Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 50 of 106
Found at i:18762043 original size:16 final size:16
Alignment explanation
Indices: 18762022--18762052 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18762012 TAGTGATGAA
*
18762022 ATATAGCTTTGTTCCC
1 ATATAGATTTGTTCCC
18762038 ATATAGATTTGTTCC
1 ATATAGATTTGTTCC
18762053 TAAATCTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (16 bp):
ATATAGATTTGTTCCC
Found at i:18764512 original size:37 final size:37
Alignment explanation
Indices: 18764470--18764547 Score: 138
Period size: 37 Copynumber: 2.1 Consensus size: 37
18764460 GATGTGTGAG
*
18764470 GATGTTGAAGTGTGCAAGTAGGGAGTGCACACATGAT
1 GATGTTGAACTGTGCAAGTAGGGAGTGCACACATGAT
*
18764507 GATGTTGAACTGTGCGAGTAGGGAGTGCACACATGAT
1 GATGTTGAACTGTGCAAGTAGGGAGTGCACACATGAT
18764544 GATG
1 GATG
18764548 AATGCATATG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.28, C:0.12, G:0.36, T:0.24
Consensus pattern (37 bp):
GATGTTGAACTGTGCAAGTAGGGAGTGCACACATGAT
Found at i:18778527 original size:196 final size:192
Alignment explanation
Indices: 18778193--18778580 Score: 614
Period size: 196 Copynumber: 2.0 Consensus size: 192
18778183 CATAGTTATC
** *
18778193 CTACCGCTAATGGTGATTCACATAGTGATTTGCCGAAATCTATTCGTTAAGAGTGTGTGAATCCC
1 CTACCGCTAATGGTGATTCACATAGTGATTTGCCGAAATCTATTCACTAAGAGTGTCTGAATCCC
*
18778258 CAAGCCAAAGTTTGTGCTAGCAAACTCTCAACTTTGAGCTCGCTTGTGTTTCTCTCTTTTTGGCT
66 CAAGCCAAAGTTTGTACTAGCAAACTCTCAACTTTGAGCTCGCTTGTGTTTCTCTCTTTTTGGCT
*
18778323 ATGATCCTATCTCAACACAAGAGAAAATAAAAACAAAACTCTTCTATATATTCAAGAGGTGGCTA
131 ATGATCCTATCTCAACACAAGAGAAAAT-AAAACAAAACTC-TCT-TATATACAAGAGGTGGCTA
*
18778388 NCTACCGCTAATGGTGATTCACATAGTGATTTGCCGAAATCTCTTCACTAAGAGTGTCTGAATCC
1 -CTACCGCTAATGGTGATTCACATAGTGATTTGCCGAAATCTATTCACTAAGAGTGTCTGAATCC
* **
18778453 CTAAGCTGAAGTTTGTACTAGCAAACTCTCAACTTTGAGCTCGCTTGTGTTTCTCTCTTTTTGGC
65 CCAAGCCAAAGTTTGTACTAGCAAACTCTCAACTTTGAGCTCGCTTGTGTTTCTCTCTTTTTGGC
* * * * *
18778518 TATGATCCTATCTCAATACATGAGAAAATAAAATAGAACTCTCTTATCTACAAGAGGTGGCTA
130 TATGATCCTATCTCAACACAAGAGAAAATAAAACAAAACTCTCTTATATACAAGAGGTGGCTA
18778581 AGGGATTCTT
Statistics
Matches: 178, Mismatches: 14, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
193 17 0.10
194 3 0.02
195 10 0.06
196 148 0.83
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.32
Consensus pattern (192 bp):
CTACCGCTAATGGTGATTCACATAGTGATTTGCCGAAATCTATTCACTAAGAGTGTCTGAATCCC
CAAGCCAAAGTTTGTACTAGCAAACTCTCAACTTTGAGCTCGCTTGTGTTTCTCTCTTTTTGGCT
ATGATCCTATCTCAACACAAGAGAAAATAAAACAAAACTCTCTTATATACAAGAGGTGGCTA
Found at i:18780758 original size:38 final size:38
Alignment explanation
Indices: 18780668--18780806 Score: 143
Period size: 38 Copynumber: 3.6 Consensus size: 38
18780658 ATCCAGCTCA
*** * * *
18780668 TGTGCATCCCCCCACATCGTGCACATAGCCGGAGTCATCG
1 TGTGCATCCCCCCACATCGTGCACA-A-TTAGTGCCACCG
* * * **
18780708 TGTGTATTCCCCCACATCATGCACAATTAGTGCCATTG
1 TGTGCATCCCCCCACATCGTGCACAATTAGTGCCACCG
*
18780746 TGTGCATCCCCCCACATCGTGCATAATTAGTGCCACCG
1 TGTGCATCCCCCCACATCGTGCACAATTAGTGCCACCG
*
18780784 TGTGCATCCCCACACATCGTGCA
1 TGTGCATCCCCCCACATCGTGCA
18780807 TAGGGGCACT
Statistics
Matches: 83, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
38 60 0.72
39 1 0.01
40 22 0.27
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.24
Consensus pattern (38 bp):
TGTGCATCCCCCCACATCGTGCACAATTAGTGCCACCG
Found at i:18786088 original size:40 final size:39
Alignment explanation
Indices: 18785994--18786095 Score: 116
Period size: 38 Copynumber: 2.6 Consensus size: 39
18785984 GAAAGTGCCC
* * *
18785994 ATGTGCACGATGTGGGGGGATGTACACGATGGCACTAAT
1 ATGTGCACGATGTGGGGGGATGCACACGATGACACGAAT
* * **
18786033 -TGTGCACAATGTGGGGGGATGCACACGATGACTCCGGCT
1 ATGTGCACGATGTGGGGGGATGCACACGATGAC-ACGAAT
*
18786072 ATGTGCACGATGTGGGGAGATGCA
1 ATGTGCACGATGTGGGGGGATGCA
18786096 TATGAGCTGG
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
38 29 0.56
39 2 0.04
40 21 0.40
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.22
Consensus pattern (39 bp):
ATGTGCACGATGTGGGGGGATGCACACGATGACACGAAT
Found at i:18789770 original size:18 final size:18
Alignment explanation
Indices: 18789747--18789784 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
18789737 ATAGTTTTCT
18789747 TACTATGGCACTAAGCAA
1 TACTATGGCACTAAGCAA
*
18789765 TACTATGGCATTAAGCAA
1 TACTATGGCACTAAGCAA
18789783 TA
1 TA
18789785 AATTGTGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.26
Consensus pattern (18 bp):
TACTATGGCACTAAGCAA
Found at i:18790356 original size:21 final size:20
Alignment explanation
Indices: 18790331--18790373 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
18790321 CCTAAGAACA
*
18790331 TAAATTTAAATGTTTTTTAT
1 TAAAATTAAATGTTTTTTAT
* *
18790351 TAAAATTAGATTTTTTTTAT
1 TAAAATTAAATGTTTTTTAT
18790371 TAA
1 TAA
18790374 TTGACATCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
TAAAATTAAATGTTTTTTAT
Found at i:18790499 original size:247 final size:246
Alignment explanation
Indices: 18789803--18790511 Score: 798
Period size: 252 Copynumber: 2.8 Consensus size: 246
18789793 AATTCTAAAA
* *
18789803 TAAATACATTTAGCCTAAGATTATAAATTTGAATAT-TTGTTTTGCATTAAAATTAGAGTTTTTT
1 TAAATACTTTTAGCCTAAGAATATAAATTT-AA-ATGTT-TTTT--ATTAAAATTAGA-TTTTTT
* *
18789867 TTACTTAATTGACTTGTTACATTAACTTTTA-ATCATTTACATTAGGATTTTAAATTTGCTTGTT
60 TTACTTAATTGACTTGTTACGTTAACTTTCACA-CATTTACATTAGGATTTTAAATTTGCTTGTT
* * * * * *
18789931 TCACCTTTATAAGTTTTTAGGTCAATTCTTACAACTTTATGTGAAGGCTTTTCAATGGTAATTTT
124 CCACC-TTATAAGTTTTTACGTCAATTCTTACAGCTTTATGTAAAGGCTTTTCAATGATAACTTT
* *
18789996 TAACTATAATTATTTTTATTCTTATTATTCTTTATTTTAAAATTAAAACTTTTATATCGT
188 TAACTATAATTA-TTTTATCCTTATTATTCTTTATTTTAAAATTAAAACTTTTATATCAT
* * * *
18790056 TAAATACTTTTAGCTTGAGAATATAAATTTAAATGTTTATTTTTTAATAAAAATAGATTTTTTTT
1 TAAATACTTTTAGCCTAAGAATATAAATTTAAATG----TTTTTTATTAAAATTAGATTTTTTTT
* * * * *
18790121 ACTTAGTTGACTTGTTGCGTTAACTTTCACACATTAATATTAGGATATTAAATTTGCTTGTTCCA
62 ACTTAATTGACTTGTTACGTTAACTTTCACACATTTACATTAGGATTTTAAATTTGCTTGTTCCA
* ** * * * * * *
18790186 TCCTTATGAGTTTTTATTTCAATTCTTACAGTTTTACGTCAAGACATTTCAATGCA-ATCTTTTA
127 -CCTTATAAGTTTTTACGTCAATTCTTACAGCTTTATGTAAAGGCTTTTCAATG-ATAACTTTTA
* *
18790250 ACTATAATTATTTTATCCTTATTGTTCTTTGTTTTAAAAATTAAAA-TTTGTATATCAT
190 ACTATAATTATTTTATCCTTATTATTCTTTATTTT-AAAATTAAAACTTT-TATATCAT
* *
18790308 TAAATATTTTTAGCCTAAGAACATAAATTTAAATGTTTTTTATTAAAATTAGATTTTTTTTA-TT
1 TAAATACTTTTAGCCTAAGAATATAAATTTAAATGTTTTTTATTAAAATTAGATTTTTTTTACTT
* * * * * * * *
18790372 AATTGACATCTTATGTTAACTCTCACACATTTGCGTTAAGATTTTAAGTTTGCTTGTTCCACCTA
66 AATTGACTTGTTACGTTAACTTTCACACATTTACATTAGGATTTTAAATTTGCTTGTTCCACCT-
* * * *
18790437 TATAAGTTTTTACGTCAATTCTTATAGCTTTATATAAAGGCTTTTTAATGATAACATTTAACTAT
130 TATAAGTTTTTACGTCAATTCTTACAGCTTTATGTAAAGGCTTTTCAATGATAACTTTTAACTAT
18790502 AATTAATTTT
195 AATT-ATTTT
18790512 TATCTGTCAA
Statistics
Matches: 381, Mismatches: 62, Indels: 31
0.80 0.13 0.07
Matches are distributed among these distances:
246 4 0.01
247 104 0.27
248 30 0.08
251 27 0.07
252 171 0.45
253 39 0.10
255 4 0.01
256 2 0.01
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.49
Consensus pattern (246 bp):
TAAATACTTTTAGCCTAAGAATATAAATTTAAATGTTTTTTATTAAAATTAGATTTTTTTTACTT
AATTGACTTGTTACGTTAACTTTCACACATTTACATTAGGATTTTAAATTTGCTTGTTCCACCTT
ATAAGTTTTTACGTCAATTCTTACAGCTTTATGTAAAGGCTTTTCAATGATAACTTTTAACTATA
ATTATTTTATCCTTATTATTCTTTATTTTAAAATTAAAACTTTTATATCAT
Found at i:18791231 original size:21 final size:22
Alignment explanation
Indices: 18791206--18791246 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
18791196 CCTAGGTGGA
*
18791206 AAAATTCAAGGGAA-AAGTGTG
1 AAAATTCAAGGAAACAAGTGTG
18791227 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAACAAGTG
18791247 ACAAAAGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.17
Consensus pattern (22 bp):
AAAATTCAAGGAAACAAGTGTG
Found at i:18791252 original size:22 final size:21
Alignment explanation
Indices: 18791206--18791252 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
18791196 CCTAGGTGGA
* **
18791206 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGGAAAAAGTGAC
18791227 AAAATTCAAGGAAACAAGTGAC
1 AAAATTCAAGGAAA-AAGTGAC
18791249 AAAA
1 AAAA
18791253 GGTAAGATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.55, C:0.09, G:0.21, T:0.15
Consensus pattern (21 bp):
AAAATTCAAGGAAAAAGTGAC
Found at i:18795169 original size:35 final size:35
Alignment explanation
Indices: 18795130--18795222 Score: 96
Period size: 35 Copynumber: 2.7 Consensus size: 35
18795120 AGAAGGCATG
*
18795130 TTGTAAAGGTTATTCCTAATCTTGCAAAAGACATA
1 TTGTAAAGGTTATGCCTAATCTTGCAAAAGACATA
* * * * * * *
18795165 TTGTAGAGGTTACGCTTGATCCTGCAAAAGGCTTA
1 TTGTAAAGGTTATGCCTAATCTTGCAAAAGACATA
* *
18795200 CTGTAAAGATTATGCCTAATCTT
1 TTGTAAAGGTTATGCCTAATCTT
18795223 ATTAAAAAGG
Statistics
Matches: 43, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Consensus pattern (35 bp):
TTGTAAAGGTTATGCCTAATCTTGCAAAAGACATA
Found at i:18796951 original size:23 final size:23
Alignment explanation
Indices: 18796921--18796966 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
18796911 AATTGAGATG
18796921 GCCCATCTTATGCATCAAATCAA
1 GCCCATCTTATGCATCAAATCAA
18796944 GCCCATCTTATGCATCAAATCAA
1 GCCCATCTTATGCATCAAATCAA
18796967 TTAAGGCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.30, G:0.09, T:0.26
Consensus pattern (23 bp):
GCCCATCTTATGCATCAAATCAA
Found at i:18797793 original size:25 final size:25
Alignment explanation
Indices: 18797765--18797816 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
18797755 TTCAAGTAAA
* *
18797765 TTATGATTTAATAAACATAATGTTC
1 TTATGATTCAATAAACATAATCTTC
18797790 TTATGATTCAATAAACATAATCTTC
1 TTATGATTCAATAAACATAATCTTC
18797815 TT
1 TT
18797817 GCCTTCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (25 bp):
TTATGATTCAATAAACATAATCTTC
Found at i:18799641 original size:13 final size:13
Alignment explanation
Indices: 18799623--18799647 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18799613 TTCCAAAAAA
18799623 TTTATAAAATCAT
1 TTTATAAAATCAT
18799636 TTTATAAAATCA
1 TTTATAAAATCA
18799648 CAATTTCTCC
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:18818078 original size:20 final size:20
Alignment explanation
Indices: 18818055--18818100 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
18818045 CTTCTAAACC
* *
18818055 TCAAATCATACTTCAATAAG
1 TCAAATCATACTCCAAGAAG
*
18818075 TCAAATTATACTCCAAGAAG
1 TCAAATCATACTCCAAGAAG
18818095 TCAAAT
1 TCAAAT
18818101 GGGGCCAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.46, C:0.20, G:0.07, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAAGAAG
Found at i:18819529 original size:20 final size:20
Alignment explanation
Indices: 18819506--18819546 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
18819496 ATCAAATCTC
*
18819506 ATTTCATTTCATATAAATCA
1 ATTTCATTTCATAAAAATCA
18819526 ATTTCATTTCATAAAAATCA
1 ATTTCATTTCATAAAAATCA
18819546 A
1 A
18819547 CAAGGCTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTTCATTTCATAAAAATCA
Found at i:18827308 original size:20 final size:22
Alignment explanation
Indices: 18827269--18827314 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
18827259 AAACCTACCT
*
18827269 CAAAGAACAGGTTAAGAAAG-A
1 CAAAGAACAGATTAAGAAAGTA
*
18827290 CAAAGAACA-ATTAATAAAGTA
1 CAAAGAACAGATTAAGAAAGTA
18827311 CAAA
1 CAAA
18827315 AAGAGGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.61, C:0.11, G:0.15, T:0.13
Consensus pattern (22 bp):
CAAAGAACAGATTAAGAAAGTA
Found at i:18834439 original size:15 final size:17
Alignment explanation
Indices: 18834421--18834459 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
18834411 AATTTTCAGA
18834421 AAATTAAT-TAAA-ACT
1 AAATTAATGTAAACACT
18834436 AAATTAATGTAAACACT
1 AAATTAATGTAAACACT
18834453 AAATTAA
1 AAATTAA
18834460 CTAACAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 8 0.36
16 4 0.18
17 10 0.45
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.31
Consensus pattern (17 bp):
AAATTAATGTAAACACT
Found at i:18837515 original size:39 final size:39
Alignment explanation
Indices: 18837472--18837567 Score: 147
Period size: 39 Copynumber: 2.5 Consensus size: 39
18837462 TCATCAATTG
* * * *
18837472 AATTTCGCTGTAGCGAGACACCTTTTGTTTCTGGGTTAC
1 AATTTCTCTGCAGCGAGAAACCTTCTGTTTCTGGGTTAC
*
18837511 AATTTCTCTGCAGCAAGAAACCTTCTGTTTCTGGGTTAC
1 AATTTCTCTGCAGCGAGAAACCTTCTGTTTCTGGGTTAC
18837550 AATTTCTCTGCAGCGAGA
1 AATTTCTCTGCAGCGAGA
18837568 TTGAATCTCG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 51 1.00
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (39 bp):
AATTTCTCTGCAGCGAGAAACCTTCTGTTTCTGGGTTAC
Found at i:18843147 original size:2 final size:2
Alignment explanation
Indices: 18843140--18843250 Score: 101
Period size: 2 Copynumber: 57.0 Consensus size: 2
18843130 CTAAGTTAGA
*
18843140 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
18843182 AT -T AGT A- AT TT NA- ACT A- AGT -T A- AG A- AT AT AT AT AT AT
1 AT AT A-T AT AT AT -AT A-T AT A-T AT AT AT AT AT AT AT AT AT AT
*
18843219 AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18843251 TGAAATTTTG
Statistics
Matches: 92, Mismatches: 6, Indels: 22
0.77 0.05 0.18
Matches are distributed among these distances:
1 7 0.08
2 82 0.89
3 3 0.03
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:18844279 original size:250 final size:247
Alignment explanation
Indices: 18843996--18845569 Score: 1426
Period size: 250 Copynumber: 6.3 Consensus size: 247
18843986 TAAACTCGTT
* *
18843996 AATATAAATTTAAATGTTTGTTTTTTATTAAAATTAGATTTTTTTACTTAATTGACATGTTACGT
1 AATATAAATTTAAATG-TT-ATTTTCATTAAAATTAGATTTTTTTACTTAATTGACATGTTACGT
* *
18844061 TTACTCTTACACATTTACGTTAGGATTTTAAATTTGCTTGTTCTACCTTTATGAGTTTTTACG-C
64 TAACTCTTACACATTTACGTTAAGATTTTAAATTTGCTTGTTCTACCTTTATGAGTTTTTACGTC
* ** * *
18844125 TAATTCTTATAGCTTTACGTCAAAGGCTTTTCAACAGAACCTTTTAACTATAATAATTTTTATCT
129 -AATTCTTACAGCTTTACGTC-AAGGCTTTTCAATGGAA-CTTTTAACTATAATTATTTTTATCC
* * * * * * * *
18844190 TTATAATTATTTATTTTAAAATTAAAAATTGCAAATCATTATATACTTTTCGCCCGAG
191 TTATTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTTTTC-CTCGAG
* * * ** *
18844248 AATATAAATTTAAATGTTATTTTCTTTAAAATTAGAATTTTGTGACTTAATTGAGTTGTTATGTT
1 AATATAAATTTAAATGTTATTTTCATTAAAATTAG-ATTTTTTTACTTAATTGACATGTTACGTT
* * * * * * * *
18844313 AA-TGCATAAACATTTATGTTAAGATTTTAAATATGTTTGTTCTGCCATTATGAGTTTTTACATC
65 AACT-CTTACACATTTACGTTAAGATTTTAAATTTGCTTGTTCTACCTTTATGAGTTTTTACGTC
* * * * * * **
18844377 AATTCTTAGAACTTTACGTCAACGCTTTTCAATGACAACTTTTAACCAAAATTATTTTTATTTTT
129 AATTCTTACAGCTTTACGTCAAGGCTTTTCAATG-GAACTTTTAACTATAATTATTTTTATCCTT
* * * *
18844442 ATTATTCTTTATTTTAAAATTAAAATTTGCATATCATTAAATACTTTTACCTTGAC
193 ATTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTTTT-CCTCGAG
* * * ** * *
18844498 AATATGAATTTAAATGTTTGTTTTTAACAAAAATAAGATTTTTTTTTACTTAATTAACATGTTAC
1 AATATAAATTTAAATG-TT-ATTTTCATTAAAATTAGA--TTTTTTTACTTAATTGACATGTTAC
* *
18844563 GTTAACT-TTCACACATTTACGTTAGGATTTTAAATTCGCTTGTT-T-CACTTCTATGAGTTTTT
62 GTTAACTCTT-ACACATTTACGTTAAGATTTTAAATTTGCTTGTTCTAC-CTT-TATGAGTTTTT
* * * * * *
18844625 ACGTTAATTCTTACAGTTTTACATCAAGGCATTTCAATGGCACCTTTTAACTATAATTATATTTA
124 ACGTCAATTCTTACAGCTTTACGTCAAGGCTTTTCAATGG-AACTTTTAACTATAATTATTTTTA
* * **
18844690 TCCTTATTATTTTTTATTTTAAAATTAAAATTTGTATATCGTTAAAT-TTTTTAATCGAG
188 TCCTTATTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTTTTCCTCGAG
* * * * * * **
18844749 AATATAAATTTAAATATTTATTTTTCCTTAAAATTAGATTTTTTTTACATAATTAACTTATTATA
1 AATATAAATTTAAAT-GTTA-TTTTCATTAAAATTAGA-TTTTTTTACTTAATTGACATGTTACG
* * * * * * *
18844814 TTAACTCTCACACATTTACATTAAGATTTTAAATTTGCTTATTCCACTTTTATAAGTTTTCACGT
63 TTAACTCTTACACATTTACGTTAAGATTTTAAATTTGCTTGTTCTACCTTTATGAGTTTTTACGT
* * * *
18844879 CAATTCTTACAACTTTACATTAAGGCTTTTCGAA-GGTAACTTTTAACTATAATTATTCTTATCC
128 CAATTCTTACAGCTTTACGTCAAGGCTTTTC-AATGG-AACTTTTAACTATAATTATTTTTATCC
* * * *
18844943 TTCTTATTCTTTATTGTAAAATTAAAATTTGTATATCGTTAAATATTTTTACCTTGAG
191 TTATTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTTTT-CCTCGAG
* * * * * *
18845001 AATGTAAATTTAAATGTTTGTTTTTCATTGAAATTATATTTTTTTTACTTACTTGACATGTTACT
1 AATATAAATTTAAATG-TT-ATTTTCATTAAAATTAGA-TTTTTTTACTTAATTGACATGTTACG
* * * * * * *
18845066 TTAAGTCTCACATATTTACGTCT-AGATTTCAAATTTGCTTGGTCTACCATTAT-ATGTTTTCAC
63 TTAACTCTTACACATTTACGT-TAAGATTTTAAATTTGCTTGTTCTACCTTTATGA-GTTTTTAC
* * * * *
18845129 ATCAATTCTTACAGCTATATGTTAAAGGGTTTTCAATGGTAACTTTTAACTATAATTATTTTTAT
126 GTCAATTCTTACAGCTTTACG-TCAAGGCTTTTCAATGG-AACTTTTAACTATAATTATTTTTAT
* *
18845194 CCTTATTATTCTTTA-TTTAAAATT-AAATTTATATATCGTTAAATACTTTTAACC-CAAG
189 CCTTATTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTTTT--CCTCGAG
* * * * * * * *
18845252 AATATAAATTTTAATGTTTGTTTTTCATAAAAATTAGAATTTTGTGACTTAATTGACTTTTTATG
1 AATATAAATTTAAATG-TT-ATTTTCATTAAAATTAG-ATTTTTTTACTTAATTGACATGTTACG
* * * * *
18845317 TTAACTC--ACACATTTACGTTAAGATTTTAAATTTGTTTCTTAC-ACATTTATAAGTTTTTATG
63 TTAACTCTTACACATTTACGTTAAGATTTTAAATTTGCTTGTT-CTACCTTTATGAGTTTTTACG
* * * *
18845379 TCAATTCTTACAGTTTTACGGCAA-GCTTTTCAAT-AATATCTTTTAACTATAATTATTTTCATC
127 TCAATTCTTACAGCTTTACGTCAAGGCTTTTCAATGGA-A-CTTTTAACTATAATTATTTTTATC
* * * * *
18845442 CTTATTATTCTTTATCTTAAAATTAAATTTTTTATATTGTTAAATACTTTTAGCAT-GAG
190 CTTATTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTTTT--CCTCGAG
* * * *
18845501 ATTATAAATTTAAATATTTACTTTTCATTAAAATTAGA-TTTTTT--TTAATTGACTTGTTATGT
1 AATATAAATTTAAAT-GTTA-TTTTCATTAAAATTAGATTTTTTTACTTAATTGACATGTTACGT
*
18845563 TAGCTCT
64 TAACTCT
18845570 CAATCATTTA
Statistics
Matches: 1081, Mismatches: 200, Indels: 88
0.79 0.15 0.06
Matches are distributed among these distances:
245 23 0.02
246 1 0.00
247 50 0.05
248 12 0.01
249 113 0.10
250 276 0.26
251 226 0.21
252 171 0.16
253 208 0.19
254 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (247 bp):
AATATAAATTTAAATGTTATTTTCATTAAAATTAGATTTTTTTACTTAATTGACATGTTACGTTA
ACTCTTACACATTTACGTTAAGATTTTAAATTTGCTTGTTCTACCTTTATGAGTTTTTACGTCAA
TTCTTACAGCTTTACGTCAAGGCTTTTCAATGGAACTTTTAACTATAATTATTTTTATCCTTATT
ATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTTTTCCTCGAG
Found at i:18844445 original size:15 final size:16
Alignment explanation
Indices: 18844427--18844456 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18844417 TTTAACCAAA
18844427 ATTATT-TTTATTTTT
1 ATTATTCTTTATTTTT
18844442 ATTATTCTTTATTTT
1 ATTATTCTTTATTTT
18844457 AAAATTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (16 bp):
ATTATTCTTTATTTTT
Found at i:18844909 original size:503 final size:499
Alignment explanation
Indices: 18843996--18845547 Score: 1748
Period size: 503 Copynumber: 3.1 Consensus size: 499
18843986 TAAACTCGTT
*
18843996 AATATAAATTTAAATGTTTGTTTTTTATTAAAATTAGA-TTTTTTTACTTAATTGACATGTTACG
1 AATATAAATTTAAATGTTTGTTTTTAATTAAAATTAGATTTTTTTTACTTAATTGACATGTTACG
*
18844060 TTTACTCTT-ACACATTTACGTTAGGATTTTAAATTTGCTTGTTCTACCTTTATGAGTTTTTACG
66 TTAACT-TTCACACATTTACGTTAGGATTTTAAATTTGCTTGTTCTACCTTTATGAGTTTTTACG
* * * ** *
18844124 CTAATTCTTATAGCTTTACGTCAAAGGCTTTTCAACAGAACCTTTTAACTATAATAATTTTTATC
130 TTAATTCTTACAGCTTTACATC-AAGGCTTTTCAATGGAACCTTTTAACTATAATTATTTTTATC
* * * * * * * ***
18844189 TTTATAATTATTTATTTTAAAATTAAAAATTGCAAATCATTATATACTTTTCGCCCGAGAATATA
194 CTTATTATTATTTATTTTAAAATTAAAATTTGTATATCGTTA-A-ATTTTTTAACCGAGAATATA
* * * *
18844254 AATTTAAATGTTA-TTTTCTTTAAAATTAGAATTTTGTGACTTAATTGAGTTGTTATGTTAATGC
257 AATTTAAATTTTATTTTTCATTAAAATTAGAATTTTGTGACTTAATTGACTTATTATGTTAAT-C
* * * * * *
18844318 AT-AAACATTTATGTTAAGATTTTAAATATGTTTGTTCTGC-CA-TTATGAGTTTTTACATCAAT
321 -TCACACATTTACGTTAAGATTTTAAATTTGTTTATTC--CACATTTATAAGTTTTTACGTCAAT
* * * * **
18844380 TCTTAGAACTTTACGTCAACGCTTTTCAATGACAACTTTTAACCAAAATTATTTTTATTTTTATT
383 TCTTACAACTTTACGTCAA-GCTTTTCAATGATAACTTTTAACTATAATTATTTTTATCCTTATT
* *
18844445 ATTCTTTATTTTAAAATTAAAATTTGCATATCATTAAATACTTTTACCTTGAC
447 ATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTTTTACCTTGAC
* ** * *
18844498 AATATGAATTTAAATGTTTGTTTTTAACAAAAATAAGATTTTTTTTTACTTAATTAACATGTTAC
1 AATATAAATTTAAATGTTTGTTTTTAATTAAAATTAGA-TTTTTTTTACTTAATTGACATGTTAC
*
18844563 GTTAACTTTCACACATTTACGTTAGGATTTTAAATTCGCTTGTT-T-CACTTCTATGAGTTTTTA
65 GTTAACTTTCACACATTTACGTTAGGATTTTAAATTTGCTTGTTCTAC-CTT-TATGAGTTTTTA
* * * *
18844626 CGTTAATTCTTACAGTTTTACATCAAGGCATTTCAATGGCACCTTTTAACTATAATTATATTTAT
128 CGTTAATTCTTACAGCTTTACATCAAGGCTTTTCAATGGAACCTTTTAACTATAATTATTTTTAT
* *
18844691 CCTTATTATTTTTTATTTTAAAATTAAAATTTGTATATCGTTAAATTTTTTAATCGAGAATATAA
193 CCTTATTATTATTTATTTTAAAATTAAAATTTGTATATCGTTAAATTTTTTAACCGAGAATATAA
* * * * * * *
18844756 ATTTAAATATTTATTTTTCCTTAAAATTAGATTTTTTTTACATAATTAACTTATTATATTAACTC
258 ATTTAAAT-TTTATTTTTCATTAAAATTAGAATTTTGTGACTTAATTGACTTATTATGTTAA-TC
* * * *
18844821 TCACACATTTACATTAAGATTTTAAATTTGCTTATTCCACTTTTATAAGTTTTCACGTCAATTCT
321 TCACACATTTACGTTAAGATTTTAAATTTGTTTATTCCACATTTATAAGTTTTTACGTCAATTCT
* * * * *
18844886 TACAACTTTACATTAAGGCTTTTCGAA-GGTAACTTTTAACTATAATTATTCTTATCCTTCTTAT
386 TACAACTTTACGTCAA-GCTTTTC-AATGATAACTTTTAACTATAATTATTTTTATCCTTATTAT
* * *
18844950 TCTTTATTGTAAAATTAAAATTTGTATATCGTTAAATATTTTTACCTTGAG
449 TCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTTTTACCTTGAC
* * * * * *
18845001 AATGTAAATTTAAATGTTTGTTTTTCATTGAAATTATATTTTTTTTACTTACTTGACATGTTACT
1 AATATAAATTTAAATGTTTGTTTTTAATTAAAATTAGATTTTTTTTACTTAATTGACATGTTACG
* * * * * * *
18845066 TTAAGTCTCACATATTTACGTCTA-GATTTCAAATTTGCTTGGTCTACCATTAT-ATGTTTTCAC
66 TTAACTTTCACACATTTACGT-TAGGATTTTAAATTTGCTTGTTCTACCTTTATGA-GTTTTTAC
* * * ** * *
18845129 ATCAATTCTTACAGCTATATGTTAAAGGGTTTTCAATGGTAA-CTTTTAACTATAATTATTTTTA
129 GTTAATTCTTACAGCTTTA-CATCAAGGCTTTTCAATGG-AACCTTTTAACTATAATTATTTTTA
* * * *
18845193 TCCTTATTATTCTTTA-TTTAAAATT-AAATTTATATATCGTTAAATACTTTTAACCCAAGAATA
192 TCCTTATTATTATTTATTTTAAAATTAAAATTTGTATATCGTTAAAT-TTTTTAA-CCGAGAATA
* * * *
18845256 TAAATTTTAATGTTTGTTTTTCATAAAAATTAGAATTTTGTGACTTAATTGACTTTTTATGTTAA
255 TAAATTTAAAT-TTTATTTTTCATTAAAATTAGAATTTTGTGACTTAATTGACTTATTATGTTAA
* * *
18845321 -CTCACACATTTACGTTAAGATTTTAAATTTGTTTCTTACACATTTATAAGTTTTTATGTCAATT
319 TCTCACACATTTACGTTAAGATTTTAAATTTGTTTATTCCACATTTATAAGTTTTTACGTCAATT
** * * * *
18845385 CTTACAGTTTTACGGCAAGCTTTTCAATAATATCTTTTAACTATAATTATTTTCATCCTTATTAT
384 CTTACAACTTTACGTCAAGCTTTTCAATGATAACTTTTAACTATAATTATTTTTATCCTTATTAT
* * * * * * *
18845450 TCTTTATCTTAAAATTAAATTTTTTATATTGTTAAATACTTTTAGCATGAG
449 TCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTTTTACCTTGAC
* * ** *
18845501 ATTATAAATTTAAATATTTACTTTTCATTAAAATTAGATTTTTTTTA
1 AATATAAATTTAAATGTTTGTTTTTAATTAAAATTAGATTTTTTTTA
18845548 ATTGACTTGT
Statistics
Matches: 882, Mismatches: 147, Indels: 44
0.82 0.14 0.04
Matches are distributed among these distances:
499 2 0.00
500 121 0.14
501 115 0.13
502 138 0.16
503 406 0.46
504 100 0.11
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (499 bp):
AATATAAATTTAAATGTTTGTTTTTAATTAAAATTAGATTTTTTTTACTTAATTGACATGTTACG
TTAACTTTCACACATTTACGTTAGGATTTTAAATTTGCTTGTTCTACCTTTATGAGTTTTTACGT
TAATTCTTACAGCTTTACATCAAGGCTTTTCAATGGAACCTTTTAACTATAATTATTTTTATCCT
TATTATTATTTATTTTAAAATTAAAATTTGTATATCGTTAAATTTTTTAACCGAGAATATAAATT
TAAATTTTATTTTTCATTAAAATTAGAATTTTGTGACTTAATTGACTTATTATGTTAATCTCACA
CATTTACGTTAAGATTTTAAATTTGTTTATTCCACATTTATAAGTTTTTACGTCAATTCTTACAA
CTTTACGTCAAGCTTTTCAATGATAACTTTTAACTATAATTATTTTTATCCTTATTATTCTTTAT
TTTAAAATTAAAATTTGTATATCGTTAAATACTTTTACCTTGAC
Found at i:18847654 original size:507 final size:506
Alignment explanation
Indices: 18846816--18848825 Score: 1158
Period size: 507 Copynumber: 4.0 Consensus size: 506
18846806 ATTCTTATAG
* * * *
18846816 CTTTACGTCAAGACTTTTTAATTGTAATTTTTAACTATAATTATTTTTATATATATTATTATTTA
1 CTTTACGTCAAGACTTTTCAATTGCAACTTTTAACTATAATTATTATTATATATATTATTATTTA
* ** * *
18846881 GTTTAAAGTTAAAATTTGCATATCATTAAATACTTTTAGCCTGAGAATATAAATTTAAATGTTTA
66 GTTTAAAATTAAAATTTGCATATCATTAAATACTTTTAGCCCAACAAAATAAATTTAAATGTTTA
* * * * * *
18846946 TTTTTTTCATAAAATTAGATTTTTATTACTTACTTGACATGTTAAGTTAACTCCCACACATTTAC
131 TGTTTTTCACAAAATTAGATTTTTATTACATAATAGACATGTTAAGTTAACTCCCACACATATAC
** *
18847011 ATTAGGATTTTAAACTTGTTTGTTTCACCTTTATGAGTTTTTACGTTAATTCTTACAGCTTTACA
196 ATTAGGATTTTAAACTTACTTGTTCCACCTTTATGAGTTTTTACGTTAATTCTTACAGCTTTACA
* * ** * **
18847076 TTAATAACTTTTCAATGGCAACTTTTAACTATAATAATTTTTATCCTTATAATTATATATTTTTC
261 TTAAGAACATTTCAATCACAACTTTTAACTATAATAACTTTTATCCTTATAATTATATATTTTAA
* * * * *
18847141 AATTAAAATTTGTGA-ATCGTTAAATACTTTT-TGCCCGAAAACATAAATTTAAATGATTGTTTT
326 AATTAAAATTTCT-ACATCATTAAATA-TTTTCAGCCAGAAAACATAAATTAAAATGATTG-TTT
* *
18847204 TTCATTAAAATAAGA-ATTTTTTACTTAATTGAGTTGTTACGTTAATGTGCACACATTTACATTA
388 TTCATTAAAATAAGATATTTTTTACTTAATTGACTTGTTAAGTTAATGTGCACACATTTACATTA
18847268 AAAGTTTAAATATGCTTGTTCCACCTTAATGAGTTTCTATGTCACCTTTTACAA
453 AAAGTTTAAATATGCTTGTTCCACCTTAATGAGTTTCTATGTCACCTTTTACAA
* * *
18847322 CTTTAGGTCAAGACTTTTCAA-TGACAACTTTTAAGTATAATTATTATTATTATTATTATTATTC
1 CTTTACGTCAAGACTTTTCAATTG-CAACTTTTAACTATAATTATTATTA-TA-TA-TATTATTA
* * *
18847386 TTTATTTTAAAATTAAAATTTGC-TCATCATTATATACTTTTAGCCCAACAAAATCAA-TTAAAT
62 TTTAGTTTAAAATTAAAATTTGCAT-ATCATTAAATACTTTTAGCCCAACAAAATAAATTTAAAT
*
18847449 -TATT-TGTTTTTCACAAAATTTAGATTCTTT-TTACATAATAGACATGTTACA-TTAACTCTCA
126 GT-TTATGTTTTTCACAAAA-TTAGATT-TTTATTACATAATAGACATGTTA-AGTTAACTCCCA
* * * *
18847510 CATATATACA-TATGATTTTTAA-TTCACTTGTTCCACCTTTATGACTTTTTTACGTTAATTCTT
187 CACATATACATTAGGATTTTAAACTT-ACTTGTTCCACCTTTATGA-GTTTTTACGTTAATTCTT
* ** * * * * *
18847573 ACAGTTTTATGTT-AGGACATTTCAATCATAACTTTTAACTATAATTACTTTTATCTTTATTATT
250 ACAGCTTTACATTAAGAACATTTCAATCACAACTTTTAACTATAATAACTTTTATCCTTATAATT
* * * * * **
18847637 CTTTATTTTAAAATTAAAATTTCTACATCATTCAATATTTTCAGCGAGAGAATTTAAATTAAAAT
315 ATATATTTTAAAATTAAAATTTCTACATCATTAAATATTTTCAGCCAGAAAACATAAATTAAAAT
* * * * * *
18847702 GTTTGTTTTTCATTAAAATTAGATTTTTTTTACTTACTTGACTTGTTAAGTTAACTCT-CATACA
380 GATTGTTTTTCATTAAAATAAGATATTTTTTACTTAATTGACTTGTTAAGTTAA-TGTGCACACA
* ** * * * * * * * * ** * *
18847766 TCTATGTTAAAATTTTAAGTTTCCTTGTT-CAACATATATAAGTTTTTACAAT-A-ATTCTTATA
444 TTTACATTAAAAGTTTAAATATGCTTGTTCCACCTTA-ATGAGTTTCTA-TGTCACCTT-TTACA
*
18847828 G
506 A
* *** * * * *
18847829 CTTTATGTCAAGACTTTTCAGGGGCAACTTTTAAATATAATTGTTCTTATCCT-TATTATTATTT
1 CTTTACGTCAAGACTTTTCAATTGCAACTTTTAACTATAATTATTATTAT-ATATATTATTATTT
* ** * * * * * *
18847893 ATTTTAAAATTAAAATTTATATATCGTTAAATGCTTTTAGCTCAAGAATATAAATTTAAATATTT
65 AGTTTAAAATTAAAATTTGCATATCATTAAATACTTTTAGCCCAACAAAATAAATTTAAATGTTT
* * * ** *
18847958 A--TTTTTCATGAAAATTAGATTTTTTTTTTTTACTTAAGT-GACATGTTATA-TTAACTGTCAT
130 ATGTTTTTCA-CAAAATTAGA----TTTTTATTACATAA-TAGACATGTTA-AGTTAACTCCCAC
* * * * * * * * *
18848019 ACATTTACATTAGGATTTTAAATTTGCATGTTCTACCGTTAT-ATGTTCTTACATCAATTCTTAC
188 ACATATACATTAGGATTTTAAACTTACTTGTTCCACCTTTATGA-GTTTTTACGTTAATTCTTAC
* * ** *** * * * * *
18848083 A-ATGTTACGTTAA-AAGGTTTTCAATGGTAACATTTAACTATAATTATTTTTATCTTTATTACT
252 AGCT-TTACATTAAGAA-CATTTCAATCACAACTTTTAACTATAATAACTTTTATCCTTA-TAAT
* * * * * * ** * * *
18848146 T-TTTATCTTAAAATTAAAATTTGTATACCATTAAATACTTTCAGCTTGATAATATAAATTTAAA
314 TATATATTTTAAAATTAAAATTTCTACATCATTAAATATTTTCAGCCAGAAAACATAAATTAAAA
* * * * ** *** *
18848210 TGTTTATTTTTCATCAAAATCAGA-ATTTTGTGCCTTAATTGACTTGTTACCATAA-GT-CTCAC
379 TGATTGTTTTTCATTAAAATAAGATATTTT-TTACTTAATTGACTTGTTAAGTTAATGTGCACAC
* * * * * **
18848272 A---A-ATT-TACG-TT--A-A------TTCCTCCTT--TGTATGTTTTTAAGTCAATTTTTACA
443 ATTTACATTAAAAGTTTAAATATGCTTGTTCCACCTTAATG-A-GTTTCTATGTCACCTTTTACA
18848320 A
506 A
* * * * * *
18848321 CTTTATGACAAGACTTTTC-ATTGGTAACTTTTAATTATAATTATGT-TTATCCT-TATTATTCT
1 CTTTACGTCAAGACTTTTCAATT-GCAACTTTTAACTATAATTAT-TATTAT-ATATATTATTAT
* * * * * * * * * *
18848383 TAATTTTGAAACTAAAATTTGTACATCATTAAATACTTTTAGCTCAAGAATATAAATTTAAATAT
63 TTAGTTTAAAATTAAAATTTGCATATCATTAAATACTTTTAGCCCAACAAAATAAATTTAAATGT
* * ** * ** * * * ** *
18848448 TTA--TTTTTAATTAAAATTAGA-GCTTATTAACACAATTCACTTATTCTA-TTAACTTTCATAC
128 TTATGTTTTTCA-CAAAATTAGATTTTTATT-ACATAATAGACATGTT-AAGTTAACTCCCACAC
* * * * * * * * * *
18848509 ATTTAGATTAAGATTTTAAATTTGCTTGTTCCACCTTTATAAGCTTTTATC-TCATTTCTTACAA
190 ATATACATTAGGATTTTAAACTTACTTGTTCCACCTTTATGAGTTTTTA-CGTTAATTCTTACAG
* * * * * * * * *
18848573 CTTTGCATCAAG-GCTTTTCAAT-AGCAACTTTTAACTATAATTATTTTTATCCTTATTATTCTT
254 CTTTACATTAAGAACATTTCAATCA-CAACTTTTAACTATAATAACTTTTATCCTTATAATTATA
* * * * * * *
18848636 TATCTTAAAATTAAAATTTCTATATCATTAAATATTTTTA-CCA-AGAATATAAATTTAAAT-AC
318 TATTTTAAAATTAAAATTTCTACATCATTAAATATTTTCAGCCAGAAAACATAAATTAAAATGAT
* ** * * *** * *
18848698 T-TTTTT-ATTAAAATTAGAGCTTTTTTACGTAATTCACTTGTTCCTTTAACTCT-CATACATTT
383 TGTTTTTCATTAAAATAAGATATTTTTTACTTAATTGACTTGTTAAGTTAA-TGTGCACACATTT
* * * * * * * * *
18848760 ACATTAAGATTTTAAATTTGTTTGTTCCACCTTTATAAGTTTTTATGTTA-TTTCTTACAA
447 ACATTAAAAGTTTAAATATGCTTGTTCCACCTTAATGAGTTTCTATGTCACCTT-TTACAA
18848820 CTTTAC
1 CTTTAC
18848826 ATAATACTAA
Statistics
Matches: 1186, Mismatches: 243, Indels: 157
0.75 0.15 0.10
Matches are distributed among these distances:
482 28 0.02
483 9 0.01
484 6 0.01
485 16 0.01
486 4 0.00
487 80 0.07
488 82 0.07
489 3 0.00
490 3 0.00
491 3 0.00
492 143 0.12
493 6 0.01
498 3 0.00
499 29 0.02
500 1 0.00
501 3 0.00
502 1 0.00
503 2 0.00
504 66 0.06
505 15 0.01
506 74 0.06
507 247 0.21
508 146 0.12
509 211 0.18
510 5 0.00
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.47
Consensus pattern (506 bp):
CTTTACGTCAAGACTTTTCAATTGCAACTTTTAACTATAATTATTATTATATATATTATTATTTA
GTTTAAAATTAAAATTTGCATATCATTAAATACTTTTAGCCCAACAAAATAAATTTAAATGTTTA
TGTTTTTCACAAAATTAGATTTTTATTACATAATAGACATGTTAAGTTAACTCCCACACATATAC
ATTAGGATTTTAAACTTACTTGTTCCACCTTTATGAGTTTTTACGTTAATTCTTACAGCTTTACA
TTAAGAACATTTCAATCACAACTTTTAACTATAATAACTTTTATCCTTATAATTATATATTTTAA
AATTAAAATTTCTACATCATTAAATATTTTCAGCCAGAAAACATAAATTAAAATGATTGTTTTTC
ATTAAAATAAGATATTTTTTACTTAATTGACTTGTTAAGTTAATGTGCACACATTTACATTAAAA
GTTTAAATATGCTTGTTCCACCTTAATGAGTTTCTATGTCACCTTTTACAA
Found at i:18847814 original size:252 final size:252
Alignment explanation
Indices: 18846679--18848825 Score: 1615
Period size: 252 Copynumber: 8.6 Consensus size: 252
18846669 AGTTTATTTC
* * * * *
18846679 ATAAATTTAAATGTTTGCTTTTCATTAAAATTTGA-TTTTTTTACATCATT-TCTTTGTTACATT
1 ATAAATTTAAATGTTTGTTTTTCATTAAAATTAGATTTTTTTTACTTAATTGAC-TTGTTACATT
* * * * * *
18846742 CACTCTCACAAATTTACGTTACAATTTT-AATTTGCTTGTTCCACCTTTATAAGTTTTAATATTA
65 AACTCTCACACATTTACATTAGAATTTTAAATTTGCTTGTTCCACCTTTATAAGTTTTTACATTA
* * * * * * *
18846806 ATTCTTATAGCTTTACGTCAAGACTTTTTAATTGTAATTTTTAACTATAATTATTTTTATATATA
130 ATTCTTACAGCTTTACGTCAAGACTTTTCAATGGCAACTTTTAACTATAATTATTTTTATCTTTA
* * *
18846871 TTATTATTTAGTTTAAAGTTAAAATTTGC-ATATCATTAAATACTTTTAGCCTGAGAAT
195 TTATTATTTATTTTAAAATTAAAATTT-CTATATCATTAAATACTTTTAGCCAGAGAAT
* * * *
18846929 ATAAATTTAAATGTTTATTTTTTTCA-TAAAATTAGATTTTTATTACTTACTTGACATGTTA-AG
1 ATAAATTTAAATG-TT-TGTTTTTCATTAAAATTAGATTTTTTTTACTTAATTGACTTGTTACA-
* * * * * * *
18846992 TTAACTCCCACACATTTACATTAGGATTTTAAACTTGTTTGTTTCACCTTTATGAGTTTTTACGT
63 TTAACTCTCACACATTTACATTAGAATTTTAAATTTGCTTGTTCCACCTTTATAAGTTTTTACAT
* * * * *
18847057 TAATTCTTACAGCTTTACATTAATAACTTTTCAATGGCAACTTTTAACTATAATAATTTTTATCC
128 TAATTCTTACAGCTTTACGTCAA-GACTTTTCAATGGCAACTTTTAACTATAATTATTTTTATCT
* * ** * * * * * *
18847122 TTATAATTATATATTTTTCAATTAAAATTTGTGA-ATCGTTAAATACTTTTTGCCCGAAAAC
192 TTATTATTATTTATTTTAAAATTAAAATTTCT-ATATCATTAAATACTTTTAGCCAGAGAAT
* * * * *
18847183 ATAAATTTAAATGATTGTTTTTTCATTAAAATAAGA-ATTTTTTACTTAATTGAGTTGTTACGTT
1 ATAAATTTAAATGTTTG-TTTTTCATTAAAATTAGATTTTTTTTACTTAATTGACTTGTTACATT
* * * * * * * ** *
18847247 AA-TGTGCACACATTTACATTAAAAGTTTAAATATGCTTGTTCCACCTTAATGAGTTTCTATGTC
65 AACTCT-CACACATTTACATTAGAATTTTAAATTTGCTTGTTCCACCTTTATAAGTTTTTACATT
* * * * *
18847311 ACCTT-TTACAACTTTAGGTCAAGACTTTTCAATGACAACTTTTAAGTATAATTATTATTATTAT
129 A-ATTCTTACAGCTTTACGTCAAGACTTTTCAATGGCAACTTTTAACTATAATTA-T-TT-TTAT
* * * *
18847375 -TATTATTATTCTTTATTTTAAAATTAAAATTTGCT-CATCATTATATACTTTTAGCCCA-ACAA
190 CT-TTATTATTATTTATTTTAAAATTAAAATTT-CTATATCATTAAATACTTTTAG-CCAGAGAA
*
18847437 A
252 T
* * * * * * *
18847438 ATCAA-TTAAATTATTTGTTTTTCA-CAAAATTTAGATTCTTTTTACATAATAGACATGTTACAT
1 ATAAATTTAAA-TGTTTGTTTTTCATTAAAA-TTAGATTTTTTTTACTTAATTGACTTGTTACAT
* * * ** ** *
18847501 TAACTCTCACATATATACA-TATG-ATTTTTAATTCACTTGTTCCACCTTTATGACTTTTTTACG
64 TAACTCTCACACATTTACATTA-GAATTTTAAATTTGCTTGTTCCACCTTTAT-AAGTTTTTACA
* * * * * *** *
18847564 TTAATTCTTACAGTTTTATGTTAGGACATTTCAATCATAACTTTTAACTATAATTACTTTTATCT
127 TTAATTCTTACAGCTTTACGTCAAGACTTTTCAATGGCAACTTTTAACTATAATTATTTTTATCT
* * * *
18847629 TTATTATTCTTTATTTTAAAATTAAAATTTCTACATCATTCAATA-TTTTCAGCGAGAGAAT
192 TTATTATTATTTATTTTAAAATTAAAATTTCTATATCATTAAATACTTTT-AGCCAGAGAAT
* * *
18847690 TTAAATTAAAATGTTTGTTTTTCATTAAAATTAGATTTTTTTTACTTACTTGACTTGTTA-AGTT
1 ATAAATTTAAATGTTTGTTTTTCATTAAAATTAGATTTTTTTTACTTAATTGACTTGTTACA-TT
* * ** * * * * * * *
18847754 AACTCTCATACATCTATGTTAAAATTTTAAGTTTCCTTGTTCAACATATATAAGTTTTTACAATA
65 AACTCTCACACATTTACATTAGAATTTTAAATTTGCTTGTTCCACCTTTATAAGTTTTTACATTA
* * ** * * * *
18847819 ATTCTTATAGCTTTATGTCAAGACTTTTCAGGGGCAACTTTTAAATATAATTGTTCTTATCCTTA
130 ATTCTTACAGCTTTACGTCAAGACTTTTCAATGGCAACTTTTAACTATAATTATTTTTATCTTTA
* * *
18847884 TTATTATTTATTTTAAAATTAAAATTTATATATCGTTAAATGCTTTTAGCTCA-AGAAT
195 TTATTATTTATTTTAAAATTAAAATTTCTATATCATTAAATACTTTTAGC-CAGAGAAT
* * * * * *
18847942 ATAAATTTAAATATTTATTTTTCATGAAAATTAGATTTTTTTTTTTTACTTAAGTGACATGTTAT
1 ATAAATTTAAATGTTTGTTTTTCATTAAAATTAGA----TTTTTTTTACTTAATTGACTTGTTAC
* * * * * * * *
18848007 ATTAACTGTCATACATTTACATTAGGATTTTAAATTTGCATGTTCTACCGTTATATGTTCTTACA
62 ATTAACTCTCACACATTTACATTAGAATTTTAAATTTGCTTGTTCCACCTTTATAAGTTTTTACA
* * * * * * *
18848072 TCAATTCTTACA-ATGTTACGTTAAAAGGTTTTCAATGGTAACATTTAACTATAATTATTTTTAT
127 TTAATTCTTACAGCT-TTACGTCAAGA-CTTTTCAATGGCAACTTTTAACTATAATTATTTTTAT
* * * * ** *
18848136 CTTTATTACTT-TTTATCTTAAAATTAAAATTTGTATACCATTAAATACTTTCAGCTTGATAAT
190 CTTTATTA-TTATTTATTTTAAAATTAAAATTTCTATATCATTAAATACTTTTAGCCAGAGAAT
* * * * * **
18848199 ATAAATTTAAATGTTTATTTTTCATCAAAATCAGAATTTTGTGCCTTAATTGACTTGTTACCA-T
1 ATAAATTTAAATGTTTGTTTTTCATTAAAATTAGATTTTTTTTACTTAATTGACTTGTTA-CATT
* * * * * *
18848263 AAGTCTCACAAATTTAC----G----TT-AA--------TTCCTCCTTTGTATGTTTTTA-AGTC
65 AACTCTCACACATTTACATTAGAATTTTAAATTTGCTTGTTCCACCTTTATAAGTTTTTACA-TT
* * * * * * * * *
18848310 AATTTTTACAACTTTATGACAAGACTTTTCATTGGTAACTTTTAATTATAATTATGTTTATCCTT
129 AATTCTTACAGCTTTACGTCAAGACTTTTCAATGGCAACTTTTAACTATAATTATTTTTATCTTT
* * * * * *
18848375 ATTATTCTTAATTTTGAAACTAAAATTTGTACATCATTAAATACTTTTAGCTCA-AGAAT
194 ATTATTATTTATTTTAAAATTAAAATTTCTATATCATTAAATACTTTTAGC-CAGAGAAT
* * * ** * * ** * *
18848434 ATAAATTTAAATATTTATTTTTAATTAAAATTAGAGCTTATTAACACAATTCACTTATT-CTATT
1 ATAAATTTAAATGTTTGTTTTTCATTAAAATTAGATTTTTTTTACTTAATTGACTTGTTAC-ATT
* * * *
18848498 AACTTTCATACATTTAGATTA-AGATTTTAAATTTGCTTGTTCCACCTTTATAAGCTTTTATC-T
65 AACTCTCACACATTTACATTAGA-ATTTTAAATTTGCTTGTTCCACCTTTATAAGTTTTTA-CAT
* * * * * * * *
18848561 CATTTCTTACAACTTTGCATCAAGGCTTTTCAATAGCAACTTTTAACTATAATTATTTTTATCCT
128 TAATTCTTACAGCTTTACGTCAAGACTTTTCAATGGCAACTTTTAACTATAATTATTTTTATCTT
* * *
18848626 TATTATTCTTTATCTTAAAATTAAAATTTCTATATCATTAAATATTTTTA-CCA-AGAAT
193 TATTATTATTTATTTTAAAATTAAAATTTCTATATCATTAAATACTTTTAGCCAGAGAAT
** ** * * * *
18848684 ATAAATTTAAAT-ACT-TTTTT-ATTAAAATTAGAGCTTTTTTACGTAATTCACTTGTTCCTTTA
1 ATAAATTTAAATGTTTGTTTTTCATTAAAATTAGATTTTTTTTACTTAATTGACTTGTTACATTA
* * **
18848746 ACTCTCATACATTTACATTA-AGATTTTAAATTTGTTTGTTCCACCTTTATAAGTTTTTATGTTA
66 ACTCTCACACATTTACATTAGA-ATTTTAAATTTGCTTGTTCCACCTTTATAAGTTTTTACATTA
* *
18848810 TTTCTTACAACTTTAC
130 ATTCTTACAGCTTTAC
18848826 ATAATACTAA
Statistics
Matches: 1491, Mismatches: 329, Indels: 157
0.75 0.17 0.08
Matches are distributed among these distances:
233 1 0.00
234 3 0.00
235 139 0.09
236 34 0.02
237 1 0.00
243 2 0.00
244 4 0.00
245 2 0.00
247 106 0.07
248 6 0.00
249 2 0.00
250 32 0.02
251 22 0.01
252 429 0.29
253 217 0.15
254 147 0.10
255 138 0.09
256 93 0.06
257 111 0.07
258 2 0.00
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (252 bp):
ATAAATTTAAATGTTTGTTTTTCATTAAAATTAGATTTTTTTTACTTAATTGACTTGTTACATTA
ACTCTCACACATTTACATTAGAATTTTAAATTTGCTTGTTCCACCTTTATAAGTTTTTACATTAA
TTCTTACAGCTTTACGTCAAGACTTTTCAATGGCAACTTTTAACTATAATTATTTTTATCTTTAT
TATTATTTATTTTAAAATTAAAATTTCTATATCATTAAATACTTTTAGCCAGAGAAT
Found at i:18848148 original size:15 final size:16
Alignment explanation
Indices: 18848125--18848154 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18848115 TTTAACTATA
18848125 ATTA-TTTTTATCTTT
1 ATTACTTTTTATCTTT
18848140 ATTACTTTTTATCTT
1 ATTACTTTTTATCTT
18848155 AAAATTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTACTTTTTATCTTT
Found at i:18848798 original size:247 final size:252
Alignment explanation
Indices: 18848346--18848823 Score: 716
Period size: 247 Copynumber: 1.9 Consensus size: 252
18848336 TTTCATTGGT
* * * *
18848346 AACTTTTAATTATAATTATGTTTATCCTTATTATTCTTAATTTTGAAACTAAAATTTGTACATCA
1 AACTTTTAACTATAATTATGTTTATCCTTATTATTCTTAATCTTAAAACTAAAATTTCTACATCA
*
18848411 TTAAATACTTTTAGCTCAAGAATATAAATTTAAATATTTATTTTTAATTAAAATTAGAGCTTATT
66 TTAAATACTTTTAGCTCAAGAATATAAATTTAAATATCTATTTTTAATTAAAATTAGAGCTTATT
* *
18848476 AACACAATTCACTTATTCTATTAACTTTCATACATTTAGATTAAGATTTTAAATTTGCTTGTTCC
131 AACACAATTCACTTATTCTATTAACTCTCATACATTTACATTAAGATTTTAAATTTGCTTGTTCC
18848541 ACCTTTATAAGCTTTTATCTCATTTCTTACAACTTTGCATCAAGGCTTTTCAATAGC
196 ACCTTTATAAGCTTTTATCTCATTTCTTACAACTTTGCATCAAGGCTTTTCAATAGC
* * * *
18848598 AACTTTTAACTATAATTATTTTTATCCTTATTATTCTTTATCTTAAAATTAAAATTTCTATATCA
1 AACTTTTAACTATAATTATGTTTATCCTTATTATTCTTAATCTTAAAACTAAAATTTCTACATCA
* *
18848663 TTAAATATTTTTA-C-CAAGAATATAAATTTAAATA-CT-TTTTT-ATTAAAATTAGAGCTTTTT
66 TTAAATACTTTTAGCTCAAGAATATAAATTTAAATATCTATTTTTAATTAAAATTAGAGCTTATT
* ** * *
18848723 TACGTAATTCACTTGTTCCT-TTAACTCTCATACATTTACATTAAGATTTTAAATTTGTTTGTTC
131 AACACAATTCACTTATT-CTATTAACTCTCATACATTTACATTAAGATTTTAAATTTGCTTGTTC
* * *
18848787 CACCTTTATAAGTTTTTATGTTATTTCTTACAACTTT
195 CACCTTTATAAGCTTTTATCTCATTTCTTACAACTTT
18848824 ACATAATACT
Statistics
Matches: 204, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
247 106 0.52
248 7 0.03
249 1 0.00
250 20 0.10
251 1 0.00
252 69 0.34
ACGTcount: A:0.33, C:0.13, G:0.05, T:0.48
Consensus pattern (252 bp):
AACTTTTAACTATAATTATGTTTATCCTTATTATTCTTAATCTTAAAACTAAAATTTCTACATCA
TTAAATACTTTTAGCTCAAGAATATAAATTTAAATATCTATTTTTAATTAAAATTAGAGCTTATT
AACACAATTCACTTATTCTATTAACTCTCATACATTTACATTAAGATTTTAAATTTGCTTGTTCC
ACCTTTATAAGCTTTTATCTCATTTCTTACAACTTTGCATCAAGGCTTTTCAATAGC
Found at i:18850465 original size:15 final size:15
Alignment explanation
Indices: 18850428--18850470 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
18850418 ACGGTGGAAG
18850428 AAAGAAAGAAAAGAA
1 AAAGAAAGAAAAGAA
*
18850443 AAAAAAAGAAAA-AA
1 AAAGAAAGAAAAGAA
18850457 ACAAGAAAGGAAAA
1 A-AAGAAA-GAAAA
18850471 TAGGCATGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 3 0.12
15 16 0.67
16 5 0.21
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAAAAGAA
Found at i:18850497 original size:27 final size:27
Alignment explanation
Indices: 18850456--18850511 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
18850446 AAAAGAAAAA
*
18850456 AACAAGAAAGGAAAATAGG-CATGGCCC
1 AACAAGAAAGAAAAAT-GGACATGGCCC
* *
18850483 AACAAGCAAGAAAAATGGACATGGTCC
1 AACAAGAAAGAAAAATGGACATGGCCC
18850510 AA
1 AA
18850512 TAAAGGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.50, C:0.18, G:0.23, T:0.09
Consensus pattern (27 bp):
AACAAGAAAGAAAAATGGACATGGCCC
Found at i:18850528 original size:25 final size:25
Alignment explanation
Indices: 18850500--18850562 Score: 92
Period size: 25 Copynumber: 2.5 Consensus size: 25
18850490 AAGAAAAATG
18850500 GACATGGTCCAATAAAGGAA-AACTA
1 GACATGGTCCAATAAAGGAAGAA-TA
*
18850525 GACATGGTCCAATAAAGGAAGAATG
1 GACATGGTCCAATAAAGGAAGAATA
*
18850550 GGCATGGTCCAAT
1 GACATGGTCCAAT
18850563 TAAAAAGAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 33 0.94
26 2 0.06
ACGTcount: A:0.41, C:0.16, G:0.25, T:0.17
Consensus pattern (25 bp):
GACATGGTCCAATAAAGGAAGAATA
Found at i:18850575 original size:25 final size:24
Alignment explanation
Indices: 18850490--18850576 Score: 79
Period size: 25 Copynumber: 3.5 Consensus size: 24
18850480 CCCAACAAGC
* *
18850490 AAGAAAAATGGACATGGTCCAATA
1 AAGAAGAATGGGCATGGTCCAATA
* *
18850514 AAGGAA-AACTAGACATGGTCCAATA
1 AA-GAAGAA-TGGGCATGGTCCAATA
18850539 AAGGAAGAATGGGCATGGTCCAATTA
1 AA-GAAGAATGGGCATGGTCCAA-TA
18850565 AA-AAGAGATGGG
1 AAGAAGA-ATGGG
18850577 AGAAGTCCAT
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
24 8 0.15
25 41 0.75
26 6 0.11
ACGTcount: A:0.46, C:0.11, G:0.26, T:0.16
Consensus pattern (24 bp):
AAGAAGAATGGGCATGGTCCAATA
Found at i:18859942 original size:27 final size:27
Alignment explanation
Indices: 18859891--18859942 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
18859881 ATGTCCTGGT
*
18859891 GGTGGAAAATTACAATTTTGCCCCTAG
1 GGTGGAAAATTACAATTTTGACCCTAG
*
18859918 GGTGGTAAAATTACCATTTT-ACCCT
1 GGTGG-AAAATTACAATTTTGACCCT
18859943 TATGCTTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTGACCCTAG
Found at i:18862224 original size:22 final size:22
Alignment explanation
Indices: 18862199--18862255 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
18862189 TATCAGAGCA
18862199 TTTGGTTTTAAAGATAAGAACT
1 TTTGGTTTTAAAGATAAGAACT
* **
18862221 TTTGGTTTTAAAGATCAGAGTT
1 TTTGGTTTTAAAGATAAGAACT
*
18862243 TTTGGGTTTAAAG
1 TTTGGTTTTAAAG
18862256 CTGGTTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.30, C:0.04, G:0.23, T:0.44
Consensus pattern (22 bp):
TTTGGTTTTAAAGATAAGAACT
Found at i:18862263 original size:11 final size:11
Alignment explanation
Indices: 18862247--18862287 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
18862237 AGAGTTTTTG
18862247 GGTTTAAAGCT
1 GGTTTAAAGCT
*
18862258 GGTTTAAAGTT
1 GGTTTAAAGCT
*
18862269 GTTTTAAAGCT
1 GGTTTAAAGCT
*
18862280 GTTTTAAA
1 GGTTTAAA
18862288 ATTTACAGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.29, C:0.05, G:0.22, T:0.44
Consensus pattern (11 bp):
GGTTTAAAGCT
Found at i:18862327 original size:5 final size:5
Alignment explanation
Indices: 18862317--18862346 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
18862307 CCCCAAGTCC
*
18862317 AGTTA AGTTA AGATA AGTTA AGTTA AGTTA
1 AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA
18862347 GGTCAAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (5 bp):
AGTTA
Found at i:18863922 original size:20 final size:20
Alignment explanation
Indices: 18863897--18863942 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
18863887 TTTTGGCCCC
18863897 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
*
18863917 ATTTGACTTATTGGAGTATG
1 ATTTGACTTATTGGAGTATA
18863937 ATTTGA
1 ATTTGA
18863943 GGTTTAGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:18893354 original size:502 final size:500
Alignment explanation
Indices: 18892215--18894381 Score: 1969
Period size: 502 Copynumber: 4.3 Consensus size: 500
18892205 GACAGTGACA
* * *
18892215 TTATTATT-TTATATTTTAAAACTAAAATTTGTAAATCGTTAAATACTTTTAATCC-GAGAATAT
1 TTATTATTATT-TATTTTAAAACTAAAATTTGTATATCGTTAAATACTTTT-AGCCTAAGAATAT
*
18892278 AAATTTAAATGTTTGCTTTTCATTAAAATTAGATTTTTTTT-CTTAATTGACTTGTT-CAGTTAA
64 AAATTTAAATGTTTGTTTTTCATTAAAATTAGATTTTTTTTACTTAATTGACTTGTTAC-GTTAA
* * * * * * * *
18892341 CTTTCACTCATTAATGTTAAGATTTTAAATTTGCTT-TTGTAATTTTTATAAG-TTTTACGTCAA
128 CTCTCACACATTTACGTTAAGATTTTAAATTT-ATTGTT-TCATCTTTATGAGTTTTTACGTCAA
** * * * * * *
18892404 TTCTTACTGCTTTACGTTAAGACTTTTCAATGGTAACTTTTAAATATAATTATTTTCATCCATAT
191 TTCTTACAACTTTACGTCAAGACATTTCAATGGCAACTTTTAACTATAATTATTTTTATCCTTAT
* *
18892469 TATTCTTTATTTTAAAATTAAAACTTT-TATATCGTTAAATACTTTTAGCTTGAGAATATAAATT
256 TATTCTTTATTTTAAAATTAAAA-TTTGTATATCGTTAAATACTTTTAGCCTAAGAATATAAATT
** * * *
18892533 TAAATATTTAATTTTTTTAAAGATTAT-ATTTATTTTGATTTAATTGACTTGTTACATTAACTTT
320 TAAATATTT--TTTCATTAAA-A-TATGATTT-TTTTGATCTAATTGACTTATTACATTAACTCT
* * * * * ***
18892597 TAATCATTTACATTAGGATTTTAAATTTGCTTGGTCCACCTTTATAAG-TTTTTGGTCAATTCTT
380 CAAACATTTACGTTAAGATTTTAAATTTGCTTGTTCCACCTTTATAAGCTTTTACATCAATTCTT
* * * * * *
18892661 ACAACATTATGTCAAGGTTTTTCAATGATAACTTTTAACTATAAGTATTTTTATCC
445 ACAACTTTAAGTCAAAGCTTTTCAATGGTAACTTTTAACTATAATTATTTTTATCC
* * * *
18892717 TTATTATT-TTTATTTTTAAA-TAAAAATTTATATATCGTTAAATACCTTTGACCCGT--GAATA
1 TTATTATTATTTATTTTAAAACT-AAAATTTGTATATCGTTAAATA-CTTTTAGCC-TAAGAATA
** *
18892778 TAAATTTAAATACTT-TTTTT-ATTAAAAATT-TATTTTTTTTACTTAATTGACTTGTTACGTTA
63 TAAATTTAAATGTTTGTTTTTCATT-AAAATTAGATTTTTTTTACTTAATTGACTTGTTACGTTA
** * * * *
18892840 ACTCTCACACATTTACGTTTGGATTTTAAATTTACTTGTTCCATCTTTTTGACTTTTTACATCAA
127 ACTCTCACACATTTACGTTAAGATTTTAAATTTA-TTGTTTCATCTTTATGAGTTTTTACGTCAA
* * * * * *
18892905 TTCTTACAACTTTATGTCAAGCCATTTCAATGTCTACTTTTGACTATAATTATATTTATCCTTAT
191 TTCTTACAACTTTACGTCAAGACATTTCAATGGCAACTTTTAACTATAATTATTTTTATCCTTAT
* * * *
18892970 TATTCTTAATTTAAAAAATTAAAATTTGTATATCGTCAAATATTTTTAGCCTAAGAATATAAATT
256 TATTCTTTATTT-TAAAATTAAAATTTGTATATCGTTAAATACTTTTAGCCTAAGAATATAAATT
* * * * *
18893035 TAAATATTTTTTCATTAAAATATGATTTTTTTTA-CTAATAGAATTATTATATTAACTCTCAAAA
320 TAAATATTTTTTCATTAAAATATGATTTTTTTGATCTAATTGACTTATTACATTAACTCTCAAAC
* * * ** * * * * *
18893099 ATTTATGTTAAAATTTT-AATTTGCTTCTTCCATTTTTATAAGTTTTTATATTAATTCTTATAAT
385 ATTTACGTTAAGATTTTAAATTTGCTTGTTCCACCTTTATAAGCTTTTACATCAATTCTTACAAC
* *
18893163 TTTAAGTCAAAGCTTTTCAATTGTAACTTTTAAATATAATTATTTTTA-CC
450 TTTAAGTCAAAGCTTTTCAATGGTAACTTTTAACTATAATTATTTTTATCC
* * *
18893213 TTTTTAGTTATTTATTTTAAAACTAAAATTTGCATATCGTTAAATACTTTTAGTCTAAGAATATA
1 TTATTA-TTATTTATTTTAAAACTAAAATTTGTATATCGTTAAATACTTTTAGCCTAAGAATATA
* * *
18893278 AATTTAAATGTTTGTTTTTCATTAAAAGTAGATTTTGTTTTCACTTAGTTGATTTGTTACGTTAA
65 AATTTAAATGTTTGTTTTTCATTAAAATTAGATTTT-TTTT-ACTTAATTGACTTGTTACGTTAA
* *
18893343 CTC-CTACACATTTACGTTAAGATTTTAAATTTGATTGTTTCACCTTTATGAGTTTTTAGGTCAA
128 CTCTC-ACACATTTACGTTAAGATTTTAAATTT-ATTGTTTCATCTTTATGAGTTTTTACGTCAA
* * * * * *
18893407 TTTTTACAACTTTACGTCAAAAGCTTTTCAATGGCCAC-TTTAACTATAATAATTTTTATACTTA
191 TTCTTACAACTTTACGTCAAGA-CATTTCAATGGCAACTTTTAACTATAATTATTTTTATCCTTA
* * * * * * * *
18893471 TAATTATTTATTTCAAAATTAAAATTTGTAAATCTTTAAATACTCTTCGCGC-AAGAATATAGAT
255 TTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTTTTAGC-CTAAGAATATAAAT
* * * * * * * *
18893535 TTCAATATTTGTTTTTCATTAAAAT-TAGAATGTTGTGA-CTTAATTGAGTTGTTATATTAACAC
319 TT-AA-ATAT-TTTTTCATTAAAATAT-GATTTTTTTGATC-TAATTGACTTATTACATTAACTC
* * * * * * * * **
18893598 GT-ACACATTT-CAGTTAAGATTATAAATATACTTATTCTATCTTTATGAGCTTTTACATTTATT
379 -TCAAACATTTAC-GTTAAGATTTTAAATTTGCTTGTTCCACCTTTATAAGCTTTTACATCAATT
* * * * * *
18893661 TTTACAACTTCATGTCAAAGCTTTTTAATGGGAACTTTTAATTATAATTATTTTTAT--
442 CTTACAACTTTAAGTCAAAGCTTTTCAATGGTAACTTTTAACTATAATTATTTTTATCC
* * * * * *
18893718 TT-TTATTACTTTATTTTAAAATTAAAATTTGTATATCATTAAATACTTCTAGCCCAACACTATA
1 TTATTATTA-TTTATTTTAAAACTAAAATTTGTATATCGTTAAATACTTTTAGCCTAAGAATATA
* ** * * *
18893782 GAA--TACAATGTTTGTTTTCCACAAAAATTAGTTTTTCTTTTACTTAATTGACATGTTACTTTA
65 -AATTTA-AATGTTTGTTTTTCATTAAAATTAGATTTT-TTTTACTTAATTGACTTGTTACGTTA
* * * ** * * * * *
18893845 AGC-CTTACATATATGTGTTAGGATTTTAAAATCATGTGTTTCAACTTTATGAGTTTTTACGTTA
127 A-CTCTCACACATTTACGTTAAGATTTTAAATTTAT-TGTTTCATCTTTATGAGTTTTTACGTCA
* * *
18893909 A-TCTTTACAATTTTACGTCAAGACATTTCAATGGCAACTTTTAATTATAATTATTTTTGTCCTT
190 ATTC-TTACAACTTTACGTCAAGACATTTCAATGGCAACTTTTAACTATAATTATTTTTATCCTT
* * * *
18893973 ATTATTCTTTATTTTAAAATTAAAATTTGTATATTGTTAAATATTTTTA-ACTCGAGAATATAAA
254 ATTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTTTTAGCCT-AAGAATATAAA
* * * * *
18894037 TTTAAATATTTATTTTCATTAAAATAAGATTTTTTTTATTTATTTGACTTATTACGTTAACT-TA
318 TTTAAATA-TT-TTTTCATTAAAATATGATTTTTTTGATCTAATTGACTTATTACATTAACTCT-
* *
18894101 CACACATTTACGTTAAGATTTTAAATTTGCTTGTTCCACCTTTATAAGCTTTTACGTCAATTCTT
380 CAAACATTTACGTTAAGATTTTAAATTTGCTTGTTCCACCTTTATAAGCTTTTACATCAATTCTT
* * * * * * * * *
18894166 ATAGCTTTTCA-TCAAGGCATTTCAAGGGCAACTTTTAACTATAATTATTCTTATGC
445 ACAAC-TTTAAGTCAAAGCTTTTCAATGGTAACTTTTAACTATAATTATTTTTATCC
* * * * * * * * *
18894222 TTATTATTTTTTATTCTAAAATTAAATTTTTTTTATTGTTAAATACTCTTA-CCTTGAGAATATA
1 TTATTATTATTTATTTTAAAACTAAAATTTGTATATCGTTAAATACTTTTAGCC-TAAGAATATA
* * * * * *
18894286 AATTTAAATCTTTATTTTTCATTAAAATTATAATTTTTTTTACTTAATTTACATGTTACATTAAC
65 AATTTAAATGTTTGTTTTTCATTAAAATTA-GATTTTTTTTACTTAATTGACTTGTTACGTTAAC
**
18894351 TCTCACACATTTAAATTAAGATTTTAAATTT
129 TCTCACACATTTACGTTAAGATTTTAAATTT
18894382 GTATTGTCAA
Statistics
Matches: 1333, Mismatches: 269, Indels: 124
0.77 0.16 0.07
Matches are distributed among these distances:
496 29 0.02
497 97 0.07
498 57 0.04
499 28 0.02
500 83 0.06
501 180 0.14
502 337 0.25
503 186 0.14
504 209 0.16
505 49 0.04
506 78 0.06
ACGTcount: A:0.33, C:0.11, G:0.08, T:0.48
Consensus pattern (500 bp):
TTATTATTATTTATTTTAAAACTAAAATTTGTATATCGTTAAATACTTTTAGCCTAAGAATATAA
ATTTAAATGTTTGTTTTTCATTAAAATTAGATTTTTTTTACTTAATTGACTTGTTACGTTAACTC
TCACACATTTACGTTAAGATTTTAAATTTATTGTTTCATCTTTATGAGTTTTTACGTCAATTCTT
ACAACTTTACGTCAAGACATTTCAATGGCAACTTTTAACTATAATTATTTTTATCCTTATTATTC
TTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTTTTAGCCTAAGAATATAAATTTAAATA
TTTTTTCATTAAAATATGATTTTTTTGATCTAATTGACTTATTACATTAACTCTCAAACATTTAC
GTTAAGATTTTAAATTTGCTTGTTCCACCTTTATAAGCTTTTACATCAATTCTTACAACTTTAAG
TCAAAGCTTTTCAATGGTAACTTTTAACTATAATTATTTTTATCC
Found at i:18893965 original size:251 final size:250
Alignment explanation
Indices: 18892215--18894379 Score: 1233
Period size: 251 Copynumber: 8.6 Consensus size: 250
18892205 GACAGTGACA
* * * ** *
18892215 TTATTATT-TTATATTTTAAAACTAAAATTTGTAAATCGTTAAATACTTTTAATCCGAGAATATA
1 TTATTATTATT-TATTTTAAAATTAAAATTTGTATATCGTTAAATACTTCTAGCCCAAGAATATA
* *
18892279 -AATTTA-AATGTTTGCTTTTCATTAAAATTAGATTTTTTTT-CTTAATTGACTTGTT-CAGTTA
65 GAA--TACAATGTTTGTTTTTCATTAAAATTAGATTTTTTTTACTTAATTGACTTGTTAC-TTTA
** * * * * * *
18892340 AC-TTTCACTCA-TTAATGTTAAGATTTTAAATTTGCTT-TTGT-AATTTTTATAAG-TTTTACG
127 ACACCT-ACACATTTAA-GTTAAGATTTTAAATAT-ATTGTT-TCAA-CTTTATGAGTTTTTACA
* * ** * * * *
18892400 TCAATTCTTACTGCTTTACGT-TAAGACTTTTCAATGGTAACTTTTAAATATAATTATTTTCATC
187 TTAATTTTTACAACTTTACGTCAAAG-CTTTTCAATGGCAACTTTTAATTATAATTATTTTTAT-
18892464 C
250 C
* * * ***
18892465 ATATTATTCTTTATTTTAAAATTAAAACTTT-TATATCGTTAAATACTTTTAGCTTGAGAATATA
1 TTATTATTATTTATTTTAAAATTAAAA-TTTGTATATCGTTAAATACTTCTAGCCCAAGAATATA
* * * * * *
18892529 -AATTTA-AATATTTAATTTTT--TTAAAGATTATATTTATTTTGATTTAATTGACTTGTTACAT
65 GAA--TACAATGTTT-GTTTTTCATTAAA-ATTAGATTT-TTTTTACTTAATTGACTTGTTACTT
*** * * * * * * * **
18892590 TAACTTTTA-ATCATTTACA-TTAGGATTTTAAATTTGCTTGGTCCACCTTTATAAGTTTTT-GG
125 TAACACCTACA-CATTTA-AGTTAAGATTTTAAATAT-ATTGTTTCAACTTTATGAGTTTTTACA
* * * * * * ** * *
18892652 TCAATTCTTACAACATTATGTCAAGGTTTTTCAATGATAACTTTTAACTATAAGTATTTTTATCC
187 TTAATTTTTACAACTTTACGTCAAAGCTTTTCAATGGCAACTTTTAATTATAATTATTTTTAT-C
* * * **
18892717 TTATTATT-TTTATTTTTAAATAAAAATTTATATATCGTTAAATACCTT-T-GACCCGTGAATAT
1 TTATTATTATTTATTTTAAAATTAAAATTTGTATATCGTTAAATA-CTTCTAG-CCCAAGAATAT
** * *
18892779 A-AATTTA-AATACTT-TTTTT-ATTAAAAATT-TATTTTTTTTACTTAATTGACTTGTTACGTT
64 AGAA--TACAATGTTTGTTTTTCATT-AAAATTAGATTTTTTTTACTTAATTGACTTGTTACTTT
* * ** * * * * * *
18892839 AAC-TCTCACACATTTACGTTTGGATTTTAAATTTACTTGTTCCATCTTTTTGACTTTTTACATC
126 AACACCT-ACACATTTAAGTTAAGATTTTAAATATA-TTGTTTCAACTTTATGAGTTTTTACATT
* * * * * * * *
18892903 AATTCTTACAACTTTATGTC-AAGCCATTTCAATGTCTACTTTTGACTATAATTATATTTATCC
189 AATTTTTACAACTTTACGTCAAAG-CTTTTCAATGGCAACTTTTAATTATAATTATTTTTAT-C
* * * * * * *
18892966 TTATTATTCTTAATTTAAAAAATTAAAATTTGTATATCGTCAAATATTTTTAGCCTAAGAATATA
1 TTATTATTATTTATTT-TAAAATTAAAATTTGTATATCGTTAAATACTTCTAGCCCAAGAATATA
** * * * * *
18893031 -AATTTAA-ATAT-TTTTTCATTAAAA-TATGATTTTTTTTAC-TAATAGAATTATTA-TATTAA
65 GAATACAATGTTTGTTTTTCATTAAAATTA-GATTTTTTTTACTTAATTGACTTGTTACT-TTAA
* * * * * * * * * ** * *
18893090 C-TCTCAAAAATTTATGTTAAAATTTT-AATTTGCTTCTTCCATTTTTATAAGTTTTTATATTAA
128 CACCT-ACACATTTAAGTTAAGATTTTAAATAT-ATTGTTTCAACTTTATGAGTTTTTACATTAA
* * * * * * * *
18893153 TTCTTATAATTTTAAGTCAAAGCTTTTCAATTGTAACTTTTAAATATAATTATTTTTACC
191 TTTTTACAACTTTACGTCAAAGCTTTTCAATGGCAACTTTTAATTATAATTATTTTTATC
* * * * * *
18893213 TTTTTAGTTATTTATTTTAAAACTAAAATTTGCATATCGTTAAATACTTTTAGTCTAAGAATATA
1 TTATTA-TTATTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTTCTAGCCCAAGAATATA
* * * *
18893278 -AATTTA-AATGTTTGTTTTTCATTAAAAGTAGATTTTGTTTTCACTTAGTTGATTTGTTACGTT
65 GAA--TACAATGTTTGTTTTTCATTAAAATTAGATTTT-TTTT-ACTTAATTGACTTGTTACTTT
* * * * ** *
18893341 AACTCCTACACATTTACGTTAAGATTTTAAATTTGATTGTTTCACCTTTATGAGTTTTTAGGTCA
126 AACACCTACACATTTAAGTTAAGATTTTAAATAT-ATTGTTTCAACTTTATGAGTTTTTACATTA
* * *
18893406 ATTTTTACAACTTTACGTCAAAAGCTTTTCAATGGCCAC-TTTAACTATAATAATTTTTATAC
190 ATTTTTACAACTTTACGTC-AAAGCTTTTCAATGGCAACTTTTAATTATAATTATTTTTAT-C
* * * * * *
18893468 TTATAATTATTTATTTCAAAATTAAAATTTGTAAATCTTTAAATAC-TCTTCGCGCAAGAATATA
1 TTATTATTATTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTTC-TAGCCCAAGAATATA
* * * * * * * *
18893532 GATTTCAATATTTGTTTTTCATTAAAATTAGAATGTTGTGACTTAATTGAGTTGTTA-TATTAAC
65 GAATACAATGTTTGTTTTTCATTAAAATTAGATTTTTTTTACTTAATTGACTTGTTACT-TTAAC
* * * * * * *
18893596 ACGTACACATTTCAGTTAAGATTATAAATATACTT-ATTCTATCTTTATGAGCTTTTACATTTAT
129 ACCTACACATTTAAGTTAAGATTTTAAATATA-TTGTTTC-AACTTTATGAGTTTTTACATTAAT
* * * *
18893660 TTTTACAACTTCATGTCAAAGCTTTTTAATGGGAACTTTTAATTATAATTATTTTTAT-
192 TTTTACAACTTTACGTCAAAGCTTTTCAATGGCAACTTTTAATTATAATTATTTTTATC
* * *
18893718 TT-TTATTACTTTATTTTAAAATTAAAATTTGTATATCATTAAATACTTCTAGCCCAACACTATA
1 TTATTATTA-TTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTTCTAGCCCAAGAATATA
* ** * *
18893782 GAATACAATGTTTGTTTTCCACAAAAATTAGTTTTTCTTTTACTTAATTGACATGTTACTTTAAG
65 GAATACAATGTTTGTTTTTCATTAAAATTAGATTTT-TTTTACTTAATTGACTTGTTACTTTAA-
* * * ** * *
18893847 C-CTTACATATATGTGTTAGGATTTTAAA-ATCATGTGTTTCAACTTTATGAGTTTTTACGTTAA
128 CACCTACACATTTAAGTTAAGATTTTAAATAT-AT-TGTTTCAACTTTATGAGTTTTTACATTAA
* * * *
18893910 TCTTTACAATTTTACGTC-AAGACATTTCAATGGCAACTTTTAATTATAATTATTTTTGTCC
191 TTTTTACAACTTTACGTCAAAG-CTTTTCAATGGCAACTTTTAATTATAATTATTTTTAT-C
* * * * * * *
18893971 TTATTATTCTTTATTTTAAAATTAAAATTTGTATATTGTTAAATATTTTTAACTCGAGAATATA-
1 TTATTATTATTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTTCTAGCCCAAGAATATAG
* * * * * * *
18894035 AATTTA-AATATTT-ATTTTCATTAAAATAAGATTTTTTTTATTTATTTGACTTATTACGTTAAC
66 AA--TACAATGTTTGTTTTTCATTAAAATTAGATTTTTTTTACTTAATTGACTTGTTACTTTAAC
* * * * * * * * *
18894098 TTA-C-ACACATTTACGTTAAGATTTTAAATTTGCTTGTTCCACCTTTATAAGCTTTTACGTCAA
129 --ACCTACACATTTAAGTTAAGATTTTAAATAT-ATTGTTTCAACTTTATGAGTTTTTACATTAA
* * * * * * * * * *
18894161 TTCTTATAGCTTTTCATCAAGGCATTTCAAGGGCAACTTTTAACTATAATTATTCTTATGC
191 TTTTTACAACTTTACGTCAAAGCTTTTCAATGGCAACTTTTAATTATAATTATTTTTAT-C
* * * * * * **
18894222 TTATTATTTTTTATTCTAAAATTAAATTTTTTTTATTGTTAAATAC-TCTTA-CCTTGAGAATAT
1 TTATTATTATTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTTC-TAGCC-CAAGAATAT
* * * * * *
18894285 A-AATTTA-AATCTTTATTTTTCATTAAAATTATAATTTTTTTTACTTAATTTACATGTTACATT
64 AGAA--TACAATGTTTGTTTTTCATTAAAATTA-GATTTTTTTTACTTAATTGACTTGTTACTTT
* *
18894348 AAC-TCTCACACATTTAAATTAAGATTTTAAAT
126 AACACCT-ACACATTTAAGTTAAGATTTTAAAT
18894380 TTGTATTGTC
Statistics
Matches: 1529, Mismatches: 302, Indels: 165
0.77 0.15 0.08
Matches are distributed among these distances:
247 52 0.03
248 150 0.10
249 134 0.09
250 205 0.13
251 415 0.27
252 254 0.17
253 155 0.10
254 142 0.09
255 22 0.01
ACGTcount: A:0.33, C:0.11, G:0.08, T:0.48
Consensus pattern (250 bp):
TTATTATTATTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTTCTAGCCCAAGAATATAG
AATACAATGTTTGTTTTTCATTAAAATTAGATTTTTTTTACTTAATTGACTTGTTACTTTAACAC
CTACACATTTAAGTTAAGATTTTAAATATATTGTTTCAACTTTATGAGTTTTTACATTAATTTTT
ACAACTTTACGTCAAAGCTTTTCAATGGCAACTTTTAATTATAATTATTTTTATC
Found at i:18894115 original size:754 final size:745
Alignment explanation
Indices: 18892385--18894379 Score: 1944
Period size: 754 Copynumber: 2.7 Consensus size: 745
18892375 TTTTGTAATT
* * *** *
18892385 TTTATAAG-TTTTACGTCAATTCTTACTGCTTTACGTTAAGACTTTTCAATGGTAACTTTTAAAT
1 TTTATAAGTTTTTACATTAATTCTTACAATTTTACGTCAAGACTTTTCAATGGTAACTTTTAAAT
* *
18892449 ATAATTATTTTCATCCATATTATTCTTTATTTTAAAATTAAAACTTT-TATATCGTTAAATACTT
66 ATAATTATTTT-TTCCTTATTATTCTTTATTTTAAAATTAAAA-TTTGTATATCGTTAAATACTT
* * * * *
18892513 TTAGCTTGAGAATATAAATTTAAATATTTAATTTT-TTTAAAGATTATATTTATTTTGATTTAAT
129 TTAACTCGAGAATATAAATTTAAATATTTAATTTTCATTAAA-A-TAGATTT-TTTTTATTTAAT
* ** * * *
18892577 TGACTTGTTACATTAACTTTTA-ATCATTTACATTAGGATTTTAAATTTGCTTGGTCCACCTTTA
191 TGACTTGTTACGTTAACTTACACA-CATTTACGTTAAGATTTTAAATTTGCTTGTTCCACCTTTA
* * * **
18892641 TAAGTTTTT-GGTCAATTCTTACAACATTATGTCAAGGTTTTTCAATGATAACTTTTAACTATAA
255 TAAGTTTTTAGGTCAATTCTTACAACTTTACGTCAAGGCTTTTCAATGGCAACTTTTAACTATAA
* ** * * *
18892705 GTATTTTTATCCTTATTATTTTTATTTTTAAATAAAAATTTATATATCGTTAAATAC-CTTTGAC
320 -TATTTTTATACTTATTATTTTTATTTCAAAATTAAAATTTATATATCTTTAAATACTCTTCG-C
* * * * * * *
18892769 CCGTGAATATAAATTTAAATACTTTTTTT-ATTAAAAATT-TATTTTTTTTACTTAATTGACTTG
383 CCGAGAATATAAATTTAAATATTTTTTTTCATT-AAAATTAGAATGTTGTGACTTAATTGACTTG
* * ** * * * *
18892832 TTACGTTAACTCTCACACATTTACGTTTGGATTTTAAATTTACTTGTTCCATCTTTTTGACTTTT
447 TTACATTAACACTCACACATTTACGTTAAGATTATAAATATACTTATTCCATCTTTATGACTTTT
* * * *
18892897 TACATCAATTCTTACAACTTTATGTCAAGCCATTTCAATGTCTACTTTTGACTATAATTATATTT
512 TACATCAATTCTTACAACTTCATGTCAAGCCATTTCAATGGCAACTTTTAACTATAATTATATTT
* * * * *
18892962 ATCCTTATTATTCTTAATTTAAAAAATTAAAATTTGTATATCGTCAAATATTTTTAGCCTAAGAA
577 AT-CTTATTATTCTTAATTTAAAAAATTAAAATTTGTATATCATCAAATACTTCTAGCCCAACAA
**
18893027 TATAAATTTAAATATTTTTTCATTAAAATATGATTTTTTTTACTAATAGAATTATTATATTAACT
641 TATAAA-TTAAATATTTTTTCACAAAAATATGATTTTTTTTACTAATAGAATTATTATATTAACT
* ** **
18893092 CTCAAAAATTTATGTTAAAATTTTAATTTGCTTCTTCCATT
705 CTCAAAAATATATGTTAAAATTTTAAAATGCTTCTTCCAAC
* * * *
18893133 TTTATAAGTTTTTATATTAATTCTTATAATTTTAAGTCAA-AGCTTTTCAATTGTAACTTTTAAA
1 TTTATAAGTTTTTACATTAATTCTTACAATTTTACGTCAAGA-CTTTTCAATGGTAACTTTTAAA
* * * * *
18893197 TATAATTATTTTTACCTTTTTAGTTATTTATTTTAAAACTAAAATTTGCATATCGTTAAATACTT
65 TATAATTATTTTTTCCTTATTA-TTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTT
* * * ** * *
18893262 TT-AGTCTAAGAATATAAATTTAAATGTTTGTTTTTCATTAAAAGTAGATTTTGTTTTCACTTAG
129 TTAACTC-GAGAATATAAATTTAAATATTTAATTTTCATTAAAA-TAGATTTT-TTTT-ATTTAA
* * * *
18893326 TTGATTTGTTACGTTAAC-TCCTACACATTTACGTTAAGATTTTAAATTTGATTGTTTCACCTTT
190 TTGACTTGTTACGTTAACTTAC-ACACATTTACGTTAAGATTTTAAATTTGCTTGTTCCACCTTT
* * * *
18893390 ATGAGTTTTTAGGTCAATTTTTACAACTTTACGTCAAAAGCTTTTCAATGGCCAC-TTTAACTAT
254 ATAAGTTTTTAGGTCAATTCTTACAACTTTACGTC-AAGGCTTTTCAATGGCAACTTTTAACTAT
* * *
18893454 AATAATTTTTATACTTATAATTATTTATTTCAAAATTAAAATTTGTAAATCTTTAAATACTCTTC
318 AAT-ATTTTTATACTTATTATT-TTTATTTCAAAATTAAAATTTATATATCTTTAAATACTCTTC
* * * * *
18893519 GCGCAAGAATATAGATTTCAATATTTGTTTTTCATTAAAATTAGAATGTTGTGACTTAATTGAGT
381 GCCCGAGAATATAAATTTAAATATTT-TTTTTCATTAAAATTAGAATGTTGTGACTTAATTGACT
* *
18893584 TGTTATATTAACACGT-ACACATTT-CAGTTAAGATTATAAATATACTTATTCTATCTTTATGAG
445 TGTTACATTAACAC-TCACACATTTAC-GTTAAGATTATAAATATACTTATTCCATCTTTATGA-
** * * * * *
18893647 C-TTTTACATTTATTTTTACAACTTCATGTCAAAG-CTTTTTAATGGGAACTTTTAATTATAATT
507 CTTTTTACATCAATTCTTACAACTTCATGTC-AAGCCATTTCAATGGCAACTTTTAACTATAATT
* * * *
18893710 ATTTTTAT-TT-TTATTACTTTATTT-TAAAATTAAAATTTGTATATCATTAAATACTTCTAGCC
571 ATATTTATCTTATTATT-CTTAATTTAAAAAATTAAAATTTGTATATCATCAAATACTTCTAGCC
* * * *
18893772 CAACACTATAGAA-TACAATGTTTGTTTTCCACAAAAAT-TAGTTTTTCTTTTACTTAATTGACA
635 CAACAATATA-AATTA-AAT-ATT-TTTT-CACAAAAATAT-GATTTT-TTTTAC-TAATAGA-A
* * * * * ** * *
18893835 -TGTTACT-TTAAGC-CTTACATATATGTGTTAGGATTTTAAAAT-CATGTGTTTCAAC
691 TTATTA-TATTAA-CTCTCAAAAATATATGTTAAAATTTTAAAATGC-T-TCTTCCAAC
* * * * *
18893890 TTTATGAGTTTTTACGTTAA-TCTTTACAATTTTACGTCAAGACATTTCAATGGCAACTTTTAAT
1 TTTATAAGTTTTTACATTAATTC-TTACAATTTTACGTCAAGACTTTTCAATGGTAACTTTTAAA
* *
18893954 TATAATTATTTTTGTCCTTATTATTCTTTATTTTAAAATTAAAATTTGTATATTGTTAAATATTT
65 TATAATTATTTTT-TCCTTATTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTT
*
18894019 TTAACTCGAGAATATAAATTTAAATATTT-ATTTTCATTAAAATAAGATTTTTTTTATTTATTTG
129 TTAACTCGAGAATATAAATTTAAATATTTAATTTTCATTAAAAT-AGATTTTTTTTATTTAATTG
*
18894083 ACTTATTACGTTAACTTACACACATTTACGTTAAGATTTTAAATTTGCTTGTTCCACCTTTATAA
193 ACTTGTTACGTTAACTTACACACATTTACGTTAAGATTTTAAATTTGCTTGTTCCACCTTTATAA
* * * * * * * *
18894148 GCTTTTACGTCAATTCTTATAGCTTTTCATCAAGGCATTTCAAGGGCAACTTTTAACTATAATTA
258 GTTTTTAGGTCAATTCTTACAACTTTACGTCAAGGCTTTTCAATGGCAACTTTTAACTATAA-TA
* * * * *
18894213 TTCTTATGCTTATTATTTTT-TATTCTAAAATTAAATTTTTTTTAT-TGTTAAATACTCTTAC-C
322 TTTTTATACTTATTATTTTTAT-TTC-AAAATTAAAATTTATATATCT-TTAAATACTCTT-CGC
** * * * * * * *
18894275 TTGAGAATATAAATTTAAATCTTTATTTTTCATTAAAATTATAATTTTTTTTACTTAATTTACAT
383 CCGAGAATATAAATTTAAATATTT-TTTTTCATTAAAATTAGAA-TGTTGTGACTTAATTGACTT
* ** *
18894340 GTTACATTAACTCTCACACATTTAAATTAAGATTTTAAAT
446 GTTACATTAACACTCACACATTTACGTTAAGATTATAAAT
18894380 TTGTATTGTC
Statistics
Matches: 1012, Mismatches: 184, Indels: 95
0.78 0.14 0.07
Matches are distributed among these distances:
748 20 0.02
749 127 0.13
750 72 0.07
751 97 0.10
752 78 0.08
753 43 0.04
754 311 0.31
755 67 0.07
756 56 0.06
757 130 0.13
758 11 0.01
ACGTcount: A:0.33, C:0.11, G:0.08, T:0.48
Consensus pattern (745 bp):
TTTATAAGTTTTTACATTAATTCTTACAATTTTACGTCAAGACTTTTCAATGGTAACTTTTAAAT
ATAATTATTTTTTCCTTATTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTTTT
AACTCGAGAATATAAATTTAAATATTTAATTTTCATTAAAATAGATTTTTTTTATTTAATTGACT
TGTTACGTTAACTTACACACATTTACGTTAAGATTTTAAATTTGCTTGTTCCACCTTTATAAGTT
TTTAGGTCAATTCTTACAACTTTACGTCAAGGCTTTTCAATGGCAACTTTTAACTATAATATTTT
TATACTTATTATTTTTATTTCAAAATTAAAATTTATATATCTTTAAATACTCTTCGCCCGAGAAT
ATAAATTTAAATATTTTTTTTCATTAAAATTAGAATGTTGTGACTTAATTGACTTGTTACATTAA
CACTCACACATTTACGTTAAGATTATAAATATACTTATTCCATCTTTATGACTTTTTACATCAAT
TCTTACAACTTCATGTCAAGCCATTTCAATGGCAACTTTTAACTATAATTATATTTATCTTATTA
TTCTTAATTTAAAAAATTAAAATTTGTATATCATCAAATACTTCTAGCCCAACAATATAAATTAA
ATATTTTTTCACAAAAATATGATTTTTTTTACTAATAGAATTATTATATTAACTCTCAAAAATAT
ATGTTAAAATTTTAAAATGCTTCTTCCAAC
Found at i:18894732 original size:20 final size:20
Alignment explanation
Indices: 18894707--18894752 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
18894697 TTTTTGCTCT
* *
18894707 ATTTGACTTATTGGAGTATG
1 ATTTGACTAATTGAAGTATG
*
18894727 ATTTGAGTAATTGAAGTATG
1 ATTTGACTAATTGAAGTATG
18894747 ATTTGA
1 ATTTGA
18894753 GGTTTAGAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.02, G:0.24, T:0.43
Consensus pattern (20 bp):
ATTTGACTAATTGAAGTATG
Found at i:18894753 original size:20 final size:20
Alignment explanation
Indices: 18894716--18894753 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
18894706 TATTTGACTT
*
18894716 ATTGGAGTATGATTTGAGTA
1 ATTGAAGTATGATTTGAGTA
18894736 ATTGAAGTATGATTTGAG
1 ATTGAAGTATGATTTGAG
18894754 GTTTAGAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.29, T:0.39
Consensus pattern (20 bp):
ATTGAAGTATGATTTGAGTA
Found at i:18897374 original size:15 final size:14
Alignment explanation
Indices: 18897350--18897382 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
18897340 AGATCAGAGA
18897350 TTTTGATTTTAAAG
1 TTTTGATTTTAAAG
18897364 TTTTGGATTTTAAAG
1 TTTT-GATTTTAAAG
18897379 TTTT
1 TTTT
18897383 TGGTTTTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.61
Consensus pattern (14 bp):
TTTTGATTTTAAAG
Found at i:18897389 original size:15 final size:14
Alignment explanation
Indices: 18897350--18897390 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
18897340 AGATCAGAGA
*
18897350 TTTTGATTTTAAAG
1 TTTTGGTTTTAAAG
18897364 TTTTGGATTTTAAAG
1 TTTTGG-TTTTAAAG
18897379 TTTTTGGTTTTA
1 -TTTTGGTTTTA
18897391 GGACTATCGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 5 0.21
15 13 0.54
16 6 0.25
ACGTcount: A:0.22, C:0.00, G:0.17, T:0.61
Consensus pattern (14 bp):
TTTTGGTTTTAAAG
Found at i:18899060 original size:43 final size:43
Alignment explanation
Indices: 18899012--18899130 Score: 159
Period size: 43 Copynumber: 2.8 Consensus size: 43
18899002 TCACCAGCTC
** * *
18899012 ATGCGCACTCCCTACTCGCACATGGCTGGGTCATCAC-CGGGTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATC-CTCGGCTT
18899055 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
* * *
18899098 ATGTGCACTCCCTACTCGCACATAGCCGAGTCA
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCA
18899131 ATATAATTAC
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 1 0.01
43 67 0.99
ACGTcount: A:0.19, C:0.37, G:0.21, T:0.23
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
Found at i:18899951 original size:19 final size:20
Alignment explanation
Indices: 18899917--18899954 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
18899907 GAAGAAGACC
*
18899917 AGCTGTTGGAAAATTCAAGA
1 AGCTGCTGGAAAATTCAAGA
18899937 AGCTGCTGG-AAATTCAAG
1 AGCTGCTGGAAAATTCAAG
18899955 GTATTTATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (20 bp):
AGCTGCTGGAAAATTCAAGA
Found at i:18901458 original size:30 final size:29
Alignment explanation
Indices: 18901419--18901489 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 29
18901409 GATCAGTAAT
18901419 AACCCATGGTTTGT-AATGGATTCAACCACA
1 AACCCATGGTTT-TCAATGGATTC-ACCACA
* *
18901449 AACCGATGGTTTTCAATGGGTTCACCACA
1 AACCCATGGTTTTCAATGGATTCACCACA
*
18901478 AACCTATGGTTT
1 AACCCATGGTTT
18901490 CCAACAAGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 18 0.49
30 19 0.51
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (29 bp):
AACCCATGGTTTTCAATGGATTCACCACA
Found at i:18901486 original size:29 final size:29
Alignment explanation
Indices: 18901419--18901510 Score: 96
Period size: 29 Copynumber: 3.1 Consensus size: 29
18901409 GATCAGTAAT
*
18901419 AACCCATGGTTTGT-AATGGATTCAACCACA
1 AACCCATGGTTT-TCAATGGGTTC-ACCACA
*
18901449 AACCGATGGTTTTCAATGGGTTCACCACA
1 AACCCATGGTTTTCAATGGGTTCACCACA
* * ***
18901478 AACCTATGGTTTCCAACAAGTTCACCACA
1 AACCCATGGTTTTCAATGGGTTCACCACA
18901507 AACC
1 AACC
18901511 AATACTAACT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
29 35 0.65
30 19 0.35
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (29 bp):
AACCCATGGTTTTCAATGGGTTCACCACA
Found at i:18902777 original size:37 final size:37
Alignment explanation
Indices: 18902736--18902813 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 37
18902726 CATATGCATT
18902736 CATCATCATGTGTGCACTCCCTACTCGCACAC-TCTAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTC-AA
*
18902773 CATCATCATGTGTGCACTCCCTACTTGCACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
18902810 CATC
1 CATC
18902814 CTCACACAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
37 37 0.95
38 2 0.05
ACGTcount: A:0.24, C:0.37, G:0.10, T:0.28
Consensus pattern (37 bp):
CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
Found at i:18904941 original size:19 final size:19
Alignment explanation
Indices: 18904917--18904954 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
18904907 CCATTTGACT
*
18904917 TATTGGAGTATGATTTGAG
1 TATTGGAGCATGATTTGAG
18904936 TATTGGAGCATGATTTGAG
1 TATTGGAGCATGATTTGAG
18904955 GTTTATAAGT
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:0.03, G:0.32, T:0.39
Consensus pattern (19 bp):
TATTGGAGCATGATTTGAG
Found at i:18917163 original size:22 final size:23
Alignment explanation
Indices: 18917115--18917167 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
18917105 TTGCAAATTA
*
18917115 AAAGCTTGATAAATACTAGAAAG
1 AAAGCTTGATAAATACAAGAAAG
* *
18917138 AAAGCTTGATAAA-GCAAGGAAG
1 AAAGCTTGATAAATACAAGAAAG
18917160 AAAGCTTG
1 AAAGCTTG
18917168 TTATTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.49, C:0.09, G:0.23, T:0.19
Consensus pattern (23 bp):
AAAGCTTGATAAATACAAGAAAG
Found at i:18919488 original size:74 final size:74
Alignment explanation
Indices: 18919393--18919555 Score: 272
Period size: 74 Copynumber: 2.2 Consensus size: 74
18919383 TGCCCAAATG
* * * *
18919393 AGAATTTGATTCTTCATGCTTTAGCTTTAGGCTTAATGCTTTCTGTTCCTCAGGAATCGAACATT
1 AGAAGTTGATTCTTCATGCTTTAGCTTTAGGCCTAATGCTCTCTATTCCTCAGGAATCGAACATT
*
18919458 CATCCATCA
66 CATCCACCA
18919467 AGAAGTTGATTCTTCATGCTTTAGCTTTAGGCCTAATGCTCTCTATTCCTCAGGAATCGAACATT
1 AGAAGTTGATTCTTCATGCTTTAGCTTTAGGCCTAATGCTCTCTATTCCTCAGGAATCGAACATT
18919532 CATCCACCA
66 CATCCACCA
*
18919541 AGAAGTTCATTCTTC
1 AGAAGTTGATTCTTC
18919556 TCGTCTTACT
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 83 1.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (74 bp):
AGAAGTTGATTCTTCATGCTTTAGCTTTAGGCCTAATGCTCTCTATTCCTCAGGAATCGAACATT
CATCCACCA
Found at i:18920977 original size:16 final size:16
Alignment explanation
Indices: 18920958--18920992 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
18920948 GTATAAATCT
*
18920958 CATTTTTATTAAAAAA
1 CATTTTAATTAAAAAA
*
18920974 CATTTTAATTAGAAAA
1 CATTTTAATTAAAAAA
18920990 CAT
1 CAT
18920993 AATATTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.40
Consensus pattern (16 bp):
CATTTTAATTAAAAAA
Found at i:18922362 original size:19 final size:19
Alignment explanation
Indices: 18922338--18922375 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
18922328 CTTCCAAACC
*
18922338 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
18922357 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
18922376 AGTTAAATGG
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:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:18923451 original size:21 final size:20
Alignment explanation
Indices: 18923419--18923457 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
18923409 GAATGGGGAG
*
18923419 AAAAAGAGAAAAACGGAAGA
1 AAAAAGAGAAAAAAGGAAGA
18923439 AAAAAGAGAAAAAAAGGAA
1 AAAAAGAG-AAAAAAGGAA
18923458 AATGAACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.74, C:0.03, G:0.23, T:0.00
Consensus pattern (20 bp):
AAAAAGAGAAAAAAGGAAGA
Found at i:18924515 original size:24 final size:24
Alignment explanation
Indices: 18924488--18924557 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 24
18924478 AATATATAAG
18924488 ATTATAATAAAAATAAAATATGAC
1 ATTATAATAAAAATAAAATATGAC
* * ** * *
18924512 ATTAAAATATATTTAAAAGATGAT
1 ATTATAATAAAAATAAAATATGAC
18924536 ATTAT-ATAAAAATTAACAATAT
1 ATTATAATAAAAA-TAA-AATAT
18924558 TAAACTTGCA
Statistics
Matches: 33, Mismatches: 11, Indels: 3
0.70 0.23 0.06
Matches are distributed among these distances:
23 4 0.12
24 25 0.76
25 4 0.12
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.34
Consensus pattern (24 bp):
ATTATAATAAAAATAAAATATGAC
Found at i:18924731 original size:15 final size:15
Alignment explanation
Indices: 18924711--18924762 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
18924701 TCTTTGTTGA
18924711 AATCACATTGATTGC
1 AATCACATTGATTGC
18924726 AATCACATT-ACTTGC
1 AATCACATTGA-TTGC
* * *
18924741 AATTACATTGCTTGT
1 AATCACATTGATTGC
18924756 AATCACA
1 AATCACA
18924763 CTACATTGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 1 0.03
15 30 0.97
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.35
Consensus pattern (15 bp):
AATCACATTGATTGC
Found at i:18929075 original size:19 final size:19
Alignment explanation
Indices: 18929053--18929094 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
18929043 TAATCATAAT
* *
18929053 AAAAATATAGAAATATATA
1 AAAAATATACAAAAATATA
18929072 AAAAATATACAAAAATATA
1 AAAAATATACAAAAATATA
18929091 AAAA
1 AAAA
18929095 TAAAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (19 bp):
AAAAATATACAAAAATATA
Found at i:18929079 original size:11 final size:10
Alignment explanation
Indices: 18929048--18929094 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
18929038 AAATATAATC
18929048 ATAATAAAAAT
1 ATAA-AAAAAT
* *
18929059 ATAGAAATAT
1 ATAAAAAAAT
18929069 AT-AAAAAAT
1 ATAAAAAAAT
*
18929078 ATACAAAAAT
1 ATAAAAAAAT
18929088 ATAAAAA
1 ATAAAAA
18929095 TAAAATATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
9 7 0.24
10 19 0.66
11 3 0.10
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (10 bp):
ATAAAAAAAT
Found at i:18929085 original size:10 final size:9
Alignment explanation
Indices: 18929053--18929094 Score: 57
Period size: 10 Copynumber: 4.4 Consensus size: 9
18929043 TAATCATAAT
18929053 AAAAATATA
1 AAAAATATA
*
18929062 GAAATATATA
1 -AAAAATATA
18929072 AAAAATATA
1 AAAAATATA
18929081 CAAAAATATA
1 -AAAAATATA
18929091 AAAA
1 AAAA
18929095 TAAAATATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 12 0.41
10 17 0.59
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (9 bp):
AAAAATATA
Found at i:18929095 original size:8 final size:8
Alignment explanation
Indices: 18929036--18929096 Score: 50
Period size: 10 Copynumber: 6.9 Consensus size: 8
18929026 TTGTTTACGA
18929036 AAAAATAT
1 AAAAATAT
**
18929044 AATCATAAT
1 AAAAAT-AT
18929053 AAAAATAT
1 AAAAATAT
18929061 AGAAATATAT
1 A-AAA-ATAT
18929071 AAAAAATAT
1 -AAAAATAT
18929080 ACAAAAATAT
1 --AAAAATAT
18929090 AAAAATA
1 AAAAATA
18929097 AAATATAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
8 14 0.33
9 13 0.30
10 15 0.35
11 1 0.02
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.25
Consensus pattern (8 bp):
AAAAATAT
Found at i:18934783 original size:21 final size:21
Alignment explanation
Indices: 18934757--18934806 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
18934747 TTTGTACTGG
18934757 GGTAAAAAGTGTTATAAAATA
1 GGTAAAAAGTGTTATAAAATA
* *
18934778 GGTAAAAAGTGTTGTAAATTA
1 GGTAAAAAGTGTTATAAAATA
*
18934799 GATAAAAA
1 GGTAAAAA
18934807 CAAGTGTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.52, C:0.00, G:0.20, T:0.28
Consensus pattern (21 bp):
GGTAAAAAGTGTTATAAAATA
Found at i:18935859 original size:21 final size:21
Alignment explanation
Indices: 18935834--18935873 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
18935824 GAATAAAGAT
18935834 AAAAAT-ACATATAAAATAACG
1 AAAAATCA-ATATAAAATAACG
18935855 AAAAATCAATATAAAATAA
1 AAAAATCAATATAAAATAA
18935874 TTTTTGCTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.70, C:0.07, G:0.03, T:0.20
Consensus pattern (21 bp):
AAAAATCAATATAAAATAACG
Found at i:18936154 original size:20 final size:21
Alignment explanation
Indices: 18936115--18936154 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
18936105 GTACAAACTG
18936115 TTATGATCAATTTAAGATGAA
1 TTATGATCAATTTAAGATGAA
18936136 TTATGAT-AATTATAA-ATGA
1 TTATGATCAATT-TAAGATGA
18936155 TAAAAATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.40
Consensus pattern (21 bp):
TTATGATCAATTTAAGATGAA
Found at i:18945935 original size:20 final size:20
Alignment explanation
Indices: 18945910--18945947 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
18945900 TAGAAATGAC
*
18945910 TTAGTCGACTAAGAGCATAG
1 TTAGTCAACTAAGAGCATAG
18945930 TTAGTCAACTAAGAGCAT
1 TTAGTCAACTAAGAGCAT
18945948 TCTGCCAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (20 bp):
TTAGTCAACTAAGAGCATAG
Found at i:18960964 original size:30 final size:29
Alignment explanation
Indices: 18960875--18961042 Score: 205
Period size: 30 Copynumber: 5.7 Consensus size: 29
18960865 TTAAGACAAC
* *
18960875 TCTTGTCATTAATTAAGACAAAACATGTTA
1 TCTTGTC-TAAATTAAGACAAAACATGTTT
*
18960905 TCCTGTCTAAATTAAGAC-AAACATGTTTT
1 TCTTGTCTAAATTAAGACAAAACATG-TTT
* *
18960934 TCTTGTCTAGATTAAGACAAAACATATTTT
1 TCTTGTCTAAATTAAGACAAAACAT-GTTT
* *
18960964 TCTTGTCTAAATTAAGATAAAACATATTT
1 TCTTGTCTAAATTAAGACAAAACATGTTT
*
18960993 TCTTGTGTTAAATTAAG-CTAAAACATGTTT
1 TCTTGT-CTAAATTAAGAC-AAAACATGTTT
18961023 TCTTGTCTAAATTAAGACAA
1 TCTTGTCTAAATTAAGACAA
18961043 GCATGTAAAA
Statistics
Matches: 119, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.06
29 48 0.40
30 64 0.54
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (29 bp):
TCTTGTCTAAATTAAGACAAAACATGTTT
Found at i:18960974 original size:59 final size:59
Alignment explanation
Indices: 18960885--18961048 Score: 208
Period size: 59 Copynumber: 2.8 Consensus size: 59
18960875 TCTTGTCATT
* *
18960885 AATTAAGACAAAACATGTTATCCTGTCTAAATTAAGACAAACATGTTTTTCTTGT-CTA
1 AATTAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAACATGTTTTTCTTGTGCTA
* * * * *
18960943 GATTAAGACAAAACATATTTTTCTTGTCTAAATTAAGATAAAACAT-ATTTTCTTGTGTTA
1 AATTAAGACAAAACAT-GTTTTCTTGTCTAAATTAAGA-CAAACATGTTTTTCTTGTGCTA
*
18961003 AATTAAG-CTAAAACATGTTTTCTTGTCTAAATTAAGACAAGCATGT
1 AATTAAGAC-AAAACATGTTTTCTTGTCTAAATTAAGACAAACATGT
18961049 AAAAGTTGCC
Statistics
Matches: 89, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
58 20 0.22
59 48 0.54
60 21 0.24
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (59 bp):
AATTAAGACAAAACATGTTTTCTTGTCTAAATTAAGACAAACATGTTTTTCTTGTGCTA
Found at i:18970427 original size:26 final size:26
Alignment explanation
Indices: 18970371--18970427 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
18970361 TGAAGACGAA
* *
18970371 AAGTAGAGTCTTTCCACATTCCACGG
1 AAGTAAAGTCTTTCCACATTCCAAGG
*
18970397 AAGTAAAGTCTTTCCACATTCTAAGG
1 AAGTAAAGTCTTTCCACATTCCAAGG
*
18970423 GAGTA
1 AAGTA
18970428 TTCTCTTTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (26 bp):
AAGTAAAGTCTTTCCACATTCCAAGG
Found at i:18975004 original size:42 final size:43
Alignment explanation
Indices: 18974944--18975047 Score: 129
Period size: 42 Copynumber: 2.4 Consensus size: 43
18974934 TTGACTTGGC
*
18974944 TATGTGCGAGTAAAGAGTGCACATAAGCCGAGGATGACCCTGT
1 TATGTGCGAGTAAAGAGTGCACATAACCCGAGGATGACCCTGT
* * * * *
18974987 TATGTGC-TGTAAAGAGTGCGCATAACCCGATGATGACCCAGC
1 TATGTGCGAGTAAAGAGTGCACATAACCCGAGGATGACCCTGT
* *
18975029 CATGTGCGAGTAAGGAGTG
1 TATGTGCGAGTAAAGAGTG
18975048 TGCATGAGTT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 35 0.69
43 16 0.31
ACGTcount: A:0.29, C:0.19, G:0.31, T:0.21
Consensus pattern (43 bp):
TATGTGCGAGTAAAGAGTGCACATAACCCGAGGATGACCCTGT
Found at i:18975488 original size:39 final size:39
Alignment explanation
Indices: 18975425--18975513 Score: 124
Period size: 39 Copynumber: 2.3 Consensus size: 39
18975415 TAGCTTCTCG
* * * *
18975425 CTGCAGCGAGAAACTTTCTTTTTCTGGGTTACAATTTCA
1 CTGCAGCGAGAAACATTCTATTTCTAGGTCACAATTTCA
*
18975464 CTGCAGCGAGAAACATTCTATTTCTAGGTCACAATTTCG
1 CTGCAGCGAGAAACATTCTATTTCTAGGTCACAATTTCA
*
18975503 CTGCAGTGAGA
1 CTGCAGCGAGA
18975514 TTGAATCTTG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (39 bp):
CTGCAGCGAGAAACATTCTATTTCTAGGTCACAATTTCA
Found at i:18978916 original size:71 final size:71
Alignment explanation
Indices: 18978745--18978916 Score: 206
Period size: 72 Copynumber: 2.4 Consensus size: 71
18978735 CTTATCACTG
* * * *
18978745 AGTATCGATACTTTTCACACAAAATGCTTCCTAAGACATTTTGTCTTCTAAGTATCAATACTTCT
1 AGTATCGATATTTTTCACACAAAATGCTACCCAAGACATTTTGTCCTCTAAGTATCAATAC-TCT
*
18978810 TTTTGTA
65 TTCTGTA
* * * *
18978817 AATATCAATATTTTTCACACAAAATGCTACCCAAGGCATTTTGTCCTCTAAGTATCGATAC-CTG
1 AGTATCGATATTTTTCACACAAAATGCTACCCAAGACATTTTGTCCTCTAAGTATCAATACTCT-
18978881 TTCT-TA
65 TTCTGTA
18978887 AGGTATCGATATTTTTGCA-ACAAAATGCTA
1 A-GTATCGATATTTTT-CACACAAAATGCTA
18978917 TTTTCTTGCC
Statistics
Matches: 86, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
70 5 0.06
71 26 0.30
72 55 0.64
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (71 bp):
AGTATCGATATTTTTCACACAAAATGCTACCCAAGACATTTTGTCCTCTAAGTATCAATACTCTT
TCTGTA
Found at i:18985065 original size:23 final size:23
Alignment explanation
Indices: 18985035--18985078 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
18985025 TGAAATGTCA
*
18985035 CTTTGACCTGAAAAAAGAGCCTT
1 CTTTGACCTGAAAAAACAGCCTT
18985058 CTTTGACCTGAAAAAACAGCC
1 CTTTGACCTGAAAAAACAGCC
18985079 ATATTTCCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (23 bp):
CTTTGACCTGAAAAAACAGCCTT
Found at i:18989428 original size:19 final size:19
Alignment explanation
Indices: 18989404--18989443 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
18989394 TAATGTGGTA
18989404 ATTGAAAACTAGCTAAGAG
1 ATTGAAAACTAGCTAAGAG
18989423 ATTGAAAACTAGCTAAGAG
1 ATTGAAAACTAGCTAAGAG
18989442 AT
1 AT
18989444 AGCTTTTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.23
Consensus pattern (19 bp):
ATTGAAAACTAGCTAAGAG
Found at i:18989861 original size:43 final size:43
Alignment explanation
Indices: 18989799--18989910 Score: 147
Period size: 43 Copynumber: 2.6 Consensus size: 43
18989789 TATTGACTCG
* *
18989799 GCTATGTGTGAGTAGGGAGTGCGCATAAGTCAAG-GATGACCC-
1 GCTATGTGCGAGTAGGGAGTGCGCATAA-CCAAGTGATGACCCA
**
18989841 GACTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCA
1 G-CTATGTGCGAGTAGGGAGTGCGCATAACCAAGTGATGACCCA
*
18989885 GCCATGTGCGAGTAGGGAGTGCGCAT
1 GCTATGTGCGAGTAGGGAGTGCGCAT
18989911 GAGCTAGTGA
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
42 3 0.05
43 58 0.94
44 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.37, T:0.20
Consensus pattern (43 bp):
GCTATGTGCGAGTAGGGAGTGCGCATAACCAAGTGATGACCCA
Found at i:19002147 original size:20 final size:20
Alignment explanation
Indices: 19002122--19002175 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
19002112 CAGAAGCAAC
19002122 TTAGTCAACTAAGATATCAG
1 TTAGTCAACTAAGATATCAG
*
19002142 TTAGTCAACTAGGATATCAG
1 TTAGTCAACTAAGATATCAG
*
19002162 TTAGTCAACAAAGA
1 TTAGTCAACTAAGA
19002176 GTATTCTGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.28
Consensus pattern (20 bp):
TTAGTCAACTAAGATATCAG
Found at i:19006621 original size:17 final size:16
Alignment explanation
Indices: 19006573--19006625 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
19006563 TCAAACAACC
*
19006573 AAAATTAAAG-ATACT
1 AAAATTAAAGAAAACT
19006588 GAAAATTAAAGAAAACT
1 -AAAATTAAAGAAAACT
*
19006605 AAAATTAAACTAAAACT
1 AAAATTAAA-GAAAACT
19006622 AAAA
1 AAAA
19006626 GCAAGAACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
16 19 0.58
17 14 0.42
ACGTcount: A:0.66, C:0.08, G:0.06, T:0.21
Consensus pattern (16 bp):
AAAATTAAAGAAAACT
Found at i:19011841 original size:17 final size:19
Alignment explanation
Indices: 19011800--19011841 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
19011790 ATATATATAT
19011800 ATGAATATATGTTGTGCATTG
1 ATGAATATATGTTGTG-A-TG
19011821 ATGAATA-ATGTTGTG-TG
1 ATGAATATATGTTGTGATG
19011838 ATGA
1 ATGA
19011842 TATTGATCCG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 6 0.29
20 8 0.38
21 7 0.33
ACGTcount: A:0.31, C:0.02, G:0.26, T:0.40
Consensus pattern (19 bp):
ATGAATATATGTTGTGATG
Found at i:19011890 original size:49 final size:49
Alignment explanation
Indices: 19011836--19011955 Score: 188
Period size: 49 Copynumber: 2.4 Consensus size: 49
19011826 TAATGTTGTG
* * *
19011836 TGATGAT-ATTGATCCGGCTATGTGCGAGTAGGGAGTGTGCATAAGCCGA
1 TGATGATGA-TGACCCGGCTATGTGCAAGTAGGGAGTGCGCATAAGCCGA
*
19011885 TGATGATGATGACCCAGCTATGTGCAAGTAGGGAGTGCGCATAAGCCGA
1 TGATGATGATGACCCGGCTATGTGCAAGTAGGGAGTGCGCATAAGCCGA
19011934 TGATGATGATGACCCGGCTATG
1 TGATGATGATGACCCGGCTATG
19011956 ACAATGAATG
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
49 64 0.98
50 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.33, T:0.24
Consensus pattern (49 bp):
TGATGATGATGACCCGGCTATGTGCAAGTAGGGAGTGCGCATAAGCCGA
Found at i:19019603 original size:32 final size:33
Alignment explanation
Indices: 19019564--19019666 Score: 104
Period size: 32 Copynumber: 3.1 Consensus size: 33
19019554 CAACCTTTAG
19019564 CAATGGTTTTTCACAAGATCAACCAAAACCCAA
1 CAATGGTTTTTCACAAGATCAACCAAAACCCAA
* * *
19019597 -AGTGGTTTTTCA-AAGGCTCAACCATAAACTACAA
1 CAATGGTTTTTCACAA-GATCAACCA-AAAC-CCAA
**
19019631 CAATGGTTTTT-ACTGGGATCAACCAAAACCCAA
1 CAATGGTTTTTCAC-AAGATCAACCAAAACCCAA
19019664 CAA
1 CAA
19019667 CCAACTTTCT
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
31 2 0.04
32 19 0.34
33 10 0.18
34 8 0.14
35 17 0.30
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.23
Consensus pattern (33 bp):
CAATGGTTTTTCACAAGATCAACCAAAACCCAA
Found at i:19020168 original size:13 final size:13
Alignment explanation
Indices: 19020150--19020180 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
19020140 CAGAGAGCAG
19020150 TTGGTCGACTAAC
1 TTGGTCGACTAAC
*
19020163 TTGGTCGACTAAG
1 TTGGTCGACTAAC
19020176 TTGGT
1 TTGGT
19020181 TTTATTTCTC
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:0.19, C:0.16, G:0.29, T:0.35
Consensus pattern (13 bp):
TTGGTCGACTAAC
Found at i:19022166 original size:20 final size:20
Alignment explanation
Indices: 19022138--19022176 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19022128 CTTCAAGCAC
* *
19022138 TATTCTCAATTATCATCAAG
1 TATTATCAATCATCATCAAG
19022158 TATTATCAATCATCATCAA
1 TATTATCAATCATCATCAA
19022177 ACATTCATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (20 bp):
TATTATCAATCATCATCAAG
Found at i:19026941 original size:67 final size:67
Alignment explanation
Indices: 19026861--19027115 Score: 377
Period size: 67 Copynumber: 3.8 Consensus size: 67
19026851 GGCTTTTCGC
* ** * *
19026861 AGGCTCAGCCACAACCTTTAGCAATGGTTTTT-CACGGGATCAACCAAAACCCAAAGTAGTTTTT
1 AGGCTCAACCACAACCTACAACAATGGTTTTTAC-CGGGATCAACCAAAACCCAAAGTGGTTTTT
*
19026925 TAA
65 CAA
* * * *
19026928 AGGCTCAACCACAACCTACAACAACGATTTTTACTGGGATCAATCAAAACCCAAAGTGGTTTTTC
1 AGGCTCAACCACAACCTACAACAATGGTTTTTACCGGGATCAACCAAAACCCAAAGTGGTTTTTC
19026993 AA
66 AA
* *
19026995 AGGCTCAACCACAACCTATAATAATGGTTTTTACCGGGATCAACCAAAACCCAAAGTGGTTTTTC
1 AGGCTCAACCACAACCTACAACAATGGTTTTTACCGGGATCAACCAAAACCCAAAGTGGTTTTTC
19027060 AA
66 AA
*
19027062 TGGCTCAACCACAACCTACAACAATGGTTTTTACCGGGATCAACCAAAACCCAA
1 AGGCTCAACCACAACCTACAACAATGGTTTTTACCGGGATCAACCAAAACCCAA
19027116 CAACCAACTT
Statistics
Matches: 168, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
67 167 0.99
68 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.24
Consensus pattern (67 bp):
AGGCTCAACCACAACCTACAACAATGGTTTTTACCGGGATCAACCAAAACCCAAAGTGGTTTTTC
AA
Found at i:19027038 original size:35 final size:34
Alignment explanation
Indices: 19026883--19027112 Score: 138
Period size: 35 Copynumber: 6.9 Consensus size: 34
19026873 AACCTTTAGC
19026883 AATGGTTTTT-CACGGGATCAACCAAAACC--CAA
1 AATGGTTTTTAC-CGGGATCAACCAAAACCTACAA
* * ** * *
19026915 AGTAGTTTTTTA-AAGGCTCAACCACAACCTACAA
1 AAT-GGTTTTTACCGGGATCAACCAAAACCTACAA
* * * *
19026949 CAACGATTTTTACTGGGATCAATCAAAACC--CAA
1 -AATGGTTTTTACCGGGATCAACCAAAACCTACAA
* ** * * *
19026982 AGTGGTTTTT-CAAAGGCTCAACCACAACCTATAA
1 AATGGTTTTTAC-CGGGATCAACCAAAACCTACAA
19027016 TAATGGTTTTTACCGGGATCAACCAAAACC--CAA
1 -AATGGTTTTTACCGGGATCAACCAAAACCTACAA
* ** * *
19027049 AGTGGTTTTT-CAATGGCTCAACCACAACCTACAA
1 AATGGTTTTTAC-CGGGATCAACCAAAACCTACAA
19027083 CAATGGTTTTTACCGGGATCAACCAAAACC
1 -AATGGTTTTTACCGGGATCAACCAAAACC
19027113 CAACAACCAA
Statistics
Matches: 143, Mismatches: 39, Indels: 29
0.68 0.18 0.14
Matches are distributed among these distances:
31 2 0.01
32 56 0.39
33 11 0.08
34 15 0.10
35 57 0.40
36 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (34 bp):
AATGGTTTTTACCGGGATCAACCAAAACCTACAA
Found at i:19036411 original size:29 final size:29
Alignment explanation
Indices: 19036334--19036526 Score: 255
Period size: 29 Copynumber: 6.7 Consensus size: 29
19036324 TTTTATCTTT
* * *
19036334 AATTAAGACAAAACATATTATCTTGTCCA
1 AATTAAGACAAAACATGTTTTCTTGTCTA
* *
19036363 AATTGAGAC-AAATATGTTTTCTTGTCTA
1 AATTAAGACAAAACATGTTTTCTTGTCTA
* * * *
19036391 GATTAAGAGAAAATATATTTTTCTTGTCCTA
1 AATTAAGACAAAACAT-GTTTTCTTGT-CTA
*
19036422 AATTAAGAC-AAACATGTTTGCTTGTCTA
1 AATTAAGACAAAACATGTTTTCTTGTCTA
*
19036450 AATTAAGACAAAATATGTTTTCTTGTCTA
1 AATTAAGACAAAACATGTTTTCTTGTCTA
19036479 AATTAAGACAAAACATGTTTTCTTGTCTA
1 AATTAAGACAAAACATGTTTTCTTGTCTA
19036508 AATTAAGACAAAACATGTT
1 AATTAAGACAAAACATGTT
19036527 AAAGTTGTCA
Statistics
Matches: 143, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
28 33 0.23
29 86 0.60
30 14 0.10
31 10 0.07
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.37
Consensus pattern (29 bp):
AATTAAGACAAAACATGTTTTCTTGTCTA
Found at i:19103132 original size:4 final size:4
Alignment explanation
Indices: 19103123--19103161 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
19103113 TGTGGCTTAT
* * *
19103123 TATA TATA TATA TATA TATA TATT TATA TGTA TTTA TAT
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TAT
19103162 GAATGATATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (4 bp):
TATA
Found at i:19103134 original size:6 final size:6
Alignment explanation
Indices: 19103123--19103161 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
19103113 TGTGGCTTAT
* * *
19103123 TATATA TATATA TATATA TATATT TATATG TATTTA TAT
1 TATATA TATATA TATATA TATATA TATATA TATATA TAT
19103162 GAATGATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (6 bp):
TATATA
Found at i:19103138 original size:10 final size:10
Alignment explanation
Indices: 19103123--19103161 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
19103113 TGTGGCTTAT
19103123 TATATATATA
1 TATATATATA
19103133 TATATATATA
1 TATATATATA
* *
19103143 TATTTATATG
1 TATATATATA
*
19103153 TATTTATAT
1 TATATATAT
19103162 GAATGATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (10 bp):
TATATATATA
Found at i:19103162 original size:10 final size:10
Alignment explanation
Indices: 19103127--19103161 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
19103117 GCTTATTATA
*
19103127 TATATATATA
1 TATATATATT
19103137 TATATATATT
1 TATATATATT
*
19103147 TATATGTATT
1 TATATATATT
19103157 TATAT
1 TATAT
19103162 GAATGATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (10 bp):
TATATATATT
Found at i:19114434 original size:2 final size:2
Alignment explanation
Indices: 19114422--19114472 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
19114412 ATTGTGTTGG
*
19114422 TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19114464 TA TA TA TA T
1 TA TA TA TA T
19114473 NCCGTGCGTG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:19130887 original size:2 final size:2
Alignment explanation
Indices: 19130882--19130968 Score: 124
Period size: 2 Copynumber: 44.0 Consensus size: 2
19130872 TATGTGTTTA
19130882 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT NAT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
* * *
19130924 TT AT AT AT GT GT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19130965 AT AT
1 AT AT
19130969 GATTTTGATT
Statistics
Matches: 80, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
1 2 0.03
2 76 0.95
3 2 0.03
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:19130948 original size:57 final size:56
Alignment explanation
Indices: 19130860--19130968 Score: 195
Period size: 55 Copynumber: 2.0 Consensus size: 56
19130850 GATGCAATGC
19130860 ATATATTTTATATATGTGTTTAATATATATATATATATATATATATATATATATAT
1 ATATATTTTATATATGTGTTTAATATATATATATATATATATATATATATATATAT
19130916 NATATATTTTATATATGTG-TT-ATATATATATATATATATATATATATATATAT
1 -ATATATTTTATATATGTGTTTAATATATATATATATATATATATATATATATAT
19130969 GATTTTGATT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
55 32 0.62
56 2 0.04
57 18 0.35
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (56 bp):
ATATATTTTATATATGTGTTTAATATATATATATATATATATATATATATATATAT
Found at i:19140551 original size:39 final size:39
Alignment explanation
Indices: 19140505--19140681 Score: 236
Period size: 39 Copynumber: 4.6 Consensus size: 39
19140495 GTGCCGGTAG
* *
19140505 TGTGCGGTGTGGGAGAGCACA-CACCGATGATATATGCCA
1 TGTGCGGTGTGGGAGAGCACATGA-TGATGATATATGCCA
*
19140544 TGTGCGGTGTGGGAGAGCACATGATGATGATAAATGCCA
1 TGTGCGGTGTGGGAGAGCACATGATGATGATATATGCCA
*
19140583 TGTGCGGTGTGGGAGAGCACATGATAATGATATATGCCA
1 TGTGCGGTGTGGGAGAGCACATGATGATGATATATGCCA
* * *
19140622 TGTGCGGTGTGGGAGTGCACATGAGGAT-AT-TA-GCTA
1 TGTGCGGTGTGGGAGAGCACATGATGATGATATATGCCA
* *
19140658 TGTGCGGCGTGGGAGTGCACATGA
1 TGTGCGGTGTGGGAGAGCACATGA
19140682 GCTGGGTTGA
Statistics
Matches: 127, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
36 26 0.20
37 2 0.02
38 2 0.02
39 96 0.76
40 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.37, T:0.24
Consensus pattern (39 bp):
TGTGCGGTGTGGGAGAGCACATGATGATGATATATGCCA
Found at i:19144963 original size:3 final size:3
Alignment explanation
Indices: 19144955--19144984 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
19144945 TACTAAAAGT
19144955 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19144985 AAATATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:19145755 original size:46 final size:46
Alignment explanation
Indices: 19145688--19145779 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
19145678 ATGTTCTAAA
19145688 ATTACAACAACAATTATTCCTCTTACAATAAATTAATAAAATCTTT
1 ATTACAACAACAATTATTCCTCTTACAATAAATTAATAAAATCTTT
*
19145734 ATTACAACAGCAATTATTCCTCTTACAATAAATTAATAAAATCTTT
1 ATTACAACAACAATTATTCCTCTTACAATAAATTAATAAAATCTTT
19145780 TTGTTCAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.45, C:0.17, G:0.01, T:0.37
Consensus pattern (46 bp):
ATTACAACAACAATTATTCCTCTTACAATAAATTAATAAAATCTTT
Found at i:19145956 original size:2 final size:2
Alignment explanation
Indices: 19145949--19145976 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19145939 AAATAATGAC
19145949 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19145977 CATACTTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19147352 original size:21 final size:21
Alignment explanation
Indices: 19147328--19147367 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19147318 CAAGGAATGA
*
19147328 GATGAAGATGAAAAAGAAATT
1 GATGAAGAAGAAAAAGAAATT
*
19147349 GATGAAGAAGAACAAGAAA
1 GATGAAGAAGAAAAAGAAA
19147368 ACCAAGATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.03, G:0.25, T:0.12
Consensus pattern (21 bp):
GATGAAGAAGAAAAAGAAATT
Found at i:19149806 original size:12 final size:13
Alignment explanation
Indices: 19149774--19149805 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
19149764 TGTTTTCCAA
*
19149774 CAAAAAAATTTGT
1 CAAAAAATTTTGT
19149787 CAAAAAATTTTGT
1 CAAAAAATTTTGT
19149800 CAAAAA
1 CAAAAA
19149806 TCCGTAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.06, T:0.28
Consensus pattern (13 bp):
CAAAAAATTTTGT
Found at i:19151344 original size:144 final size:144
Alignment explanation
Indices: 19151072--19151348 Score: 394
Period size: 144 Copynumber: 1.9 Consensus size: 144
19151062 GAGCATTTCA
*
19151072 ACATGTTGATAATCCCATACAATCCTTGAACAAAATTAAGATTACTATATGCTAGTATGCATTTG
1 ACATGTTGATAATCCCATACAATCCTTGAACAAAATTAAGATGACTATATGCTAGTATGCATTTG
* *
19151137 TTGATATTTGTGATGGTACAAGCAATTGTTATACACAAAAGCTAACATCAAATAATTGTAATTGT
66 TAGATATTTGTGATGGTACAAGCAATTGTTATACACAAAAGCTAACATCAAATAATTGAAATTGT
19151202 CAAGCTGATTTCTT
131 CAAGCTGATTTCTT
* * * *
19151216 ACATGTTGATAATCCTATACAGTCCTTGAACAAAATTAAGATGCCTATCTGCT-GATATGCATTT
1 ACATGTTGATAATCCCATACAATCCTTGAACAAAATTAAGATGACTATATGCTAG-TATGCATTT
* * * * * * * * *
19151280 GTAGATATTTGTGATGGTAGAGGTAGTTGTTATATACAAAAGTTAAGATCAGATAGTTGAAATTG
65 GTAGATATTTGTGATGGTACAAGCAATTGTTATACACAAAAGCTAACATCAAATAATTGAAATTG
19151345 TCAA
130 TCAA
19151349 ACTGCTTATA
Statistics
Matches: 116, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
143 1 0.01
144 115 0.99
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (144 bp):
ACATGTTGATAATCCCATACAATCCTTGAACAAAATTAAGATGACTATATGCTAGTATGCATTTG
TAGATATTTGTGATGGTACAAGCAATTGTTATACACAAAAGCTAACATCAAATAATTGAAATTGT
CAAGCTGATTTCTT
Found at i:19152324 original size:463 final size:456
Alignment explanation
Indices: 19151461--19152374 Score: 1282
Period size: 463 Copynumber: 2.0 Consensus size: 456
19151451 TATAAGGCAA
* * *
19151461 TGTGAGTCTCCATCGTGGGTAGAACTCCTGAATTTCTCAACATCAAGGGTCACTAGAAAATGCTT
1 TGTGAGTCTCCATCGTGGGTAGAACTCCTGAATTTCTCAACATCAAAGGTCACCAAAAAATGCTT
** ** *
19151526 CAGAAAGGGTATTCTTTGATATGTGGGTTGTCTTGGAGGATCTCTGCATGTAAAATATTAAATGA
66 CAGAAAGGACATTCTTTGATATGTGGGTTACCTTGGAGGATCTCTACATGTAAAATATTAAATGA
* *
19151591 AAAGTTAGATTTAATAAATAGTTCTTAAGGAAAGGAATGAAGTTGAGATTGATATTAGTATTACC
131 AAAGTTAGATTTAATAAATAGTTCATAAGGAAAAGAATGAAGTTGAGATTGATATTAGTATTACC
* * *
19151656 TGAAAGATAGAGAAGGAAAAATAGTAGAGTATTATTAAAGGAAAGGCATTTAGTAATAAATTGTG
196 TGAAAGATAGAGAAGGAAAAATAGTAGAGTATTATTAAAGGAAAAGCATTTACTAATAAATTGAG
*
19151721 ATAGTAACATTATTAACGGGAGTGACACTAAACCACCATAACCCAACCACTATAATGATGGTCTA
261 ATAGTAACATTATTAACGAGAGTGACACTAAACCACCATAACCCAACCACTATAATGATGGTCTA
* * * *
19151786 TACATCAATTGTTTATAACAAAATATATCACCTTAGTATTCTCAAAGGTCAAACAAAAGACAAAA
326 TACATCAACTATTTACAACAAAATATATCACCCTAGTATTCTCAAAGGTCAAACAAAAGACAAAA
* * * **
19151851 CCAAGTCCCAACAAATAAACAAAAGAAATC-AGGGTTTAAAAGTAAAATCCTCTATAAGAAAGTA
391 CCAAGTCCCAACAAACAAACAAAAGAAATCAAGGATTGAAAAACAAAATCCTCTATAAGAAAGTA
19151915 G
456 G
* ** **
19151916 TGTGAGTCTCCGTCGTGGGTAGAA-TTTTAGAATTTCTCGGCATCAAAGGTCACCAAAAAATGCT
1 TGTGAGTCTCCATCGTGGGTAGAACTCCT-GAATTTCTCAACATCAAAGGTCACCAAAAAATGCT
*
19151980 TCA-AGAAGGACATTCTTTGATTTGTGGGTTACCTTGCG-GGATCCTCTACATGTAAAAAATATT
65 TCAGA-AAGGACATTCTTTGATATGTGGGTTACCTTG-GAGGAT-CTCTACATGT--AAAATATT
* * * *
19152043 AAATGAAAAGTTATG-TTTAGTAAATAGTTCATGAGGAAAAGAATGACGTTGATATTGATATTAG
125 AAATGAAAAGTTA-GATTTAATAAATAGTTCATAAGGAAAAGAATGAAGTTGAGATTGATATTAG
* *
19152107 TATTACTTGGAAA-ATAGAGATGGAAAAATGGTATAGTAGAGTATTATTAAAGGAAAAGCATTTA
189 TATTACCT-GAAAGATAGAGAAGG-AAAA----ATAGTAGAGTATTATTAAAGGAAAAGCATTTA
* *
19152171 CTAATAAATTGAGATAGTAATATTATTAACGAGAGTGAGACTAAACCACCATAACCCAACCACTA
248 CTAATAAATTGAGATAGTAACATTATTAACGAGAGTGACACTAAACCACCATAACCCAACCACTA
** *
19152236 TAATGATGGTCTATACATTGACTATTTACAACAAAATATATCACCCTAGTATTCTCAAAGTTCAA
313 TAATGATGGTCTATACATCAACTATTTACAACAAAATATATCACCCTAGTATTCTCAAAGGTCAA
* * *
19152301 ACAAAAGACAAAGCTAGGTCCCAACAAACAAACAAAAGAAATCAAGGATTGAAAAACAAAATCCT
378 ACAAAAGACAAAACCAAGTCCCAACAAACAAACAAAAGAAATCAAGGATTGAAAAACAAAATCCT
19152366 CTATAAGAA
443 CTATAAGAA
19152375 GTGTAAACCT
Statistics
Matches: 402, Mismatches: 43, Indels: 19
0.87 0.09 0.04
Matches are distributed among these distances:
454 3 0.01
455 86 0.21
456 10 0.02
458 80 0.20
459 9 0.02
463 188 0.47
464 26 0.06
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.28
Consensus pattern (456 bp):
TGTGAGTCTCCATCGTGGGTAGAACTCCTGAATTTCTCAACATCAAAGGTCACCAAAAAATGCTT
CAGAAAGGACATTCTTTGATATGTGGGTTACCTTGGAGGATCTCTACATGTAAAATATTAAATGA
AAAGTTAGATTTAATAAATAGTTCATAAGGAAAAGAATGAAGTTGAGATTGATATTAGTATTACC
TGAAAGATAGAGAAGGAAAAATAGTAGAGTATTATTAAAGGAAAAGCATTTACTAATAAATTGAG
ATAGTAACATTATTAACGAGAGTGACACTAAACCACCATAACCCAACCACTATAATGATGGTCTA
TACATCAACTATTTACAACAAAATATATCACCCTAGTATTCTCAAAGGTCAAACAAAAGACAAAA
CCAAGTCCCAACAAACAAACAAAAGAAATCAAGGATTGAAAAACAAAATCCTCTATAAGAAAGTA
G
Found at i:19155412 original size:17 final size:17
Alignment explanation
Indices: 19155379--19155426 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
19155369 AAAAAATGAC
19155379 AAACAAATGAA-CATAG
1 AAACAAATGAATCATAG
**
19155395 AAACCCATGAATCATAG
1 AAACAAATGAATCATAG
19155412 AAACAAATGAATCAT
1 AAACAAATGAATCAT
19155427 TTATGATAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 9 0.33
17 18 0.67
ACGTcount: A:0.56, C:0.17, G:0.10, T:0.17
Consensus pattern (17 bp):
AAACAAATGAATCATAG
Found at i:19164475 original size:28 final size:27
Alignment explanation
Indices: 19164444--19164496 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
19164434 ATTTGGAGTA
19164444 TAGGAGTAAAATGGTAATTTTACCACTC
1 TAGGAGTAAAATGGTAATTTT-CCACTC
* *
19164472 TAGGGGTAAAATTGTAATTTTCCAC
1 TAGGAGTAAAATGGTAATTTTCCAC
19164497 CACCAGGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (27 bp):
TAGGAGTAAAATGGTAATTTTCCACTC
Found at i:19169678 original size:19 final size:19
Alignment explanation
Indices: 19169654--19169690 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
19169644 CCATTTGACT
19169654 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
19169673 TATTGGAGTATGATTTGA
1 TATTGGAGTATGATTTGA
19169691 CATTTAGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.30, T:0.43
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:19170080 original size:21 final size:22
Alignment explanation
Indices: 19170043--19170085 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
19170033 GTGAGGAATT
*
19170043 TCAAGAGAAAAAGAGTGGAAAA
1 TCAAGAGAAAAAGAGTGAAAAA
19170065 TCAAG-GAAAACA-AGTGAAAAA
1 TCAAGAGAAAA-AGAGTGAAAAA
19170086 GGTAGGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.60, C:0.07, G:0.23, T:0.09
Consensus pattern (22 bp):
TCAAGAGAAAAAGAGTGAAAAA
Found at i:19172371 original size:33 final size:32
Alignment explanation
Indices: 19172312--19172395 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 32
19172302 TTTTAATGTC
* **
19172312 ATATTTTTTTTTATTTTTTATTATAATCTTAT
1 ATATTTTATTTTATTTTTTAAAATAATCTTAT
* *
19172344 ATATTTTATTTTCATTTTTTAAAATAATTTTCT
1 ATATTTTATTTT-ATTTTTTAAAATAATCTTAT
19172377 ATATTATATATTTTATTTT
1 ATATT-T-TATTTTATTTT
19172396 AATTTCCTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
32 11 0.25
33 21 0.48
34 6 0.14
35 6 0.14
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.68
Consensus pattern (32 bp):
ATATTTTATTTTATTTTTTAAAATAATCTTAT
Found at i:19174566 original size:33 final size:35
Alignment explanation
Indices: 19174511--19174575 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 35
19174501 GTGTGCTTGA
*
19174511 AGGTGTTAAGGTTCTAACTTAGC-CTTGAAAAGTT
1 AGGTGTTAAGGTTCTAACTTAGCTCGTGAAAAGTT
* **
19174545 AGGTGTT-AGGTTTTAGTTTAGCTCGTGAAAA
1 AGGTGTTAAGGTTCTAACTTAGCTCGTGAAAA
19174576 ACTAATGTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
33 12 0.46
34 14 0.54
ACGTcount: A:0.28, C:0.09, G:0.26, T:0.37
Consensus pattern (35 bp):
AGGTGTTAAGGTTCTAACTTAGCTCGTGAAAAGTT
Found at i:19177220 original size:13 final size:13
Alignment explanation
Indices: 19177202--19177226 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19177192 TTTCAGAAAA
19177202 TTTATAAAATCAT
1 TTTATAAAATCAT
19177215 TTTATAAAATCA
1 TTTATAAAATCA
19177227 CAATTTCTCC
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:19184432 original size:18 final size:18
Alignment explanation
Indices: 19184409--19184445 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
19184399 CCACTGCAGC
19184409 ACCACCAA-CAGAGGGAAA
1 ACCACCAACCA-AGGGAAA
19184427 ACCACCAACCAAGGGAAA
1 ACCACCAACCAAGGGAAA
19184445 A
1 A
19184446 AAGACTATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.51, C:0.30, G:0.19, T:0.00
Consensus pattern (18 bp):
ACCACCAACCAAGGGAAA
Found at i:19191937 original size:32 final size:31
Alignment explanation
Indices: 19191870--19191938 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
19191860 TTTTAATGTC
*
19191870 ATATATTTTATTTTTATTTTTATTATAATCTT
1 ATATATTTTATTTTCATTTTTA-TATAATCTT
* *
19191902 ATATATTTTGTTTTCATTTTTA-ATAATTTT
1 ATATATTTTATTTTCATTTTTATATAATCTT
*
19191932 CTATATT
1 ATATATT
19191939 AAATATTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 13 0.39
32 20 0.61
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (31 bp):
ATATATTTTATTTTCATTTTTATATAATCTT
Found at i:19196536 original size:21 final size:19
Alignment explanation
Indices: 19196495--19196531 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
19196485 GCTCAATTTA
19196495 TCAACTAGACGAGGGTTTC
1 TCAACTAGACGAGGGTTTC
*
19196514 TCAACTAGCCGAGGGTTT
1 TCAACTAGACGAGGGTTT
19196532 TTCTCTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (19 bp):
TCAACTAGACGAGGGTTTC
Found at i:19196972 original size:2 final size:2
Alignment explanation
Indices: 19196967--19196998 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
19196957 ACATATTTAC
19196967 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19196999 GCACATCATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19197113 original size:42 final size:41
Alignment explanation
Indices: 19197025--19197157 Score: 185
Period size: 42 Copynumber: 3.1 Consensus size: 41
19197015 ACCATCCCAC
* * *
19197025 CATCATCAGCTCATATGCACTCCCCATTTGCACATAGTTGGGT
1 CATCATCAGCTCATGTGCACT-CCCA-CTGCACATAGCTGGGT
* *
19197068 CATCATCAGCTCATGTGCACTCTACACCGCACATAGCTGGGT
1 CATCATCAGCTCATGTGCACTC-CCACTGCACATAGCTGGGT
19197110 CATCATCAGCTCATGTGCACTCCCACATGCACATAGCTGGGT
1 CATCATCAGCTCATGTGCACTCCCAC-TGCACATAGCTGGGT
19197152 CATCAT
1 CATCAT
19197158 GATCACATAA
Statistics
Matches: 81, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
41 3 0.04
42 56 0.69
43 22 0.27
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.26
Consensus pattern (41 bp):
CATCATCAGCTCATGTGCACTCCCACTGCACATAGCTGGGT
Found at i:19204692 original size:22 final size:22
Alignment explanation
Indices: 19204662--19204707 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
19204652 GAAAAATTGA
*
19204662 TGCTGATATATTTATGGTACTT
1 TGCTGATATATTCATGGTACTT
* * *
19204684 TGCTTATATGTTCATGGTATTT
1 TGCTGATATATTCATGGTACTT
19204706 TG
1 TG
19204708 ATGCTGATGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.09, G:0.20, T:0.52
Consensus pattern (22 bp):
TGCTGATATATTCATGGTACTT
Found at i:19205065 original size:17 final size:17
Alignment explanation
Indices: 19205040--19205076 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
19205030 AGCAAAATAT
19205040 GCACACACTAAGGGGGA
1 GCACACACTAAGGGGGA
* *
19205057 GCACTCACTTAGGGGGA
1 GCACACACTAAGGGGGA
19205074 GCA
1 GCA
19205077 ATCCTCATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.30, C:0.24, G:0.35, T:0.11
Consensus pattern (17 bp):
GCACACACTAAGGGGGA
Found at i:19223196 original size:25 final size:25
Alignment explanation
Indices: 19223162--19223223 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
19223152 AAGAAAATAA
*
19223162 AATCCTTATAATTATGATGA-TTCT
1 AATCCCTATAATTATGATGATTTCT
*
19223186 GAATCCCTATAATTATGGTGATTTCT
1 -AATCCCTATAATTATGATGATTTCT
*
19223212 AATTCCTATAAT
1 AATCCCTATAAT
19223224 CGTGTTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
25 29 0.88
26 4 0.12
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.44
Consensus pattern (25 bp):
AATCCCTATAATTATGATGATTTCT
Found at i:19229970 original size:29 final size:31
Alignment explanation
Indices: 19229895--19229974 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 31
19229885 TATTGACACT
* *
19229895 AGAAAGCACAGA-ACAACAAGAGTGTAACTAT
1 AGAAA-CACAGACACAACAAGACTGTAACTAG
* *
19229926 AGAAACACAAAACACAACAAGTCTGTAACTAG
1 AGAAACAC-AGACACAACAAGACTGTAACTAG
19229958 AG-AA-ACAGACACAACAA
1 AGAAACACAGACACAACAA
19229975 TGAGACTGTA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
29 10 0.24
30 5 0.12
31 9 0.21
32 18 0.43
ACGTcount: A:0.55, C:0.20, G:0.15, T:0.10
Consensus pattern (31 bp):
AGAAACACAGACACAACAAGACTGTAACTAG
Found at i:19230700 original size:31 final size:30
Alignment explanation
Indices: 19230643--19230702 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
19230633 TAATAAAGAT
* *
19230643 AGAAAAAGAATCCCAAACTAAATAAAATAA
1 AGAAAAAAAATCCCAAACCAAATAAAATAA
* *
19230673 AGAAAATAAAATCCTAAACCAACTAAAATA
1 AGAAAA-AAAATCCCAAACCAAATAAAATA
19230703 CTAAATAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 6 0.24
31 19 0.76
ACGTcount: A:0.65, C:0.15, G:0.05, T:0.15
Consensus pattern (30 bp):
AGAAAAAAAATCCCAAACCAAATAAAATAA
Found at i:19231177 original size:63 final size:64
Alignment explanation
Indices: 19231057--19231178 Score: 156
Period size: 63 Copynumber: 1.9 Consensus size: 64
19231047 TTAATTGGAC
* * * * *
19231057 CCTCAAAAGTTTAAGGGTCAAATGAGTTTAAATATTGTGGAGGACCCTTTTTATGTGCATAGAG
1 CCTCAAAAGTTTAAGGGCCAAATAAGTTTAAAAATTGTAGAGGACCCTTTTGATGTGCATAGAG
* * * *
19231121 CCTCACAAG-TTAAGGGCCAAATAAGTTTAAAAATTTTAGAGGATCCTTTTGGTGTGCA
1 CCTCAAAAGTTTAAGGGCCAAATAAGTTTAAAAATTGTAGAGGACCCTTTTGATGTGCA
19231179 ATGACCACAA
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
63 41 0.84
64 8 0.16
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (64 bp):
CCTCAAAAGTTTAAGGGCCAAATAAGTTTAAAAATTGTAGAGGACCCTTTTGATGTGCATAGAG
Found at i:19232732 original size:45 final size:45
Alignment explanation
Indices: 19232668--19232757 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
19232658 CATGGTGTGT
*
19232668 GACACAATTGGCCCCAAAAGGTGCCAATAACATCCTGATGAGTGC
1 GACACAATCGGCCCCAAAAGGTGCCAATAACATCCTGATGAGTGC
* *
19232713 GACACAATCGGCCCCAAAAGGTGCCAATCACATCGTGATGAGTGC
1 GACACAATCGGCCCCAAAAGGTGCCAATAACATCCTGATGAGTGC
19232758 ACTGAACAGG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.32, C:0.28, G:0.23, T:0.17
Consensus pattern (45 bp):
GACACAATCGGCCCCAAAAGGTGCCAATAACATCCTGATGAGTGC
Found at i:19233241 original size:28 final size:27
Alignment explanation
Indices: 19233180--19233257 Score: 106
Period size: 28 Copynumber: 2.9 Consensus size: 27
19233170 GTATTGGAGA
*
19233180 ATGAATCCTAAAGTAATAGTT--AAGC
1 ATGAATTCTAAAGTAATAGTTAAAAGC
19233205 ATGAATTCTAAAGTAATAGTTAAGAAGC
1 ATGAATTCTAAAGTAATAGTTAA-AAGC
* *
19233233 ATGAATTCTCAAGTAATGGTTAAAA
1 ATGAATTCTAAAGTAATAGTTAAAA
19233258 AATGTGGTGG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
25 20 0.43
27 2 0.04
28 25 0.53
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.29
Consensus pattern (27 bp):
ATGAATTCTAAAGTAATAGTTAAAAGC
Found at i:19241290 original size:2 final size:2
Alignment explanation
Indices: 19241283--19241322 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
19241273 ATGATATGAT
19241283 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19241323 NNNNNNNNNN
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19245382 original size:6 final size:6
Alignment explanation
Indices: 19245373--19245397 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19245363 GGCTGGGAGG
19245373 AGGGAA AGGGAA AGGGAA AGGGAA A
1 AGGGAA AGGGAA AGGGAA AGGGAA A
19245398 CGGATCAGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (6 bp):
AGGGAA
Done.