Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 133 of 318
Found at i:41153932 original size:55 final size:53
Alignment explanation
Indices: 41153872--41153994 Score: 203
Period size: 55 Copynumber: 2.3 Consensus size: 53
41153862 ATATTAAGTC
*
41153872 CGCACACTCAGTGCTATATAATC-AACTCGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTA-ATAATCAAACTCGCACACTTAGTGCTA-ATAATC-AACT
41153927 CGCACACTTAGTGCTAATAATCAAACTCGCACACTTAGTGCTAATAATCAACT
1 CGCACACTTAGTGCTAATAATCAAACTCGCACACTTAGTGCTAATAATCAACT
41153980 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41153995 GTACAATTTA
Statistics
Matches: 66, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
53 19 0.29
54 12 0.18
55 35 0.53
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (53 bp):
CGCACACTTAGTGCTAATAATCAAACTCGCACACTTAGTGCTAATAATCAACT
Found at i:41154013 original size:55 final size:55
Alignment explanation
Indices: 41153872--41154019 Score: 185
Period size: 55 Copynumber: 2.7 Consensus size: 55
41153862 ATATTAAGTC
* * *
41153872 CGCACACTCAGTGCTATATAATC-AACTCGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTA-ACAATCAAACCCGCACACTTAGTGCTATATAATCAAACT
* *
41153927 CGCACACTTAGTGCTAATAATCAAACTCGCACACTTAGTGCTA-ATAATC-AACT
1 CGCACACTTAGTGCTAACAATCAAACCCGCACACTTAGTGCTATATAATCAAACT
* *
41153980 CGCACACTTAGTGCTGTACAATTTAAACCCGCACACTTAG
1 CGCACACTTAGTGCT-AACAA-TCAAACCCGCACACTTAG
41154020 CGCCAATCTC
Statistics
Matches: 85, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
53 19 0.22
54 15 0.18
55 51 0.60
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTAACAATCAAACCCGCACACTTAGTGCTATATAATCAAACT
Found at i:41175403 original size:28 final size:28
Alignment explanation
Indices: 41175340--41175490 Score: 214
Period size: 28 Copynumber: 5.4 Consensus size: 28
41175330 ATATTAAGTC
*
41175340 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
41175367 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
41175395 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTATATAATCAAACT
*
41175423 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
41175451 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
41175480 CGCACACTTAG
1 CGCACACTTAG
41175491 CGCCAATCTC
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.19
28 75 0.66
29 16 0.14
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:41183422 original size:28 final size:28
Alignment explanation
Indices: 41183359--41183509 Score: 214
Period size: 28 Copynumber: 5.4 Consensus size: 28
41183349 ATATTAAGTC
*
41183359 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
41183386 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
41183414 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
41183442 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
41183470 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
41183499 CGCACACTTAG
1 CGCACACTTAG
41183510 CGCCAATCTC
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.19
28 76 0.67
29 15 0.13
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:41185286 original size:21 final size:21
Alignment explanation
Indices: 41185260--41185307 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
41185250 ACTCCCCACA
41185260 TGGAGTGTAG-GGCTGGTAGGG
1 TGGAGTGTAGTGGCTGGT-GGG
*
41185281 TGGAGTGTAGTGGTTGGTGGG
1 TGGAGTGTAGTGGCTGGTGGG
*
41185302 TTGAGT
1 TGGAGT
41185308 AGTCTCCCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.12, C:0.02, G:0.54, T:0.31
Consensus pattern (21 bp):
TGGAGTGTAGTGGCTGGTGGG
Found at i:41186326 original size:26 final size:26
Alignment explanation
Indices: 41186297--41186404 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
41186287 TGGTACAAAT
41186297 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
41186323 TGATAATGGGTTAGGTAAATATTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
41186349 TTATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
41186375 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
41186401 TGAT
1 TGAT
41186405 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:41187943 original size:26 final size:25
Alignment explanation
Indices: 41187891--41187943 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 25
41187881 TTTACAGTTG
41187891 TACCCCTAGTAGGTAAATTACCGAAA
1 TACCCCTAG-AGGTAAATTACCGAAA
*
41187917 TACCCCTAG-GGTTAAATTGACCTAAA
1 TACCCCTAGAGG-TAAATT-ACCGAAA
41187943 T
1 T
41187944 GCCTGTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 2 0.08
25 6 0.25
26 16 0.67
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (25 bp):
TACCCCTAGAGGTAAATTACCGAAA
Found at i:41193423 original size:26 final size:26
Alignment explanation
Indices: 41193394--41193501 Score: 198
Period size: 26 Copynumber: 4.2 Consensus size: 26
41193384 TGATACAAAT
41193394 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
41193420 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
41193446 TGATAATGAGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
41193472 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
41193498 TGAT
1 TGAT
41193502 GGGCATTTCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:41195259 original size:21 final size:21
Alignment explanation
Indices: 41195233--41195280 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
41195223 ACTCCCCACA
41195233 TGGAGTGTAG-GGCTGGTAGGG
1 TGGAGTGTAGTGGCTGGT-GGG
*
41195254 TGGAGTGTAGTGGTTGGTGGG
1 TGGAGTGTAGTGGCTGGTGGG
*
41195275 TTGAGT
1 TGGAGT
41195281 AGTCTCCCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.12, C:0.02, G:0.54, T:0.31
Consensus pattern (21 bp):
TGGAGTGTAGTGGCTGGTGGG
Found at i:41198701 original size:26 final size:27
Alignment explanation
Indices: 41198642--41198695 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
41198632 ACATATATAT
* * *
41198642 TATTTTATTTTTTAAATTTTTTTTACA
1 TATTGTATATTTTAAATTTTTTATACA
41198669 TATTGTATATTTTAAATTTTTATATAC
1 TATTGTATATTTTAAATTTTT-TATAC
41198696 TATGTAGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.65
Consensus pattern (27 bp):
TATTGTATATTTTAAATTTTTTATACA
Found at i:41200797 original size:109 final size:105
Alignment explanation
Indices: 41200650--41201401 Score: 590
Period size: 102 Copynumber: 7.1 Consensus size: 105
41200640 GTCAAATAAA
* * * * *
41200650 TAAAAAAACAGATAAAATTACATTATAACAAATCACAATACACATTAAACTAAACAAATAATTTA
1 TAAAAAAACA-AAAAAATTACATCATAAC-AATAACAATA-ACACTAAACTAAACAAACAATTTA
*
41200715 TAACCTAATCATAAATTACTAGCAAAATAACTTTAAAATAATT
63 TAACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATT
* * *
41200758 TAAAAAACACAAAAAAATTGCATTTATAACAAGTAACAATAAATACTAAACTAAACACAAACAAT
1 TAAAAAA-ACAAAAAAATTACA-TCATAACAA-TAACAAT-AACACTAAACT-AA-ACAAACAAT
* *
41200823 TTATAATCTAATCATAAATTACTAACAAAATAAATTTAAAATAA-T
60 TTATAACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATT
** * * **
41200868 T--AAAAA-AATTACATT-CAT-A-AAAAATCGCAATAAACACTAAACTAAACACAATCAATTTA
1 TAAAAAAACAAAAAAATTACATCATAACAATAACAAT-AACACTAAACTAAACA-AA-CAATTTA
* *
41200927 TAATCTAATCATAAATTACTAACAAAATAACTTTCAAATAA-T
63 TAACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATT
* * * * *
41200969 TAAAAAAATAAAAAATTTTACATTCATAAAAAAACACAATAAACATTAAACTAAACAAAAACAAT
1 TAAAAAAACAAAAAA-ATTACA-TCATAACAATA-ACAAT-AACACTAAACTAAAC--AAACAAT
* *
41201034 TTATAACCTAACCATAAATTACTAACAAAATGACTTTAAAATAATT
60 TTATAACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATT
* * *
41201080 TAAAAAATACAAAAAAATTACAATCATAAACAATCATAA-AACACTAAACTAAATATAAACAATT
1 TAAAAAA-ACAAAAAAATTAC-ATCAT-AACAATAACAATAACACTAAACT-AA-ACAAACAATT
* *
41201144 TATAACCTAATCATAACTTACTAACAAAATAACTATAAAATAATT
61 TATAACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATT
** ** * * * *
41201189 TTTAAAAA-AATTATATT-CAT-A-AAAAATCACAA-AACACTCAACTAAACACAAACAATTTAT
1 TAAAAAAACAAAAAAATTACATCATAACAATAACAATAACACTAAACT-AA-ACAAACAATTTAT
** * * *
41201249 AATATAATCATAAATTACTAAAAAAATAACTATAATATAATT
64 AACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATT
**** ** * * * * *
41201291 TTTTTAAA-AATTACATT-CATAAAAAATCACAAAACACTAA-ACTAAA-T--ACAAACAATTTA
1 TAAAAAAACAAAAAAATTACAT-CATAA-CA-ATAACAATAACACTAAACTAAACAAACAATTTA
* *
41201350 TAACCTAATCATAAATTACTAACAAAATAACTATAAAAAAATTT
63 TAACCTAATCATAAATTACTAACAAAATAACTTTAAAATAA-TT
41201394 TAAAAAAA
1 TAAAAAAA
41201402 TTTACATTCA
Statistics
Matches: 538, Mismatches: 74, Indels: 69
0.79 0.11 0.10
Matches are distributed among these distances:
99 3 0.01
100 4 0.01
101 64 0.12
102 140 0.26
103 12 0.02
104 6 0.01
105 8 0.01
106 11 0.02
107 17 0.03
108 26 0.05
109 93 0.17
110 70 0.13
111 71 0.13
112 13 0.02
ACGTcount: A:0.58, C:0.14, G:0.01, T:0.27
Consensus pattern (105 bp):
TAAAAAAACAAAAAAATTACATCATAACAATAACAATAACACTAAACTAAACAAACAATTTATAA
CCTAATCATAAATTACTAACAAAATAACTTTAAAATAATT
Found at i:41200983 original size:110 final size:107
Alignment explanation
Indices: 41200858--41201454 Score: 643
Period size: 102 Copynumber: 5.7 Consensus size: 107
41200848 CAAAATAAAT
* * * *
41200858 TTAAAATAATTAAAAAAATTACATTCATAAAAAATCGCAATAAACACTAAACTAAACACAATCAA
1 TTAAAAAAATAAAAAAAATTACATTCATAAAAAATCAC-A-AAACACTAAACTAAACACAAACAA
* *
41200923 TTTATAATCTAATCATAAATTACTAACAAAATAACTTTCAAATAA
64 TTTATAACCTAATCATAAATTACTAACAAAATAACTAT-AAATAA
** * * *
41200968 TTAAAAAAATAAAAAATTTTACATTCATAAAAAAACACAATAAACATTAAACTAAACAAAAACAA
1 TTAAAAAAATAAAAAAAATTACATTCATAAAAAATCAC-A-AAACACTAAACTAAACACAAACAA
* * *
41201033 TTTATAACCTAACCATAAATTACTAACAAAATGACTTTAAAATAA
64 TTTATAACCTAATCATAAATTACTAACAAAATAACTAT-AAATAA
* * * * * *
41201078 TTTAAAAAATACAAAAAAATTACAATCATAAACAATCATAAAACACTAAACTAAATATAAACAAT
1 TTAAAAAAATA-AAAAAAATTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAAT
*
41201143 TTATAACCTAATCATAACTTACTAACAAAATAACTATAAAATAA
65 TTATAACCTAATCATAAATTACTAACAAAATAACTAT-AAATAA
* * * *
41201187 TT------TTTAAAAAAATTATATTCATAAAAAATCACAAAACACTCAACTAAACACAAACAATT
1 TTAAAAAAATAAAAAAAATTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATT
** *
41201246 TATAATATAATCATAAATTACTAAAAAAATAACTATAATATAA
66 TATAACCTAATCATAAATTACTAACAAAATAACTATAA-ATAA
* *** *
41201289 TT------TTTTTAAAAATTACATTCATAAAAAATCACAAAACACTAAACTAAATACAAACAATT
1 TTAAAAAAATAAAAAAAATTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATT
41201348 TATAACCTAATCATAAATTACTAACAAAATAACTAT--A-AA
66 TATAACCTAATCATAAATTACTAACAAAATAACTATAAATAA
*** * * *
41201387 --AAAATTTTAAAAAAATTTACATTCATAAAAAATCACAAAACACTAAACCAAACACAAAAAATT
1 TTAAAAAAATAAAAAAAATTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATT
41201450 TATAA
66 TATAA
41201455 TAATTAATAA
Statistics
Matches: 424, Mismatches: 55, Indels: 24
0.84 0.11 0.05
Matches are distributed among these distances:
98 2 0.00
99 1 0.00
101 2 0.00
102 225 0.53
103 1 0.00
109 64 0.15
110 108 0.25
111 21 0.05
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.27
Consensus pattern (107 bp):
TTAAAAAAATAAAAAAAATTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATT
TATAACCTAATCATAAATTACTAACAAAATAACTATAAATAA
Found at i:41201052 original size:211 final size:208
Alignment explanation
Indices: 41200663--41201455 Score: 832
Period size: 211 Copynumber: 3.8 Consensus size: 208
41200653 AAAAACAGAT
* * * *
41200663 AAAATTACATT-ATAACAAATCACAATACACATTAAACT-AA-ACAAATAATTTATAACCTAATC
1 AAAATTACATTCATAAAAAATCAC-ATAAACACTAAACTAAACACAAACAATTTATAACCTAATC
* * * *
41200725 ATAAATTACTAGCAAAATAACTTTAAAATAATTTAAAAAACACAAAAAAATTGCATTTATAACAA
65 ATAAATTACTAACAAAATAACTTTAAAATAA-TTAAAAAA-ATAAAAAAATTACATTCATAA-AA
* * *
41200790 GTAACA-ATAAATACTAAACTAAACACAAACAATTTATAATCTAATCATAAATTACTAACAAAAT
127 -AAACACA-AAACACTAAACTAAACAAAAACAATTTATAATCTAATCATAAATTACTAACAAAAT
*
41200854 AAATTTAAAATAA-TTAAA
190 AACTTTAAAATAATTTAAA
* * *
41200872 AAAATTACATTCATAAAAAATCGCAATAAACACTAAACTAAACACAATCAATTTATAATCTAATC
1 AAAATTACATTCATAAAAAATCAC-ATAAACACTAAACTAAACACAAACAATTTATAACCTAATC
* *
41200937 ATAAATTACTAACAAAATAACTTTCAAATAATTAAAAAAATAAAAAATTTTACATTCATAAAAAA
65 ATAAATTACTAACAAAATAACTTTAAAATAATTAAAAAAATAAAAAA-ATTACATTCATAAAAAA
* * * *
41201002 ACACAATAAACATTAAACTAAACAAAAACAATTTATAACCTAACCATAAATTACTAACAAAATGA
129 ACAC-A-AAACACTAAACTAAACAAAAACAATTTATAATCTAATCATAAATTACTAACAAAATAA
41201067 CTTTAAAATAATTTAAAAAATACAAA
192 CTTTAAAATAA-TT------T--AAA
* * * * *
41201093 AAAATTACAATCATAAACAATCATA-AAACACTAAACTAAATATAAACAATTTATAACCTAATCA
1 AAAATTACATTCATAAAAAATCACATAAACACTAAACTAAACACAAACAATTTATAACCTAATCA
* * ** * *
41201157 TAACTTACTAACAAAATAACTATAAAATAATT-----TTTAAAAAAATTATATTCATAAAAAATC
66 TAAATTACTAACAAAATAACTTTAAAATAATTAAAAAAATAAAAAAATTACATTCATAAAAAAAC
* * * * *
41201217 ACAAAACACTCAACTAAACACAAACAATTTATAATATAATCATAAATTACTAAAAAAATAACTAT
131 ACAAAACACTAAACTAAACAAAAACAATTTATAATCTAATCATAAATTACTAACAAAATAACTTT
* **
41201282 AATATAATTTTTTTA
196 AAAATAA--TTTAAA
*
41201297 AAAATTACATTCATAAAAAATCACA-AAACACTAAACTAAATACAAACAATTTATAACCTAATCA
1 AAAATTACATTCATAAAAAATCACATAAACACTAAACTAAACACAAACAATTTATAACCTAATCA
* * * *
41201361 TAAATTACTAACAAAATAACTATAAAAAAATT------TTAAAAAAATTTACATTCATAAAAAAT
66 TAAATTACTAACAAAATAACTTTAAAATAATTAAAAAAATAAAAAAA-TTACATTCATAAAAAAA
*
41201420 CACAAAACACTAAACCAAACACAAAA-AATTTATAAT
130 CACAAAACACTAAACTAAACA-AAAACAATTTATAAT
41201456 AATTAATAAC
Statistics
Matches: 506, Mismatches: 59, Indels: 43
0.83 0.10 0.07
Matches are distributed among these distances:
203 9 0.02
204 136 0.27
205 3 0.01
206 1 0.00
209 15 0.03
210 32 0.06
211 143 0.28
212 52 0.10
213 19 0.04
214 7 0.01
219 65 0.13
220 1 0.00
221 23 0.05
ACGTcount: A:0.58, C:0.14, G:0.01, T:0.27
Consensus pattern (208 bp):
AAAATTACATTCATAAAAAATCACATAAACACTAAACTAAACACAAACAATTTATAACCTAATCA
TAAATTACTAACAAAATAACTTTAAAATAATTAAAAAAATAAAAAAATTACATTCATAAAAAAAC
ACAAAACACTAAACTAAACAAAAACAATTTATAATCTAATCATAAATTACTAACAAAATAACTTT
AAAATAATTTAAA
Found at i:41207116 original size:3 final size:3
Alignment explanation
Indices: 41207108--41207137 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
41207098 ACTAATAAAT
41207108 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
41207138 CAACAACATT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:41212591 original size:11 final size:11
Alignment explanation
Indices: 41212575--41212600 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
41212565 AAAAAGTACC
41212575 GGCGTATTTGG
1 GGCGTATTTGG
41212586 GGCGTATTTGG
1 GGCGTATTTGG
41212597 GGCG
1 GGCG
41212601 AGATCTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.12, G:0.50, T:0.31
Consensus pattern (11 bp):
GGCGTATTTGG
Found at i:41222538 original size:16 final size:16
Alignment explanation
Indices: 41222514--41222569 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
41222504 GGTTAGGGGG
41222514 AATGGAATAGAGCTGT
1 AATGGAATAGAGCTGT
*
41222530 AATGTAATAGAGCTGT
1 AATGGAATAGAGCTGT
*
41222546 AATGGAATAGACCTGT
1 AATGGAATAGAGCTGT
41222562 AAT-GAATA
1 AATGGAATA
41222570 ATTCAGTTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
15 5 0.14
16 32 0.86
ACGTcount: A:0.41, C:0.07, G:0.25, T:0.27
Consensus pattern (16 bp):
AATGGAATAGAGCTGT
Found at i:41222599 original size:46 final size:44
Alignment explanation
Indices: 41222546--41222636 Score: 112
Period size: 44 Copynumber: 2.0 Consensus size: 44
41222536 ATAGAGCTGT
41222546 AATGGAATAGACCTGTAATGAATAATTCAGT-TGTTTGGTTGAATGG
1 AATGGAATAGACCTGTAAT-AAT-ATTC-GTGTGTTTGGTTGAATGG
** * *
41222592 AATGGAATAGAGTTGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGACCTGTAATAATATTCGTGTGTTTGGTTGAATGG
41222636 A
1 A
41222637 GTAGATGTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
43 1 0.03
44 20 0.50
45 2 0.05
46 17 0.43
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.37
Consensus pattern (44 bp):
AATGGAATAGACCTGTAATAATATTCGTGTGTTTGGTTGAATGG
Found at i:41222877 original size:36 final size:36
Alignment explanation
Indices: 41222808--41222887 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
41222798 TTAACATAAG
* * *
41222808 TATTATTAAATACAATTTAATAACATTCTTAATAT-
1 TATTATTAAATACAATTTAATAAAAATCATAATATA
**
41222843 TATTATTAAATTATGATTTAATAAAAATCATAATATA
1 TATTATTAAA-TACAATTTAATAAAAATCATAATATA
*
41222880 TAATATTA
1 TATTATTA
41222888 TAAAAATAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
35 10 0.27
36 20 0.54
37 7 0.19
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (36 bp):
TATTATTAAATACAATTTAATAAAAATCATAATATA
Found at i:41232133 original size:31 final size:31
Alignment explanation
Indices: 41232097--41232158 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
41232087 TTGACAAATA
41232097 AGTTTTTATTGAATTATTTGAAATTGTGTAT
1 AGTTTTTATTGAATTATTTGAAATTGTGTAT
41232128 AGTTTTTATTGAATTATTTGAAATTGTGTAT
1 AGTTTTTATTGAATTATTTGAAATTGTGTAT
41232159 GTCGCTGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (31 bp):
AGTTTTTATTGAATTATTTGAAATTGTGTAT
Found at i:41232682 original size:148 final size:148
Alignment explanation
Indices: 41232511--41232780 Score: 432
Period size: 148 Copynumber: 1.8 Consensus size: 148
41232501 ACTGTTTTGG
* * * * *
41232511 ATTTGTTTGTATTTAATTGTTTGGTTATTGTACATGACAGAAATGCATTTCTTTGTGTTAAATTA
1 ATTTATTTGTATTAAATTATTTGGTTATTGTACATAACAGAAATGCATTTCTTTGTATTAAATTA
* * *
41232576 TTTTTGTATTGGTTATTATCTGCCATTGCTTAGGTTGTATTAAAGTGTTTGGTTATTGTCTGCTA
66 TTCTTGTATTGGTTATTATCTGACATTGCTTAGGTTGTATTAAAATGTTTGGTTATTGTCTGCTA
41232641 TGTATACGACAGAAATGA
131 TGTATACGACAGAAATGA
* * *
41232659 ATTTATTTGTATTAAATTATTTGGTTATTGTACATAACAGAAATGGATTTGTTTGTATTAAATTG
1 ATTTATTTGTATTAAATTATTTGGTTATTGTACATAACAGAAATGCATTTCTTTGTATTAAATTA
*
41232724 TTCTTGTATTGGTTATTGTCTGACATTGCTTAGGTTGTATTAAAATGTTTGGTTATT
66 TTCTTGTATTGGTTATTATCTGACATTGCTTAGGTTGTATTAAAATGTTTGGTTATT
41232781 ATCTACCATT
Statistics
Matches: 110, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
148 110 1.00
ACGTcount: A:0.25, C:0.07, G:0.19, T:0.49
Consensus pattern (148 bp):
ATTTATTTGTATTAAATTATTTGGTTATTGTACATAACAGAAATGCATTTCTTTGTATTAAATTA
TTCTTGTATTGGTTATTATCTGACATTGCTTAGGTTGTATTAAAATGTTTGGTTATTGTCTGCTA
TGTATACGACAGAAATGA
Found at i:41235338 original size:49 final size:48
Alignment explanation
Indices: 41235231--41235351 Score: 147
Period size: 49 Copynumber: 2.5 Consensus size: 48
41235221 ATGCCGACGC
*
41235231 CATGTCCCAGACATGGTCTTACACTGGCTAACACATCAAAGTCGATGT
1 CATGTCCCAGACATGGTCTTACACTGGCTAACACATCAAAGTCAATGT
* ** **
41235279 CATGTCCCAGACAT-GTTTTACACTGGCTCTCATCTATCAGTGTCAATGT
1 CATGTCCCAGACATGGTCTTACACTGGCTAACA-C-ATCAAAGTCAATGT
*
41235328 CATGTCCCAGATA-GGTCTTACACT
1 CATGTCCCAGACATGGTCTTACACT
41235352 AGCTTGTATA
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
47 15 0.24
48 15 0.24
49 32 0.52
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (48 bp):
CATGTCCCAGACATGGTCTTACACTGGCTAACACATCAAAGTCAATGT
Found at i:41235395 original size:48 final size:48
Alignment explanation
Indices: 41235328--41235448 Score: 197
Period size: 48 Copynumber: 2.5 Consensus size: 48
41235318 GTGTCAATGT
* * * *
41235328 CATGTCCCAGATAGGTCTTACACTAGCTTGTATATCTTGAGGCTGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCGAGGCCGATG
*
41235376 CATGTCCCAGACATATCTTACACTAGCTTGTATATCTCGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCGAGGCCGATG
41235424 CATGTCCCAGACATGTCTTACACTA
1 CATGTCCCAGACATGTCTTACACTA
41235449 ACACACATAT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 67 1.00
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.31
Consensus pattern (48 bp):
CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCGAGGCCGATG
Found at i:41235459 original size:48 final size:48
Alignment explanation
Indices: 41235359--41235459 Score: 130
Period size: 48 Copynumber: 2.1 Consensus size: 48
41235349 ACTAGCTTGT
* * * ****
41235359 ATATCTTGAGGCTGATGCATGTCCCAGACATATCTTACACTAGCTTGT
1 ATATCTCGAGGCCGATGCATGTCCCAGACATATCTTACACTAACACAC
*
41235407 ATATCTCGAGGCCGATGCATGTCCCAGACATGTCTTACACTAACACAC
1 ATATCTCGAGGCCGATGCATGTCCCAGACATATCTTACACTAACACAC
41235455 ATATC
1 ATATC
41235460 ACCCAATGTC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.29
Consensus pattern (48 bp):
ATATCTCGAGGCCGATGCATGTCCCAGACATATCTTACACTAACACAC
Found at i:41235969 original size:31 final size:31
Alignment explanation
Indices: 41235934--41235997 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
41235924 TTTCACACAA
41235934 GTACAACATATTTTATAACTTTTATAAAATG
1 GTACAACATATTTTATAACTTTTATAAAATG
41235965 GTACAACATATTTTATAACTTTTATAAAATG
1 GTACAACATATTTTATAACTTTTATAAAATG
41235996 GT
1 GT
41235998 CCTTTTAGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (31 bp):
GTACAACATATTTTATAACTTTTATAAAATG
Found at i:41240626 original size:19 final size:19
Alignment explanation
Indices: 41240602--41240640 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
41240592 TGTAGGCAAA
41240602 TTTGGCAATAGTTTGCCTT
1 TTTGGCAATAGTTTGCCTT
*
41240621 TTTGGCAATATTTTGCCTT
1 TTTGGCAATAGTTTGCCTT
41240640 T
1 T
41240641 CTTTTTGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.15, G:0.18, T:0.51
Consensus pattern (19 bp):
TTTGGCAATAGTTTGCCTT
Found at i:41241073 original size:47 final size:47
Alignment explanation
Indices: 41240978--41241075 Score: 117
Period size: 47 Copynumber: 2.1 Consensus size: 47
41240968 ATACTCTCTT
* * *
41240978 AATACCAACAATCACATAAGTTGGTTTTCTATTTCAATAACAACAAC
1 AATACCAACAATCACATAAGCTGGTTTTCTATTTAAACAACAACAAC
* * **
41241025 AATACCAGCTATCACATAAGCTGGTTTT-TCATTTAAACAACAGGAAC
1 AATACCAACAATCACATAAGCTGGTTTTCT-ATTTAAACAACAACAAC
41241072 AATA
1 AATA
41241076 TTACAAATAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
46 1 0.02
47 42 0.98
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.29
Consensus pattern (47 bp):
AATACCAACAATCACATAAGCTGGTTTTCTATTTAAACAACAACAAC
Found at i:41249815 original size:135 final size:138
Alignment explanation
Indices: 41249654--41249967 Score: 413
Period size: 140 Copynumber: 2.3 Consensus size: 138
41249644 TCTTATTTAA
*
41249654 ATTTGTATTTTTTTATTTCATGTTGCTTCAAGTTTTTTAAATTTTT-A-AT-TTTTTTAA-TTTA
1 ATTTGTA-TTTTTTATTTCATGTTGCTTCAAGTTTTTTAAATTTTTAATATGTTTTTTAACATT-
* * * * *
41249715 TTAGTTCTTTAGTTAGATGGTTAGATAGTTGTAATTACATTATTGAGTCTCGAATTTGACTCCTC
64 TTAATTCTTTAGTTAGATGGTTAGATAGTTGCAATTACATCACTGAGTCTCGAATTCGACTCCTC
* *
41249780 TCTTACTTTT
129 TATTACTTAT
* **
41249790 ATTTGTATTTTTTATTTTATGTTGCTTCAAGCGTTTTAAATTTTTAATTGATGTTTTTTAACATT
1 ATTTGTATTTTTTATTTCATGTTGCTTCAAGTTTTTTAAATTTTTAA-T-ATGTTTTTTAACATT
* * * *
41249855 TTAATTCTTTTGTTAGATGGTTAGATAGTTGCAATTACATCACTGAGTCTCGAGTTCGATTTCTC
64 TTAATTCTTTAGTTAGATGGTTAGATAGTTGCAATTACATCACTGAGTCTCGAATTCGACTCCTC
41249920 TATTACTTAT
129 TATTACTTAT
*
41249930 ATTTGTATTTTTT-TTTCATGTTGCTTCAATTTTTTTAA
1 ATTTGTATTTTTTATTTCATGTTGCTTCAAGTTTTTTAA
41249968 TTAATATTTT
Statistics
Matches: 153, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
135 35 0.23
136 8 0.05
139 23 0.15
140 85 0.56
141 2 0.01
ACGTcount: A:0.23, C:0.10, G:0.12, T:0.55
Consensus pattern (138 bp):
ATTTGTATTTTTTATTTCATGTTGCTTCAAGTTTTTTAAATTTTTAATATGTTTTTTAACATTTT
AATTCTTTAGTTAGATGGTTAGATAGTTGCAATTACATCACTGAGTCTCGAATTCGACTCCTCTA
TTACTTAT
Found at i:41250154 original size:15 final size:16
Alignment explanation
Indices: 41250125--41250158 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
41250115 TTTATGATAT
*
41250125 TTTTTAATTATTTTTA
1 TTTTTAACTATTTTTA
41250141 TTTTTAACTA-TTTTA
1 TTTTTAACTATTTTTA
41250156 TTT
1 TTT
41250159 ATAAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTAACTATTTTTA
Found at i:41255861 original size:46 final size:44
Alignment explanation
Indices: 41255756--41255875 Score: 125
Period size: 46 Copynumber: 2.7 Consensus size: 44
41255746 GTGCCTATGC
* *
41255756 CATGTCCCAGACATGGTCTTACACTGACACATCTCGTAGCTGATG
1 CATGTCCCAGACAT-GTCTTACACTGACACATCTCGTAGCTAAAG
* * *
41255801 CATGTCCCAAACATGTCTTACACTGGCTTACGTCTCG-AGGCTAAAG
1 CATGTCCCAGACATGTCTTACACTGAC--ACATCTCGTA-GCTAAAG
* * *
41255847 CATGTCTCAGACATGTCTTGCACTAACAC
1 CATGTCCCAGACATGTCTTACACTGACAC
41255876 TCGTCTCAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
44 14 0.23
45 14 0.23
46 34 0.55
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (44 bp):
CATGTCCCAGACATGTCTTACACTGACACATCTCGTAGCTAAAG
Found at i:41257238 original size:30 final size:31
Alignment explanation
Indices: 41257202--41257259 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
41257192 TTTCTAAGCC
41257202 TAGGGGCAAAATCATAATTTTG-CAAAGGTT
1 TAGGGGCAAAATCATAATTTTGTCAAAGGTT
**
41257232 TAGGGGCAAAATTTTAATTTTGTCAAAG
1 TAGGGGCAAAATCATAATTTTGTCAAAG
41257260 TTTGAGTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (31 bp):
TAGGGGCAAAATCATAATTTTGTCAAAGGTT
Found at i:41257864 original size:44 final size:44
Alignment explanation
Indices: 41257799--41257882 Score: 100
Period size: 44 Copynumber: 1.9 Consensus size: 44
41257789 TTGATATCTC
* * *
41257799 AAAGTCCATGGTTGTACCATGGTGA-TTAAGGAAGAATTGATGAA
1 AAAGTCCATGGTTATAACATGG-CATTTAAGGAAGAATTGATGAA
*
41257843 AAAGTCCAT-GTTCATAACATGGCATTTAAGGAGGAATTGA
1 AAAGTCCATGGTT-ATAACATGGCATTTAAGGAAGAATTGA
41257883 CGGTTAAGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
43 4 0.12
44 30 0.88
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.27
Consensus pattern (44 bp):
AAAGTCCATGGTTATAACATGGCATTTAAGGAAGAATTGATGAA
Found at i:41258204 original size:55 final size:54
Alignment explanation
Indices: 41258075--41258271 Score: 254
Period size: 54 Copynumber: 3.6 Consensus size: 54
41258065 TTGGTAAGAT
* * *
41258075 AAGGATATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
* * *
41258129 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTT-CTATAAGGC
* * **
41258184 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGGGAGTTC-ATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
* *
41258237 AAGGATACCACGTAAGACCATGTCAAGACATGGCA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCA
41258272 ATGGTAAGTT
Statistics
Matches: 125, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
52 4 0.03
53 33 0.26
54 42 0.34
55 42 0.34
56 4 0.03
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
Found at i:41264441 original size:29 final size:29
Alignment explanation
Indices: 41264407--41264464 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
41264397 CCACTGGTAG
*
41264407 GTCGAATCTCTCAAGAGCTATACTGCACA
1 GTCGAATCTCTCAAAAGCTATACTGCACA
41264436 GTCGAATCTCTCAAAAGCTATACTGCACA
1 GTCGAATCTCTCAAAAGCTATACTGCACA
41264465 CTTCATGCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.24
Consensus pattern (29 bp):
GTCGAATCTCTCAAAAGCTATACTGCACA
Found at i:41266440 original size:16 final size:17
Alignment explanation
Indices: 41266409--41266441 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
41266399 TTCATAAGTA
41266409 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
41266426 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
41266442 GCACCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:41266789 original size:46 final size:46
Alignment explanation
Indices: 41266727--41267046 Score: 435
Period size: 46 Copynumber: 7.0 Consensus size: 46
41266717 TTTGACATGA
* * * * *
41266727 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATATCAGGT
* * * * *
41266773 TGCCATGGTATTTTTCAACCATGGTCTTATTCATTTCATGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
* * *** *
41266819 TGCCATGGTATCTTTCAACCATTGTCTTATTCATTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
*
41266865 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
*
41266911 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
*
41266957 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
* *
41267003 TGTCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAG
41267047 AGAGCACACT
Statistics
Matches: 252, Mismatches: 21, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
45 4 0.02
46 248 0.98
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
Found at i:41281347 original size:38 final size:39
Alignment explanation
Indices: 41281256--41281347 Score: 123
Period size: 40 Copynumber: 2.4 Consensus size: 39
41281246 CGGTACCATT
* *
41281256 TGGTGTGTAGGGTTGGATGAGTTGATTATATCCCCATACT
1 TGGTGTGTAGGGTTGGATGAGTCGATTATATCCCCA-ACA
* *
41281296 TGGTGTGTAGGGTTGGATGGGTCGATTTTATCCCC-ACA
1 TGGTGTGTAGGGTTGGATGAGTCGATTATATCCCCAACA
*
41281334 TGGTGTGTTGGGTT
1 TGGTGTGTAGGGTT
41281348 TGACGGAGAT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 15 0.32
40 32 0.68
ACGTcount: A:0.15, C:0.12, G:0.35, T:0.38
Consensus pattern (39 bp):
TGGTGTGTAGGGTTGGATGAGTCGATTATATCCCCAACA
Found at i:41282278 original size:13 final size:13
Alignment explanation
Indices: 41282260--41282285 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41282250 GCAGGGGAGA
41282260 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
41282273 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
41282286 GGAAAATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AAAAGAAAGAAAG
Found at i:41285150 original size:21 final size:21
Alignment explanation
Indices: 41285095--41285151 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
41285085 ACACGCCAAT
* *
41285095 AGAAGCTCATAAGAGCTGAAC
1 AGAAGCTCATAATAGCTAAAC
*
41285116 AGAAGCTCGTAATAGCTAAAC
1 AGAAGCTCATAATAGCTAAAC
*
41285137 AGAAGCTCAAAATAG
1 AGAAGCTCATAATAG
41285152 TTGATCCACT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.16
Consensus pattern (21 bp):
AGAAGCTCATAATAGCTAAAC
Found at i:41287812 original size:15 final size:15
Alignment explanation
Indices: 41287757--41287813 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
41287747 TTTATACTAC
*
41287757 AAAACATTTATTATT
1 AAAATATTTATTATT
* *
41287772 AACATATTTATAATTCT
1 AAAATATTTATTA-T-T
41287789 AATAAATATTTATTATT
1 -A-AAATATTTATTATT
41287806 AAAATATT
1 AAAATATT
41287814 AATATTGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 17 0.52
16 2 0.06
17 2 0.06
18 2 0.06
19 10 0.30
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (15 bp):
AAAATATTTATTATT
Found at i:41287919 original size:16 final size:16
Alignment explanation
Indices: 41287894--41287945 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
41287884 TAAAATTGAA
41287894 ATATTAAATAATTTATT
1 ATATT-AATAATTTATT
* *
41287911 AAATTAATAA---AGT
1 ATATTAATAATTTATT
41287924 ATATTAATAATTTATT
1 ATATTAATAATTTATT
41287940 ATATTA
1 ATATTA
41287946 TTATATATAG
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
13 11 0.39
16 13 0.46
17 4 0.14
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
ATATTAATAATTTATT
Found at i:41289649 original size:37 final size:37
Alignment explanation
Indices: 41289588--41289770 Score: 307
Period size: 37 Copynumber: 5.0 Consensus size: 37
41289578 TACGTATGAT
* *
41289588 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
41289623 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
41289660 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
41289697 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
* *
41289734 CACTTATCACTCTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
41289771 TAAAGCTATC
Statistics
Matches: 140, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
35 9 0.06
36 3 0.02
37 128 0.91
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:41289813 original size:52 final size:52
Alignment explanation
Indices: 41289734--41290100 Score: 461
Period size: 52 Copynumber: 7.2 Consensus size: 52
41289724 TAAGTGTAGC
* * **
41289734 CACTTATCACTCTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTAT
1 CACTTTTCACT-TGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
41289787 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* *
41289839 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* ** *
41289885 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* *
41289937 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* * *
41289983 CACTTTCCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* ** *
41290035 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
41290087 CACTTTGTCACTTG
1 CACTTT-TCACTTG
41290101 ATCAGAAGTA
Statistics
Matches: 276, Mismatches: 25, Indels: 26
0.84 0.08 0.08
Matches are distributed among these distances:
46 83 0.30
49 1 0.00
52 176 0.64
53 16 0.06
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
Found at i:41289875 original size:98 final size:98
Alignment explanation
Indices: 41289734--41290092 Score: 511
Period size: 98 Copynumber: 3.6 Consensus size: 98
41289724 TAAGTGTAGC
* * * * *
41289734 CACTTATCACTCTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTCCACTT
41289799 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
41289832 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTCCACTT
** *
41289897 GTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
41289930 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTCCACTT
*
41289995 GTCACTTGATCAGATAAGTATAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* * * *
41290028 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTT
41290093 GTCACTTGAT
Statistics
Matches: 235, Mismatches: 20, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
98 191 0.81
100 1 0.00
104 43 0.18
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTCCACTT
GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:41290101 original size:150 final size:144
Alignment explanation
Indices: 41289741--41290106 Score: 579
Period size: 150 Copynumber: 2.5 Consensus size: 144
41289731 AGCCACTTAT
* *
41289741 CACTCTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTTCACTTGTCACTT
1 CACT-TGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC---T---TTGTCACTT
*
41289806 GATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCG
59 GATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCG
41289871 AAGCTATTACTTATCACTTTC
124 AAGCTATTACTTATCACTTTC
41289892 CACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGA
1 CACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGA
*
41289957 TAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTATAGCCGA
66 TAAGTATAGCCGAAGCTATCACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCGA
41290022 AGCTATTACTTATCACTTTC
125 AGCTATTACTTATCACTTTC
41290042 CACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGA
1 CACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGA
41290107 AGTACTCAAA
Statistics
Matches: 205, Mismatches: 4, Indels: 13
0.92 0.02 0.06
Matches are distributed among these distances:
144 43 0.21
146 1 0.00
147 1 0.00
150 156 0.76
151 4 0.02
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (144 bp):
CACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGA
TAAGTATAGCCGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
TACTTATCACTTTC
Found at i:41292415 original size:3 final size:3
Alignment explanation
Indices: 41292407--41292450 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
41292397 TATATTTTTC
* *
41292407 TTA TTA TTA CTA TTA TTA TT- TTA CCTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT
41292451 TATATATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 31 0.89
4 2 0.06
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:41292427 original size:24 final size:24
Alignment explanation
Indices: 41292399--41292451 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
41292389 CTTGTACATA
* *
41292399 TATTTTTCTTATTATTACTATTAT
1 TATTTTACCTATTATTACTATTAT
*
41292423 TATTTTACCTATTATTATTATTAT
1 TATTTTACCTATTATTACTATTAT
41292447 TATTT
1 TATTT
41292452 ATATATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (24 bp):
TATTTTACCTATTATTACTATTAT
Found at i:41292434 original size:15 final size:15
Alignment explanation
Indices: 41292407--41292464 Score: 66
Period size: 15 Copynumber: 3.8 Consensus size: 15
41292397 TATATTTTTC
41292407 TTATTATTACTATTA
1 TTATTATTACTATTA
41292422 TTATT-TTACCTATTA
1 TTATTATTA-CTATTA
*
41292437 TTATTATTATTATTTA
1 TTATTATTACTA-TTA
41292453 TATATT-TTACTA
1 T-TATTATTACTA
41292465 CAAATTGCAC
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
14 3 0.08
15 18 0.49
16 12 0.32
17 4 0.11
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATTATTACTATTA
Found at i:41294184 original size:22 final size:22
Alignment explanation
Indices: 41294156--41294199 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
41294146 TCAGGTATTA
41294156 ACCAAATCAACCGTTTGAACAT
1 ACCAAATCAACCGTTTGAACAT
*
41294178 ACCAAATCTACCGTTTGAACAT
1 ACCAAATCAACCGTTTGAACAT
41294200 TCCTACTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.25
Consensus pattern (22 bp):
ACCAAATCAACCGTTTGAACAT
Found at i:41301551 original size:19 final size:19
Alignment explanation
Indices: 41301532--41301569 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 19
41301522 AGGGGATAAT
41301532 AAAAGAAAAATAATTAAATA
1 AAAAG-AAAATAATTAAATA
41301552 AAAAGAAAATAATTAAAT
1 AAAAGAAAATAATTAAAT
41301570 TGTTCAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (19 bp):
AAAAGAAAATAATTAAATA
Found at i:41302719 original size:8 final size:8
Alignment explanation
Indices: 41302706--41302734 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
41302696 CAATAAATAA
41302706 AAAATATT
1 AAAATATT
41302714 AAAATATT
1 AAAATATT
41302722 -AAATATT
1 AAAATATT
41302729 AAAATA
1 AAAATA
41302735 AAAAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
AAAATATT
Found at i:41302760 original size:11 final size:13
Alignment explanation
Indices: 41302732--41302763 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
41302722 AAATATTAAA
41302732 ATAAAAAAATTTT
1 ATAAAAAAATTTT
41302745 ATAAAAAAATTTT
1 ATAAAAAAATTTT
41302758 A-AAAAA
1 ATAAAAA
41302764 TAATATGGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAAAAAAATTTT
Found at i:41308367 original size:24 final size:25
Alignment explanation
Indices: 41308316--41308372 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
41308306 ATGTGAATTG
*
41308316 ATTTATAACAATAAAAATAAATAAA
1 ATTTTTAACAATAAAAATAAATAAA
* **
41308341 ATTTTTAACAA-AAAAATTAATTTA
1 ATTTTTAACAATAAAAATAAATAAA
41308365 ATTTTTAA
1 ATTTTTAA
41308373 TTTAATACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 18 0.64
25 10 0.36
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.39
Consensus pattern (25 bp):
ATTTTTAACAATAAAAATAAATAAA
Found at i:41309153 original size:29 final size:31
Alignment explanation
Indices: 41309089--41309153 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 31
41309079 ACATAATAAC
* *
41309089 AATAAAAATATATTAAAAATTCTACAAAGTA
1 AATAAAAATATATTAAAAATTCTAAAAAATA
*
41309120 AATAAAAAT-TA-TAAAAGTTC-AAAAAATA
1 AATAAAAATATATTAAAAATTCTAAAAAATA
41309148 ATATAA
1 A-ATAA
41309154 TTAATAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 7 0.23
29 12 0.40
30 2 0.07
31 9 0.30
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (31 bp):
AATAAAAATATATTAAAAATTCTAAAAAATA
Found at i:41309557 original size:29 final size:27
Alignment explanation
Indices: 41309495--41309554 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
41309485 TTATTTTATA
* *
41309495 ATTTATTTTTAAATTTTTATAGTTTTT
1 ATTTGTTTTTAAATTTTTATAATTTTT
41309522 ATTTGTTTTTAGAATTTTTAATATATTTTT
1 ATTTGTTTTTA-AATTTTT-ATA-ATTTTT
41309552 ATT
1 ATT
41309555 GTTAATACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 10 0.36
28 7 0.25
29 3 0.11
30 8 0.29
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (27 bp):
ATTTGTTTTTAAATTTTTATAATTTTT
Found at i:41317644 original size:24 final size:24
Alignment explanation
Indices: 41317600--41317647 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
41317590 AAATAAAGAC
***
41317600 TAATGAAATAAAAATCTATTTAAA
1 TAATGAAATAAAAAAAAATTTAAA
41317624 TAATGAAATAAAAAAAAATTTAAA
1 TAATGAAATAAAAAAAAATTTAAA
41317648 AGGTAATGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (24 bp):
TAATGAAATAAAAAAAAATTTAAA
Found at i:41318464 original size:14 final size:14
Alignment explanation
Indices: 41318445--41318486 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
41318435 AAACAATTTA
41318445 AAAATATAC-AAAAG
1 AAAATA-ACAAAAAG
41318459 AAAATAACAAAAAG
1 AAAATAACAAAAAG
*
41318473 AAAAAAACTAAAAA
1 AAAATAAC-AAAAA
41318487 AAACTAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 2 0.08
14 18 0.72
15 5 0.20
ACGTcount: A:0.79, C:0.07, G:0.05, T:0.10
Consensus pattern (14 bp):
AAAATAACAAAAAG
Found at i:41325034 original size:131 final size:131
Alignment explanation
Indices: 41324899--41325200 Score: 331
Period size: 132 Copynumber: 2.3 Consensus size: 131
41324889 TTGTCTGCTT
* * *
41324899 AAAACAATCAAATATCCCTTCAAAATTTCACTCATATCTT-TTAAAAATCCTTT-AAAACGAAGG
1 AAAACAATCGAATATCCCTTCAGAATTTCACTCATAT-TTATTAAAAA-CCTTTCAAAACAAAGG
* ** * *
41324962 CAATACTCGAGGTTTGACAATTCGGGAATCATGCCCTATCGTGCTGGGTTGTGATTTCTTATTTG
64 CAATACTCGAGGTTTGACAATTCGAGAATCATGCCCTATCGTGCTGGGTTGCAATCTCTCATTTG
41325027 TTC
129 TTC
** * * *
41325030 AAAACAATCGAATATTCCCTT-AGGTTTTTTACTTATGTTTATTAAAAACCTTTCAAAACAAAGG
1 AAAACAATCGAATA-TCCCTTCA-GAATTTCACTCATATTTATTAAAAACCTTTCAAAACAAAGG
* ** * * * *
41325094 CTATGTTCGATGTTTGGCAATTCGAGAATCGTGCCCTATCGTGCTGGGTTGCAATCTCTCGTTTG
64 CAATACTCGAGGTTTGACAATTCGAGAATCATGCCCTATCGTGCTGGGTTGCAATCTCTCATTTG
41325159 TTC
129 TTC
* * * *
41325162 AAAACAATCGAACATCTCTTCGGAATTTCACTCGTATTT
1 AAAACAATCGAATATCCCTTCAGAATTTCACTCATATTT
41325201 TCTAAGGTGA
Statistics
Matches: 137, Mismatches: 29, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
131 37 0.27
132 100 0.73
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.35
Consensus pattern (131 bp):
AAAACAATCGAATATCCCTTCAGAATTTCACTCATATTTATTAAAAACCTTTCAAAACAAAGGCA
ATACTCGAGGTTTGACAATTCGAGAATCATGCCCTATCGTGCTGGGTTGCAATCTCTCATTTGTT
C
Found at i:41326752 original size:19 final size:19
Alignment explanation
Indices: 41326730--41326777 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
41326720 TCATCCCATG
* *
41326730 CATTTGCATTGCATTGTAT
1 CATTTGCATTGCATTGAAC
41326749 CATTTGCATTGCATTGAAC
1 CATTTGCATTGCATTGAAC
41326768 CATTTGCATT
1 CATTTGCATT
41326778 AGATTTTCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.44
Consensus pattern (19 bp):
CATTTGCATTGCATTGAAC
Found at i:41330921 original size:88 final size:88
Alignment explanation
Indices: 41330805--41331213 Score: 696
Period size: 88 Copynumber: 4.7 Consensus size: 88
41330795 CTGACCTTCA
* *
41330805 TTGAAGCAGATCCAAGATGATCTGGCATCTCTGTATTAGGCGGGGAGCAGATCGAAGACATAGCT
1 TTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATCAGGCGGGGAGCAGATCGAAGACATAGCT
41330870 GATTTGGATTTCACGTGTTTACG
66 GATTTGGATTTCACGTGTTTACG
*
41330893 TTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATCAGGTGGGGAGCAGATCGAAGACATAGCT
1 TTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATCAGGCGGGGAGCAGATCGAAGACATAGCT
*
41330958 GATTTGGCTTTCACGTGTTTACG
66 GATTTGGATTTCACGTGTTTACG
41330981 TTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATCAGGCGGGGAGCAGATCGAAGACATAGCT
1 TTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATCAGGCGGGGAGCAGATCGAAGACATAGCT
*
41331046 GATTTGGCTTTCACGTGTTTACG
66 GATTTGGATTTCACGTGTTTACG
* *
41331069 TTGAAGCAGATCCAAGATGATTTGGCATCTTTATATCAGGCGGGGAGCAGATCGAAGACATAGCT
1 TTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATCAGGCGGGGAGCAGATCGAAGACATAGCT
*
41331134 AATTT-GACTTTCACGTGTTTACG
66 GATTTGGA-TTTCACGTGTTTACG
* * *
41331157 TTGAAGCAGATCCAAGATGATTTGGCATCTCTGTAGC-GGCGGAGAGTAGATCGAAGA
1 TTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATCAGGCGGGGAGCAGATCGAAGA
41331214 TAACAGATTT
Statistics
Matches: 306, Mismatches: 14, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
87 19 0.06
88 287 0.94
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (88 bp):
TTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATCAGGCGGGGAGCAGATCGAAGACATAGCT
GATTTGGATTTCACGTGTTTACG
Found at i:41330942 original size:41 final size:41
Alignment explanation
Indices: 41330897--41331126 Score: 117
Period size: 41 Copynumber: 5.3 Consensus size: 41
41330887 TTTACGTTGA
41330897 AGCAGATCCAAGATGATTTGGCATCTCTGTATCAGGTGGGG
1 AGCAGATCCAAGATGATTTGGCATCTCTGTATCAGGTGGGG
* * * * * * *
41330938 AGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGT-TTACGT-TGA
1 AGCAGATC-----CA-AGATGATTTGGC-ATCTC-TGTATCAGGTGGGG
*
41330985 AGCAGATCCAAGATGATTTGGCATCTCTGTATCAGGCGGGG
1 AGCAGATCCAAGATGATTTGGCATCTCTGTATCAGGTGGGG
* * * * * * *
41331026 AGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGT-TTACGT-TGA
1 AGCAGATC-----CA-AGATGATTTGGC-ATCTC-TGTATCAGGTGGGG
* * *
41331073 AGCAGATCCAAGATGATTTGGCATCTTTATATCAGGCGGGG
1 AGCAGATCCAAGATGATTTGGCATCTCTGTATCAGGTGGGG
*
41331114 AGCAGATCGAAGA
1 AGCAGATCCAAGA
41331127 CATAGCTAAT
Statistics
Matches: 135, Mismatches: 34, Indels: 40
0.65 0.16 0.19
Matches are distributed among these distances:
39 5 0.04
40 11 0.08
41 52 0.39
42 4 0.03
46 4 0.03
47 40 0.30
48 13 0.10
49 6 0.04
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (41 bp):
AGCAGATCCAAGATGATTTGGCATCTCTGTATCAGGTGGGG
Found at i:41330989 original size:47 final size:47
Alignment explanation
Indices: 41330850--41331085 Score: 173
Period size: 47 Copynumber: 5.3 Consensus size: 47
41330840 TTAGGCGGGG
*
41330850 AGCAGATCGAAGACATAGCTGATTTGGATTTCACGTGTTTACGTTGA
1 AGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGA
* * * * * * *
41330897 AGCAGATC-----CA-AGATGATTTGGC-ATCTC-TGTATCAGGTGGGG
1 AGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGT-TTACGT-TGA
41330938 AGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGA
1 AGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGA
* * * * * *
41330985 AGCAGATC-----CA-AGATGATTTGGC-ATCTC-TGTATCAGGCG-GGG
1 AGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGT-TTA--CGTTGA
41331026 AGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGA
1 AGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGA
*
41331073 AGCAGATCCAAGA
1 AGCAGATCGAAGA
41331086 TGATTTGGCA
Statistics
Matches: 139, Mismatches: 28, Indels: 44
0.66 0.13 0.21
Matches are distributed among these distances:
39 6 0.04
40 12 0.09
41 39 0.28
42 6 0.04
46 6 0.04
47 52 0.37
48 12 0.09
49 6 0.04
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (47 bp):
AGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGA
Found at i:41331232 original size:44 final size:44
Alignment explanation
Indices: 41331175--41331544 Score: 488
Period size: 44 Copynumber: 8.4 Consensus size: 44
41331165 GATCCAAGAT
* * * *
41331175 GATTTGGCATCTCTGTAGCGGCGGAGAGTAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTATCGGCAGAGAGCAGATCGAAGATAACA
* * *
41331219 GATTTGGCGTCTCTGTAACGGTAGAGAGCAGATCAAAGATAACA
1 GATTTGGCGTCTCTGTATCGGCAGAGAGCAGATCGAAGATAACA
* * **
41331263 GATTTGGCGTCTCTGTATTGGCAGAGAGTAGATCGAAGATAGTA
1 GATTTGGCGTCTCTGTATCGGCAGAGAGCAGATCGAAGATAACA
* * *
41331307 GATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCAAAGATAGCA
1 GATTTGGCGTCTCTGTATCGGCAGAGAGCAGATCGAAGATAACA
* * **
41331351 GATTTGGCGTCTCTGTATTGCCAGAGAGCAGATCGAAGATAGTA
1 GATTTGGCGTCTCTGTATCGGCAGAGAGCAGATCGAAGATAACA
* * *
41331395 GATTTGGCGTCTCTGTATTGTCAGAGGGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTATCGGCAGAGAGCAGATCGAAGATAACA
*
41331439 GATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTATCGGCAGAGAGCAGATCGAAGATAACA
* * * * * *
41331483 TATTTGGCGGCTCCGTAACGGCAGAGAGTAGATCGAAGATAGCA
1 GATTTGGCGTCTCTGTATCGGCAGAGAGCAGATCGAAGATAACA
41331527 GATTTGGCGTCTCTGTAT
1 GATTTGGCGTCTCTGTAT
41331545 TGGGATAGCA
Statistics
Matches: 289, Mismatches: 37, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 289 1.00
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.25
Consensus pattern (44 bp):
GATTTGGCGTCTCTGTATCGGCAGAGAGCAGATCGAAGATAACA
Found at i:41331320 original size:132 final size:132
Alignment explanation
Indices: 41331175--41331779 Score: 652
Period size: 132 Copynumber: 4.7 Consensus size: 132
41331165 GATCCAAGAT
* * *
41331175 GATTTGGCATCTCTGTAGCGGCGGAGAGTAGATCGAAGATAACAGATTTGGCGTCTCTGTAACGG
1 GATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAACGG
* * * * *
41331240 TAGAGAGCAGATCAAAGATAACAGATTTGGCGTCTCTGTATTGGCAGAGAGTAGATCGAAGATAG
66 CAGAGAGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAA
*
41331305 TA
131 CA
** * * ** *
41331307 GATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCAAAGATAGCAGATTTGGCGTCTCTGTATTGC
1 GATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAACGG
* * *
41331372 CAGAGAGCAGATCGAAGATAGTAGATTTGGCGTCTCTGTATTGTCAGAGGGCAGATCGAAGATAA
66 CAGAGAGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAA
41331437 CA
131 CA
* * *
41331439 GATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACATATTTGGCGGCTCCGTAACGG
1 GATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAACGG
*
41331504 CAGAGAGTAGATCGAAGATAGCAGATTTGGCGTCTCTGTATT------G-G--GAT---AG----
66 CAGAGAGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAA
41331553 CA
131 CA
* ** *
41331555 GATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGGTAACAGATTTGGTATCTCTGTAGCGG
1 GATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAACGG
* * * * *
41331620 CGGAGAGTAGATCGAAGATAGCAGATTTGAG-GTCTCCGTAATTGTCAGAGGGCAGATCGAAGAT
66 CAGAGAGCAGATCGAAGATAGCAGATTTG-GCGTCTCTGT-ATTGGCAGAGAGCAGATCGAAGAT
**
41331684 AGTA
129 AACA
* * * * * * * **
41331688 GATTTGGCATCTCTAT-GTTGACAGAGAGCAGATCAAAGATGACAGATTTGGCATCTCTGTATTG
1 GATTTGGCGTCTCTGTAG-CGGCAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAACG
* *
41331752 GCAGAGAGCAGATCGAAAATAACAGATT
65 GCAGAGAGCAGATCGAAGATAGCAGATT
41331780 GGTGTTCTTG
Statistics
Matches: 399, Mismatches: 55, Indels: 37
0.81 0.11 0.08
Matches are distributed among these distances:
116 95 0.24
117 4 0.01
120 2 0.01
123 4 0.01
124 1 0.00
125 1 0.00
126 4 0.01
129 2 0.01
132 209 0.52
133 77 0.19
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.25
Consensus pattern (132 bp):
GATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTAACGG
CAGAGAGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAA
CA
Found at i:41331587 original size:30 final size:28
Alignment explanation
Indices: 41331523--41331587 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 28
41331513 GATCGAAGAT
** *
41331523 AGCAGATTTGGCGTCTCTGTATTGGGAT
1 AGCAGATTTGGCGTCTCTGTAGCGGGAG
41331551 AGCAGATTTGGCGTCTCTGTAGCGGCAGAG
1 AGCAGATTTGGCGTCTCTGTAGCGG--GAG
41331581 AGCAGAT
1 AGCAGAT
41331588 CGAAGGTAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 23 0.72
30 9 0.28
ACGTcount: A:0.22, C:0.17, G:0.34, T:0.28
Consensus pattern (28 bp):
AGCAGATTTGGCGTCTCTGTAGCGGGAG
Found at i:41331616 original size:44 final size:44
Alignment explanation
Indices: 41331548--41331779 Score: 225
Period size: 44 Copynumber: 5.2 Consensus size: 44
41331538 TCTGTATTGG
* * *
41331548 GATAGCAGATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAA
1 GATAACAGATTTGGCATCTCTGTAGTGGCAGAGAGCAGATCGAA
* * * * *
41331592 GGTAACAGATTTGGTATCTCTGTAGCGGCGGAGAGTAGATCGAA
1 GATAACAGATTTGGCATCTCTGTAGTGGCAGAGAGCAGATCGAA
* * * * * *
41331636 GATAGCAGATTTGAG-GTCTCCGTAATTGTCAGAGGGCAGATCGAA
1 GATAACAGATTTG-GCATCTCTGT-AGTGGCAGAGAGCAGATCGAA
** * * *
41331681 GATAGTAGATTTGGCATCTCTAT-GTTGACAGAGAGCAGATCAAA
1 GATAACAGATTTGGCATCTCTGTAG-TGGCAGAGAGCAGATCGAA
* *
41331725 GATGACAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAA
1 GATAACAGATTTGGCATCTCTGTAGTGGCAGAGAGCAGATCGAA
*
41331769 AATAACAGATT
1 GATAACAGATT
41331780 GGTGTTCTTG
Statistics
Matches: 150, Mismatches: 33, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
44 117 0.78
45 33 0.22
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.25
Consensus pattern (44 bp):
GATAACAGATTTGGCATCTCTGTAGTGGCAGAGAGCAGATCGAA
Found at i:41331655 original size:116 final size:116
Alignment explanation
Indices: 41331432--41331648 Score: 353
Period size: 116 Copynumber: 1.9 Consensus size: 116
41331422 GCAGATCGAA
* *
41331432 GATAACAGATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACATATTTGGCGGCTCC
1 GATAACAGATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACAGATTTGGCAGCTCC
41331497 GTAACGGCAGAGAGTAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGG
66 GTAACGGCAGAGAGTAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGG
* * * * *
41331548 GATAGCAGATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGGTAACAGATTTGGTATCTCT
1 GATAACAGATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACAGATTTGGCAGCTCC
* *
41331613 GTAGCGGCGGAGAGTAGATCGAAGATAGCAGATTTG
66 GTAACGGCAGAGAGTAGATCGAAGATAGCAGATTTG
41331649 AGGTCTCCGT
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
116 92 1.00
ACGTcount: A:0.28, C:0.16, G:0.32, T:0.24
Consensus pattern (116 bp):
GATAACAGATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACAGATTTGGCAGCTCC
GTAACGGCAGAGAGTAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGG
Found at i:41331659 original size:160 final size:161
Alignment explanation
Indices: 41331388--41331701 Score: 434
Period size: 160 Copynumber: 2.0 Consensus size: 161
41331378 GCAGATCGAA
* ** * * *
41331388 GATAGTAGATTTGGCGTCTCTGTATTGTCAGAGGGCAGATCGAAGATAACAGATTTGGCGTCTCT
1 GATAGCAGATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACAGATTTGGCATCTCT
* *
41331453 GTAGCGGCAGAGAGCAGATCGAAGATAACATATTTGGCGGCTCCGTAA-CGGCAGAGAGTAGATC
66 GTAGCGGCAGAGAGCAGATCGAAGATAACAGATTTGGCGGCTCCGTAATCGGCAGAGAGCAGATC
*
41331517 GAAGATAGCAGATTTGGCGTCTCTGTATTGG
131 GAAGATAGCAGATTTGGCATCTCTGTATTGG
* *
41331548 GATAGCAGATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGGTAACAGATTTGGTATCTCT
1 GATAGCAGATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACAGATTTGGCATCTCT
* * * * * * *
41331613 GTAGCGGCGGAGAGTAGATCGAAGATAGCAGATTTGAG-GTCTCCGTAATTGTCAGAGGGCAGAT
66 GTAGCGGCAGAGAGCAGATCGAAGATAACAGATTTG-GCGGCTCCGTAATCGGCAGAGAGCAGAT
*
41331677 CGAAGATAGTAGATTTGGCATCTCT
130 CGAAGATAGCAGATTTGGCATCTCT
41331702 ATGTTGACAG
Statistics
Matches: 133, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
160 98 0.74
161 35 0.26
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (161 bp):
GATAGCAGATTTGGCGTCTCTGTAGCGGCAGAGAGCAGATCGAAGATAACAGATTTGGCATCTCT
GTAGCGGCAGAGAGCAGATCGAAGATAACAGATTTGGCGGCTCCGTAATCGGCAGAGAGCAGATC
GAAGATAGCAGATTTGGCATCTCTGTATTGG
Found at i:41333242 original size:11 final size:11
Alignment explanation
Indices: 41333226--41333250 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41333216 TTAGCTCATT
41333226 TATTTTAATTG
1 TATTTTAATTG
41333237 TATTTTAATTG
1 TATTTTAATTG
41333248 TAT
1 TAT
41333251 CCTTTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (11 bp):
TATTTTAATTG
Found at i:41334927 original size:132 final size:133
Alignment explanation
Indices: 41334684--41334927 Score: 285
Period size: 132 Copynumber: 1.8 Consensus size: 133
41334674 TTAAAATTCT
* ** * * *
41334684 TTAAATCGAAGGCGATATTCGATACTTGGTAATTCGTGGAATCGTGCGCTAACATGTTGGGTTGC
1 TTAAATCGAAGGCGATATTCGATACTTGGGAATTCACGGAATCGTACCCTAACATGCTGGGTTGC
* ** * * * * *
41334749 AATTCCTCGTTTGCTCAAAGTAATCGAAGGTCCTTTTAGAATTTCACCCACGGCTATTAAAAAAT
66 AATTCCTCGTCTGCTCAAAAAAATCAAAGATCCCTTCAAAATTTCACCCACGGCTATTAAAAAAT
41334814 CCC
131 CCC
* *
41334817 TTAAA-CGAAGGCGATATGT-GATATTTGGGAATTCACGGAATCGTACCCTAACGTGCTGGGTTG
1 TTAAATCGAAGGCGATAT-TCGATACTTGGGAATTCACGGAATCGTACCCTAACATGCTGGGTTG
* * * *
41334880 CAATTTCTTGTCTGCTTAAAAAAATCAAATATCCCTTCAAAATTTCAC
65 CAATTCCTCGTCTGCTCAAAAAAATCAAAGATCCCTTCAAAATTTCAC
41334928 TCATATCTTT
Statistics
Matches: 90, Mismatches: 20, Indels: 3
0.80 0.18 0.03
Matches are distributed among these distances:
132 84 0.93
133 6 0.07
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Consensus pattern (133 bp):
TTAAATCGAAGGCGATATTCGATACTTGGGAATTCACGGAATCGTACCCTAACATGCTGGGTTGC
AATTCCTCGTCTGCTCAAAAAAATCAAAGATCCCTTCAAAATTTCACCCACGGCTATTAAAAAAT
CCC
Found at i:41334982 original size:132 final size:131
Alignment explanation
Indices: 41334846--41335198 Score: 356
Period size: 132 Copynumber: 2.7 Consensus size: 131
41334836 GATATTTGGG
* * * * * *
41334846 AATTCACGGAATCGTACCCTAACGTGCTGGGTTGCAATTTCTTGTCTGCTT-AAAAAAATCAAAT
1 AATTC-CGGAATCGTGCCCTATCGTGCTGGGTTGCAATTTCTCGTTTG-TTCAAAACAATCGAAT
* *
41334910 ATCCCTTCAAAATTTCACTCATATCTT-TTAAAAATCCTTT-AAAACGAAGGCAATACTCGGGGT
64 ATCCCTTCAAAATTTCACTCATAT-TTATTAAAAA-CCTTTCAAAACAAAGGCAATACTCGAGGT
41334973 TTGAC
127 TTGAC
* * ** **
41334978 AATTCGGGAATCATGCCCTATTATGCTGGGTTGTGATTTCTCGTTTGTTCAAAACAATCGAATAT
1 AATTCCGGAATCGTGCCCTATCGTGCTGGGTTGCAATTTCTCGTTTGTTCAAAACAATCGAATA-
*** * * * ** *
41335043 TCCCTT-AGGTTTTTTACTCATGTTTATTAAAAACCTTTCAAAACAAAGGCTATGTTCGATGTTT
65 TCCCTTCA-AAATTTCACTCATATTTATTAAAAACCTTTCAAAACAAAGGCAATACTCGAGGTTT
*
41335107 GGC
129 GAC
*
41335110 AATT-CGAGAATCGTGCCCTATCGTGCTGGGTTGCAATCTCTCGTTTGTTCAAAACAATCGAATA
1 AATTCCG-GAATCGTGCCCTATCGTGCTGGGTTGCAATTTCTCGTTTGTTCAAAACAATCGAATA
* * *
41335174 TCTCTTCGAAATTTCACTCGTATTT
65 TCCCTTCAAAATTTCACTCATATTT
41335199 TCTAAGGTGA
Statistics
Matches: 175, Mismatches: 39, Indels: 15
0.76 0.17 0.07
Matches are distributed among these distances:
130 2 0.01
131 69 0.39
132 104 0.59
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.35
Consensus pattern (131 bp):
AATTCCGGAATCGTGCCCTATCGTGCTGGGTTGCAATTTCTCGTTTGTTCAAAACAATCGAATAT
CCCTTCAAAATTTCACTCATATTTATTAAAAACCTTTCAAAACAAAGGCAATACTCGAGGTTTGA
C
Found at i:41350614 original size:8 final size:8
Alignment explanation
Indices: 41350601--41350627 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
41350591 GGCTATTACA
41350601 ACATATAT
1 ACATATAT
41350609 ACATATAT
1 ACATATAT
41350617 ACATATAT
1 ACATATAT
41350625 ACA
1 ACA
41350628 ATAATGCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (8 bp):
ACATATAT
Found at i:41351976 original size:28 final size:28
Alignment explanation
Indices: 41351936--41351993 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
41351926 GCTTGTAACA
41351936 GTTTCCTTCATTGGATTTTTGACACATT
1 GTTTCCTTCATTGGATTTTTGACACATT
**
41351964 GTTTCCTTCATTGGATTTTTGTTACATT
1 GTTTCCTTCATTGGATTTTTGACACATT
41351992 GT
1 GT
41351994 CCATTAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.53
Consensus pattern (28 bp):
GTTTCCTTCATTGGATTTTTGACACATT
Found at i:41354152 original size:174 final size:174
Alignment explanation
Indices: 41353862--41354210 Score: 689
Period size: 174 Copynumber: 2.0 Consensus size: 174
41353852 TAACCCATAG
41353862 TCCTTATATATGAGAAAATTTGCAAGGTTCTACTAGGATTACAAGAGGTAAAATAATAATATTTT
1 TCCTTATATATGAGAAAATTTGCAAGGTTCTACTAGGATTACAAGAGGTAAAATAATAATATTTT
41353927 AATAAAAAACTTAAAAAGTTCTAACAAAACTACATATGGTGGGCAACACACCCACACTGGAAATA
66 AATAAAAAACTTAAAAAGTTCTAACAAAACTACATATGGTGGGCAACACACCCACACTGGAAATA
*
41353992 TTTAGTGTGCCGCCCACCCTTTTAGTACAGCAGGCTTATTAGGC
131 TTTAGTGTGCCGCCCACCCTTTTAGTACAGCAGACTTATTAGGC
41354036 TCCTTATATATGAGAAAATTTGCAAGGTTCTACTAGGATTACAAGAGGTAAAATAATAATATTTT
1 TCCTTATATATGAGAAAATTTGCAAGGTTCTACTAGGATTACAAGAGGTAAAATAATAATATTTT
41354101 AATAAAAAACTTAAAAAGTTCTAACAAAACTACATATGGTGGGCAACACACCCACACTGGAAATA
66 AATAAAAAACTTAAAAAGTTCTAACAAAACTACATATGGTGGGCAACACACCCACACTGGAAATA
41354166 TTTAGTGTGCCGCCCACCCTTTTAGTACAGCAGACTTATTAGGC
131 TTTAGTGTGCCGCCCACCCTTTTAGTACAGCAGACTTATTAGGC
41354210 T
1 T
41354211 ATTAATGTAT
Statistics
Matches: 174, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
174 174 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (174 bp):
TCCTTATATATGAGAAAATTTGCAAGGTTCTACTAGGATTACAAGAGGTAAAATAATAATATTTT
AATAAAAAACTTAAAAAGTTCTAACAAAACTACATATGGTGGGCAACACACCCACACTGGAAATA
TTTAGTGTGCCGCCCACCCTTTTAGTACAGCAGACTTATTAGGC
Found at i:41363166 original size:25 final size:27
Alignment explanation
Indices: 41363129--41363182 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
41363119 TCAAACATGC
41363129 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACACCTAGGGGT
* **
41363155 ATTTCGGT-AATTTTGCACCTAGGGGT
1 ATTTAGGTCAATTTAACACCTAGGGGT
41363181 AT
1 AT
41363183 AACAGTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACACCTAGGGGT
Found at i:41363190 original size:26 final size:27
Alignment explanation
Indices: 41363146--41363221 Score: 82
Period size: 26 Copynumber: 2.8 Consensus size: 27
41363136 TCAATTTAAC
* * *
41363146 CCTAGGGGTATTTCGGTAATTTTGC-A
1 CCTAGGGGTATTACAGTAATTTTCCAA
*
41363172 CCTAGGGGTATAACAGTAATTTTCCATA
1 CCTAGGGGTATTACAGTAATTTTCCA-A
* *
41363200 CATAGGGGTATTATAGTAATTT
1 CCTAGGGGTATTACAGTAATTT
41363222 ATCTATTCTT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 21 0.51
28 20 0.49
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (27 bp):
CCTAGGGGTATTACAGTAATTTTCCAA
Found at i:41364697 original size:26 final size:26
Alignment explanation
Indices: 41364667--41364748 Score: 155
Period size: 26 Copynumber: 3.2 Consensus size: 26
41364657 TGAAATTCCC
41364667 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
41364693 ATCATGGAACATTTACGTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
41364719 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
41364745 ATCA
1 ATCA
41364749 ATTTGTACCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:41368625 original size:21 final size:22
Alignment explanation
Indices: 41368566--41368629 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 22
41368556 CAGAAGCAGT
* *
41368566 ATACGACACATAAAGTGCTTGA
1 ATACGACACATATAGTGCCTGA
** *
41368588 A-ACGACACACGTGGTGCCT-A
1 ATACGACACATATAGTGCCTGA
41368608 ATACGACACATATAGTGCCTGA
1 ATACGACACATATAGTGCCTGA
41368630 TCGGCAAAGC
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 2 0.06
21 28 0.88
22 2 0.06
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (22 bp):
ATACGACACATATAGTGCCTGA
Found at i:41368739 original size:6 final size:6
Alignment explanation
Indices: 41368728--41368773 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
41368718 AAATAATTTC
* *
41368728 TCAATT TCAATT TCAATT TCACTT TCAATGT ACAA-T TCAA-T TCAAT
1 TCAATT TCAATT TCAATT TCAATT TCAAT-T TCAATT TCAATT TCAAT
41368774 GCAATTTTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
5 9 0.26
6 21 0.62
7 4 0.12
ACGTcount: A:0.35, C:0.20, G:0.02, T:0.43
Consensus pattern (6 bp):
TCAATT
Found at i:41369600 original size:7 final size:7
Alignment explanation
Indices: 41369590--41369632 Score: 86
Period size: 7 Copynumber: 6.1 Consensus size: 7
41369580 ACTATATATA
41369590 ATATAAT
1 ATATAAT
41369597 ATATAAT
1 ATATAAT
41369604 ATATAAT
1 ATATAAT
41369611 ATATAAT
1 ATATAAT
41369618 ATATAAT
1 ATATAAT
41369625 ATATAAT
1 ATATAAT
41369632 A
1 A
41369633 AAACATAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATATAAT
Found at i:41369608 original size:21 final size:21
Alignment explanation
Indices: 41369582--41369632 Score: 86
Period size: 21 Copynumber: 2.4 Consensus size: 21
41369572 TTTACTTTAC
41369582 TATAT-ATAATATAATATATAA
1 TATATAAT-ATATAATATATAA
41369603 TATATAATATATAATATATAA
1 TATATAATATATAATATATAA
41369624 TATATAATA
1 TATATAATA
41369633 AAACATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 27 0.93
22 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TATATAATATATAATATATAA
Found at i:41370089 original size:22 final size:23
Alignment explanation
Indices: 41370061--41370110 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
41370051 TTATTTAATA
41370061 ATAATAAT-TTTA-ATATAAAAT
1 ATAATAATATTTATATATAAAAT
*
41370082 CATAATAATATTTATATATAATAT
1 -ATAATAATATTTATATATAAAAT
41370106 ATAAT
1 ATAAT
41370111 CGAAGAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 8 0.32
23 9 0.36
24 8 0.32
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
ATAATAATATTTATATATAAAAT
Found at i:41370286 original size:20 final size:19
Alignment explanation
Indices: 41370240--41370286 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
41370230 AGTCTTTTTT
*
41370240 CCTAATTTCTCCTAATTAAG
1 CCTAA-TTCACCTAATTAAG
41370260 -CTAAATTCACCTAATTAAAG
1 CCT-AATTCACCTAATT-AAG
41370280 CCTAATT
1 CCTAATT
41370287 AAATATACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
19 12 0.52
20 9 0.39
21 2 0.09
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.36
Consensus pattern (19 bp):
CCTAATTCACCTAATTAAG
Found at i:41371493 original size:21 final size:22
Alignment explanation
Indices: 41371467--41371512 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
41371457 CTATTTTAAT
41371467 TTTATTTATTTATTATTATT-A
1 TTTATTTATTTATTATTATTCA
*
41371488 TTTATTTTTTTATTATTATTCA
1 TTTATTTATTTATTATTATTCA
41371510 TTT
1 TTT
41371513 TCTGATCTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTATTTATTTATTATTATTCA
Found at i:41371502 original size:18 final size:18
Alignment explanation
Indices: 41371468--41371513 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
41371458 TATTTTAATT
41371468 TTATTTA-TTTATTATTA
1 TTATTTATTTTATTATTA
*
41371485 TTATTTATTTTTTTATTA
1 TTATTTATTTTATTATTA
*
41371503 TTATTCATTTT
1 TTATTTATTTT
41371514 CTGATCTTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 7 0.27
18 19 0.73
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (18 bp):
TTATTTATTTTATTATTA
Found at i:41371654 original size:3 final size:3
Alignment explanation
Indices: 41371641--41371681 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
41371631 CTCTAGCTCT
*
41371641 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
41371682 CTATACATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:41374670 original size:7 final size:7
Alignment explanation
Indices: 41374630--41374676 Score: 58
Period size: 7 Copynumber: 6.4 Consensus size: 7
41374620 ACTTTACTAT
41374630 ATATATA
1 ATATATA
41374637 ATATAATA
1 ATAT-ATA
41374645 ATAATATA
1 AT-ATATA
* *
41374653 GTATCTA
1 ATATATA
41374660 ATATATA
1 ATATATA
41374667 ATATATA
1 ATATATA
41374674 ATA
1 ATA
41374677 AAACATAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
7 23 0.68
8 9 0.26
9 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (7 bp):
ATATATA
Found at i:41375893 original size:14 final size:15
Alignment explanation
Indices: 41375865--41375893 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41375855 ACATTAAGCA
41375865 AACAAATGTGTTTTT
1 AACAAATGTGTTTTT
41375880 AACAAATG-GTTTTT
1 AACAAATGTGTTTTT
41375894 GGAAAACGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (15 bp):
AACAAATGTGTTTTT
Found at i:41389460 original size:33 final size:33
Alignment explanation
Indices: 41389306--41389462 Score: 111
Period size: 33 Copynumber: 4.8 Consensus size: 33
41389296 TGTATATATG
** * *
41389306 TAAGACCATAGTTGGGTTATGGCATAT-TGATGA
1 TAAGACCATAGCCGGGCTATGGCAT-TCTAATGA
** * * *
41389339 TAAGACTGTAG-CTGACTATAGCATTCTAATGA
1 TAAGACCATAGCCGGGCTATGGCATTCTAATGA
* * * * *
41389371 TAAGACTATAGCGGGGCTATGTCATACTGATGA
1 TAAGACCATAGCCGGGCTATGGCATTCTAATGA
* * *
41389404 TAAGAACATAGCTGGGCTCTGGCATTCTAATGA
1 TAAGACCATAGCCGGGCTATGGCATTCTAATGA
* * *
41389437 TAAGGCCATAACCGGGTTATGGCATT
1 TAAGACCATAGCCGGGCTATGGCATT
41389463 ATGAACGTAA
Statistics
Matches: 93, Mismatches: 29, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
31 1 0.01
32 23 0.25
33 69 0.74
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (33 bp):
TAAGACCATAGCCGGGCTATGGCATTCTAATGA
Found at i:41393361 original size:31 final size:31
Alignment explanation
Indices: 41393323--41393385 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
41393313 AAAAAAAGAA
41393323 AAAAGAGAGAAAGTCTTTTGGTATGTTATAG
1 AAAAGAGAGAAAGTCTTTTGGTATGTTATAG
41393354 AAAAGAGAGAAAGTCTTTTGGTATGTTATAG
1 AAAAGAGAGAAAGTCTTTTGGTATGTTATAG
41393385 A
1 A
41393386 CAAAATAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.32
Consensus pattern (31 bp):
AAAAGAGAGAAAGTCTTTTGGTATGTTATAG
Found at i:41398241 original size:24 final size:24
Alignment explanation
Indices: 41398214--41398263 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
41398204 GTTGATGAAC
*
41398214 CTCTTTGGGTTCGTGTTCTCAGAT
1 CTCTTTAGGTTCGTGTTCTCAGAT
41398238 CTCTTTAGGTTCGTGTTCTCAGAT
1 CTCTTTAGGTTCGTGTTCTCAGAT
41398262 CT
1 CT
41398264 AAGTATGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.46
Consensus pattern (24 bp):
CTCTTTAGGTTCGTGTTCTCAGAT
Found at i:41399645 original size:12 final size:12
Alignment explanation
Indices: 41399630--41399669 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
41399620 TATTTAAATA
41399630 TAATTAATTATC
1 TAATTAATTATC
*
41399642 TAATTAA--ATA
1 TAATTAATTATC
41399652 TAATTAATTATC
1 TAATTAATTATC
41399664 TAATTA
1 TAATTA
41399670 TTTGAGTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 9 0.38
12 15 0.62
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (12 bp):
TAATTAATTATC
Found at i:41399648 original size:22 final size:22
Alignment explanation
Indices: 41399623--41399669 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
41399613 AAATGGATAT
41399623 TTAAATATAATTAATTATCTAA
1 TTAAATATAATTAATTATCTAA
41399645 TTAAATATAATTAATTATCTAA
1 TTAAATATAATTAATTATCTAA
41399667 TTA
1 TTA
41399670 TTTGAGTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (22 bp):
TTAAATATAATTAATTATCTAA
Found at i:41406118 original size:18 final size:17
Alignment explanation
Indices: 41406100--41406132 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41406090 TATGATGATT
41406100 TTTTA-ATATAAAAATA
1 TTTTATATATAAAAATA
*
41406116 TTTTATATATTAAAATA
1 TTTTATATATAAAAATA
41406133 ATAAAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTATATATAAAAATA
Found at i:41408313 original size:45 final size:45
Alignment explanation
Indices: 41408257--41408348 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
41408247 AACAAATCAC
41408257 TATATTCATCGTCCATATATGTCACCTAAAAGCACACCAAATTTT
1 TATATTCATCGTCCATATATGTCACCTAAAAGCACACCAAATTTT
*
41408302 TATATTCATCGTCCATGTATGTCACCTAAAAGCACACCAAATTTT
1 TATATTCATCGTCCATATATGTCACCTAAAAGCACACCAAATTTT
41408347 TA
1 TA
41408349 CATTGAGAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.34
Consensus pattern (45 bp):
TATATTCATCGTCCATATATGTCACCTAAAAGCACACCAAATTTT
Found at i:41409806 original size:21 final size:21
Alignment explanation
Indices: 41409781--41409825 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
41409771 CCAATCAATT
* * *
41409781 AACCTATTCAAAATATGATAA
1 AACCTACTAAAAACATGATAA
*
41409802 AACCTACTAAAAACATGCTAA
1 AACCTACTAAAAACATGATAA
41409823 AAC
1 AAC
41409826 AATCATCTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.53, C:0.20, G:0.04, T:0.22
Consensus pattern (21 bp):
AACCTACTAAAAACATGATAA
Found at i:41411779 original size:13 final size:14
Alignment explanation
Indices: 41411756--41411784 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
41411746 ATGTCCACTC
41411756 TTCTCTTCTTTCTT
1 TTCTCTTCTTTCTT
41411770 TTCT-TTCTTTCTT
1 TTCTCTTCTTTCTT
41411783 TT
1 TT
41411785 ATTTTGCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
TTCTCTTCTTTCTT
Found at i:41430992 original size:40 final size:40
Alignment explanation
Indices: 41430955--41431072 Score: 175
Period size: 40 Copynumber: 3.0 Consensus size: 40
41430945 GCTACTCGTT
* *
41430955 CAAATACCTTCGGGACATAGCCCGGTTATAGTGACTCGCA
1 CAAATACCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
41430995 CAAATACCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATACCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
41431035 CAAATGCCTTCGAGACTTAACCCGGATT-TAGTAACTCG
1 CAAATACCTTCGGGACTTAGCCCGG-TTATAGTAACTCG
41431073 AATTTAGATC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
40 70 0.97
41 2 0.03
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (40 bp):
CAAATACCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:41435985 original size:6 final size:7
Alignment explanation
Indices: 41435971--41436030 Score: 61
Period size: 7 Copynumber: 8.6 Consensus size: 7
41435961 GTTTTTTAGT
41435971 TTTTAAA
1 TTTTAAA
*
41435978 TTTTAAT
1 TTTTAAA
* *
41435985 TTTTTAT
1 TTTTAAA
41435992 TTTTAAA
1 TTTTAAA
41435999 TTTTAATA
1 TTTTAA-A
41436007 TTTTAATA
1 TTTTAA-A
41436015 TTTT-AA
1 TTTTAAA
41436021 TTTT-AA
1 TTTTAAA
41436027 TTTT
1 TTTT
41436031 TTGAGTTTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
6 11 0.23
7 24 0.50
8 13 0.27
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
TTTTAAA
Found at i:41435987 original size:22 final size:22
Alignment explanation
Indices: 41435956--41436038 Score: 107
Period size: 22 Copynumber: 3.8 Consensus size: 22
41435946 TTTTTAAGTT
*
41435956 TTTTAGTTTTTTAGTTTTTAAA
1 TTTTAATTTTTTAGTTTTTAAA
41435978 TTTTAATTTTTTA-TTTTTAAA
1 TTTTAATTTTTTAGTTTTTAAA
* *
41435999 TTTTAATATTTTAATATTTT-AA
1 TTTTAATTTTTTAGT-TTTTAAA
41436021 TTTTAATTTTTTGAGTTT
1 TTTTAATTTTTT-AGTTT
41436039 ATTTTTATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
21 20 0.37
22 28 0.52
23 6 0.11
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.69
Consensus pattern (22 bp):
TTTTAATTTTTTAGTTTTTAAA
Found at i:41436009 original size:8 final size:8
Alignment explanation
Indices: 41435971--41436021 Score: 65
Period size: 7 Copynumber: 6.9 Consensus size: 8
41435961 GTTTTTTAGT
41435971 TTTTAA-A
1 TTTTAATA
41435978 TTTTAAT-
1 TTTTAATA
*
41435985 TTTTTAT-
1 TTTTAATA
41435992 TTTTAA-A
1 TTTTAATA
41435999 TTTTAATA
1 TTTTAATA
41436007 TTTTAATA
1 TTTTAATA
41436015 TTTTAAT
1 TTTTAAT
41436022 TTTAATTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
7 23 0.59
8 16 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTTAATA
Found at i:41436032 original size:8 final size:8
Alignment explanation
Indices: 41435939--41436032 Score: 67
Period size: 8 Copynumber: 12.5 Consensus size: 8
41435929 TATTGATTAA
*
41435939 TTTTAAAT
1 TTTTAATT
41435947 TTTTAAGTT
1 TTTTAA-TT
*
41435956 TTTTAGTT
1 TTTTAATT
*
41435964 TTTT-AGT
1 TTTTAATT
*
41435971 TTTTAA-A
1 TTTTAATT
41435978 TTTTAATT
1 TTTTAATT
41435986 TTTT-A-T
1 TTTTAATT
*
41435992 TTTTAA-A
1 TTTTAATT
*
41435999 TTTTAATA
1 TTTTAATT
*
41436007 TTTTAATA
1 TTTTAATT
41436015 TTTTAA--
1 TTTTAATT
41436021 TTTTAATT
1 TTTTAATT
41436029 TTTT
1 TTTT
41436033 GAGTTTATTT
Statistics
Matches: 72, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
6 11 0.15
7 19 0.26
8 36 0.50
9 6 0.08
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (8 bp):
TTTTAATT
Found at i:41436032 original size:14 final size:14
Alignment explanation
Indices: 41435964--41436032 Score: 75
Period size: 14 Copynumber: 4.9 Consensus size: 14
41435954 TTTTTTAGTT
* *
41435964 TTTTAGTTTTTAAA
1 TTTTAATTTTTTAA
*
41435978 TTTTAATTTTTTAT
1 TTTTAATTTTTTAA
* *
41435992 TTTTAAATTTTAATA
1 TTTTAATTTTTTA-A
*
41436007 TTTTAATATTTTAA
1 TTTTAATTTTTTAA
41436021 TTTTAATTTTTT
1 TTTTAATTTTTT
41436033 GAGTTTATTT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
14 34 0.77
15 10 0.23
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (14 bp):
TTTTAATTTTTTAA
Found at i:41436986 original size:41 final size:41
Alignment explanation
Indices: 41436921--41437101 Score: 204
Period size: 41 Copynumber: 4.4 Consensus size: 41
41436911 GGGATTATAT
* *
41436921 GACTTTTAGCGGCATTGTACCAAAAGCGCCACTATTGCTCC
1 GACTTTTAGCGGCGTTTTACCAAAAGCGCCACTATTGCTCC
* ** * *
41436962 GACTTTTAGTGGTTTTTTAGCAAAAGCGCCGCTATTGCTCC
1 GACTTTTAGCGGCGTTTTACCAAAAGCGCCACTATTGCTCC
* *
41437003 GACTTTTAGCGGCGTTTTACCAAAA-CACCACTATTGCTCT
1 GACTTTTAGCGGCGTTTTACCAAAAGCGCCACTATTGCTCC
* * * * *
41437043 GACTTTTAGCAGCGTTTTAACAAAAAACGCCGCTATTGCTCT
1 GACTTTTAGCGGCGTTTT-ACCAAAAGCGCCACTATTGCTCC
*
41437085 G-TTTTTAGCGGCGTTTT
1 GACTTTTAGCGGCGTTTT
41437102 TGGTAGAACA
Statistics
Matches: 119, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
40 29 0.24
41 76 0.64
42 14 0.12
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (41 bp):
GACTTTTAGCGGCGTTTTACCAAAAGCGCCACTATTGCTCC
Found at i:41437061 original size:81 final size:83
Alignment explanation
Indices: 41436921--41437101 Score: 233
Period size: 81 Copynumber: 2.2 Consensus size: 83
41436911 GGGATTATAT
* * * ** ** *
41436921 GACTTTTAGCGGCATTGTACCAAAAGCGCCACTATTGCTCCGACTTTTAGTGGTTTTTTAGC-AA
1 GACTTTTAGCGGCGTTTTACCAAAAGCACCACTATTGCTCCGACTTTTAGCAGCGTTTTAACAAA
*
41436985 AAGCGCCGCTATTGCTCC
66 AAACGCCGCTATTGCTCC
*
41437003 GACTTTTAGCGGCGTTTTACCAAAA-CACCACTATTGCTCTGACTTTTAGCAGCGTTTTAACAAA
1 GACTTTTAGCGGCGTTTTACCAAAAGCACCACTATTGCTCCGACTTTTAGCAGCGTTTTAACAAA
*
41437067 AAACGCCGCTATTGCTCT
66 AAACGCCGCTATTGCTCC
*
41437085 G-TTTTTAGCGGCGTTTT
1 GACTTTTAGCGGCGTTTT
41437102 TGGTAGAACA
Statistics
Matches: 86, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
81 44 0.51
82 42 0.49
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (83 bp):
GACTTTTAGCGGCGTTTTACCAAAAGCACCACTATTGCTCCGACTTTTAGCAGCGTTTTAACAAA
AAACGCCGCTATTGCTCC
Found at i:41437171 original size:12 final size:12
Alignment explanation
Indices: 41437156--41437182 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
41437146 GTTTTTTGAT
41437156 AAAACGCCGCTA
1 AAAACGCCGCTA
41437168 AAAACGCCGCTA
1 AAAACGCCGCTA
41437180 AAA
1 AAA
41437183 CCCTATTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.30, G:0.15, T:0.07
Consensus pattern (12 bp):
AAAACGCCGCTA
Found at i:41447567 original size:46 final size:47
Alignment explanation
Indices: 41447327--41447596 Score: 198
Period size: 46 Copynumber: 5.7 Consensus size: 47
41447317 GGGTAAGTTA
* * * * *
41447327 CCGATGCCATGTGCCAGACATGGTCTTACACT-GGATATCATCATCGAGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCA-CTCGTC-TC-ATG
* * *
41447376 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGCATATCTGTG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCG--TCTC-ATG
* * * *
41447426 CCGATGCCACGTCCTAGACATGGTCTTACACT-G-ACACATCTCATAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCGTCTCAT-G
* * * * *
41447472 CCGATG-CATGTCCCAAACAT-GTCTTACATTGGCTTA-T-GTGTCGAGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGC--ACTCGTCTC-ATG
*
41447518 CCGATG-CATTTCCCAGACAT-GTCTTACACTAGCACTCGTCTCAATG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCGTCTC-ATG
* *
41447564 CCGATGCCATGTCCTAGACATGGCCTTACACTA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTA
41447597 AATTTCATAA
Statistics
Matches: 174, Mismatches: 34, Indels: 27
0.74 0.14 0.11
Matches are distributed among these distances:
44 10 0.06
45 14 0.08
46 55 0.32
47 13 0.07
48 13 0.07
49 34 0.20
50 34 0.20
51 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (47 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCGTCTCATG
Found at i:41447634 original size:140 final size:141
Alignment explanation
Indices: 41447370--41447639 Score: 354
Period size: 140 Copynumber: 1.9 Consensus size: 141
41447360 GATATCATCA
* **
41447370 TCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGCATATCTGTGCCGATGCCA
1 TCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCG-ATATCAATGCCGATGCCA
* *
41447435 CGTCCTAGACATGGTCTTACACTGACACATCTCATAGCCGATGCATGTCCCAAACATGTCTTACA
65 CGTCCTAGACATGGCCTTACACTGACACATCTCATAGCCAATGCATGTCCCAAACATGTCTTACA
41447500 TTGGCTTATGTG
130 TTGGCTTATGTG
* * *
41447512 TCGAGGCCGATG-CATTTCCCAGACAT-GTCTTACACTAGCACTCG-TCTCAATGCCGATGCCAT
1 TCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCGATATCAATGCCGATGCCAC
* *
41447574 GTCCTAGACATGGCCTTACACT-A-A-ATTTCATAATGTGGCCAATGCATGTCCCAGACATGTCT
66 GTCCTAGACATGGCCTTACACTGACACATCTCAT-A----GCCAATGCATGTCCCAAACATGTCT
41447636 TACA
126 TACA
41447640 CTAGCCCACA
Statistics
Matches: 113, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
135 6 0.05
136 2 0.02
137 1 0.01
138 35 0.31
140 44 0.39
141 13 0.12
142 12 0.11
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.27
Consensus pattern (141 bp):
TCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCGATATCAATGCCGATGCCAC
GTCCTAGACATGGCCTTACACTGACACATCTCATAGCCAATGCATGTCCCAAACATGTCTTACAT
TGGCTTATGTG
Found at i:41452979 original size:16 final size:16
Alignment explanation
Indices: 41452924--41452980 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
41452914 TGTCATATTG
*
41452924 CCATGGTATCTTTCAA
1 CCATGGTATTTTTCAA
* * * *
41452940 CCATGGTCTTGTGCATTG
1 CCATGGTATTTTTCA--A
41452958 CCATGGTATTTTTCAA
1 CCATGGTATTTTTCAA
41452974 CCATGGT
1 CCATGGT
41452981 CTTATTCATT
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
16 18 0.60
18 12 0.40
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (16 bp):
CCATGGTATTTTTCAA
Found at i:41453168 original size:46 final size:46
Alignment explanation
Indices: 41452955--41453177 Score: 333
Period size: 46 Copynumber: 4.9 Consensus size: 46
41452945 GTCTTGTGCA
*
41452955 TTGCCATGGTATTTTTCAACCATGGTCTTATTCA-TTC-TCGTCATG
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCAT-GTCATG
* *
41453000 TTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACG
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATG
* *
41453046 TTGCCATGATATCTTTCAACCATGGTCTTATTCTTTTCATGTCATG
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATG
** *
41453092 TTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATG
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATG
**
41453138 TTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCAT
41453178 TTCAGAAAGC
Statistics
Matches: 166, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
45 32 0.19
46 133 0.80
47 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (46 bp):
TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCATG
Found at i:41454050 original size:51 final size:51
Alignment explanation
Indices: 41453985--41454100 Score: 196
Period size: 51 Copynumber: 2.3 Consensus size: 51
41453975 CTCAAACTTA
* *
41453985 CTTCATACTTCATCTGAAATTATTACTTTGTTGCTCTAGCTTCAACAAGAG
1 CTTCATATTTCATCTGAAATTATTACTTTATTGCTCTAGCTTCAACAAGAG
*
41454036 CTTCATATTTCATCTGGAATTATTACTTTATTGCTCTAGCTTCAACAAGAG
1 CTTCATATTTCATCTGAAATTATTACTTTATTGCTCTAGCTTCAACAAGAG
*
41454087 TTTCATATTTCATC
1 CTTCATATTTCATC
41454101 CAGATAACTT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (51 bp):
CTTCATATTTCATCTGAAATTATTACTTTATTGCTCTAGCTTCAACAAGAG
Found at i:41456304 original size:20 final size:20
Alignment explanation
Indices: 41456275--41456317 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
41456265 GGTTCTAGAA
* *
41456275 GTTGCGTTCTGTCTGTTCTT
1 GTTGCATTCTGTCGGTTCTT
41456295 GTTGCATTCTGTCGGTTCTT
1 GTTGCATTCTGTCGGTTCTT
41456315 GTT
1 GTT
41456318 CTATTTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.02, C:0.19, G:0.26, T:0.53
Consensus pattern (20 bp):
GTTGCATTCTGTCGGTTCTT
Found at i:41457050 original size:9 final size:9
Alignment explanation
Indices: 41457038--41457067 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
41457028 TGAGGAACAA
41457038 GAGGAGGTG
1 GAGGAGGTG
41457047 GAGGAGGTG
1 GAGGAGGTG
*
41457056 GGGGAGGTG
1 GAGGAGGTG
41457065 GAG
1 GAG
41457068 TGTTTGGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.70, T:0.10
Consensus pattern (9 bp):
GAGGAGGTG
Found at i:41458892 original size:46 final size:47
Alignment explanation
Indices: 41458737--41458999 Score: 217
Period size: 46 Copynumber: 5.6 Consensus size: 47
41458727 GTAAGTTACC
* *
41458737 GATGCCATGTGCCAGACATGGTCTTACACTGGCTATCATCATCGAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTA-CATC-TCGAGGCA
* *
41458786 GATGCCATGTCCCAGACATGGTCTTACACTGAC-ACATCTCGTA-GCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTACATCTCG-AGGCA
* * *
41458832 GATG-CATGTCCCAGACAT-GACTTACACTGGCTTACGTCTTGAGGCA
1 GATGCCATGTCCCAGACATGGTCTTACACTGGC-TACATCTCGAGGCA
* * * * *
41458878 GATG-CATGTCCCAGACAT-GTCTTGCACTAGC-ACTCCTCTCAATGTC-
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTA--CATCTCGA-GGCA
* * *
41458924 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GCA-GCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCT-ACAT-CTCG-AGGCA
41458972 GATG-CATGTCCCAGACAT-GTCTTACACT
1 GATGCCATGTCCCAGACATGGTCTTACACT
41459000 AGCCCAAAAT
Statistics
Matches: 178, Mismatches: 22, Indels: 31
0.77 0.10 0.13
Matches are distributed among these distances:
44 12 0.07
45 15 0.08
46 64 0.36
47 36 0.20
48 18 0.10
49 33 0.19
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (47 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTACATCTCGAGGCA
Found at i:41458976 original size:94 final size:93
Alignment explanation
Indices: 41458736--41459002 Score: 307
Period size: 94 Copynumber: 2.9 Consensus size: 93
41458726 GGTAAGTTAC
*
41458736 CGATGCCATGTGCCAGACATGGTCTTACACTGGCTATCATCAT-CGAGGCCGATGCCATGTCCCA
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCT-TCATCATGC-AGGCCGATG-CATGTCCCA
*
41458800 GACATGGTCTTACACT-G-ACACATCTCGTAG
63 GACAT-GTCTTACACTAGCACACATCTCATAG
* * * *
41458830 CTGATG-CATGTCCCAGACAT-GACTTACACTGGCTTACGTCTTG-AGGCAGATGCATGTCCCAG
1 C-GATGCCATGTCCCAGACATGGTCTTACACTGGCTT-CATCATGCAGGCCGATGCATGTCCCAG
* * *
41458892 ACATGTCTTGCACTAGCACTCCTCTCA-ATG
64 ACATGTCTTACACTAGCACACATCTCATA-G
*
41458922 TCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGCA-GCCGATGCATGTCCCAG
1 -CGATGCCATGTCCCAGACATGGTCTTACACTGGCT-TCATCATGCAGGCCGATGCATGTCCCAG
41458986 ACATGTCTTACACTAGC
64 ACATGTCTTACACTAGC
41459003 CCAAAATAGC
Statistics
Matches: 147, Mismatches: 15, Indels: 22
0.80 0.08 0.12
Matches are distributed among these distances:
90 9 0.06
91 16 0.11
92 21 0.14
93 32 0.22
94 63 0.43
95 6 0.04
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (93 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTTCATCATGCAGGCCGATGCATGTCCCAGAC
ATGTCTTACACTAGCACACATCTCATAG
Found at i:41461403 original size:27 final size:27
Alignment explanation
Indices: 41461340--41461416 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
41461330 AGAACTACCA
* *
41461340 AAATAAAATAAAATAAAAACAAATAAAC
1 AAAT-AAATAAAAGAAAAAGAAATAAAC
* *
41461368 AAA-ATAATAAAAGATAAAGAAATAAAT
1 AAATA-AATAAAAGAAAAAGAAATAAAC
41461395 AAATAAAT-AAAGAAAAAGAAAT
1 AAATAAATAAAAGAAAAAGAAAT
41461417 GATAAAAGGG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
26 14 0.33
27 24 0.57
28 4 0.10
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.16
Consensus pattern (27 bp):
AAATAAATAAAAGAAAAAGAAATAAAC
Found at i:41461406 original size:26 final size:27
Alignment explanation
Indices: 41461346--41461416 Score: 83
Period size: 26 Copynumber: 2.7 Consensus size: 27
41461336 ACCAAAATAA
* *
41461346 AATAAAATAAAAACAAATAAACAAAAT
1 AATAAAAGAAAAAGAAATAAACAAAAT
* *
41461373 AATAAAAGATAAAGAAATAAA-TAAAT
1 AATAAAAGAAAAAGAAATAAACAAAAT
41461399 AA-ATAAAGAAAAAGAAAT
1 AATA-AAAGAAAAAGAAAT
41461417 GATAAAAGGG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
25 1 0.03
26 19 0.50
27 18 0.47
ACGTcount: A:0.76, C:0.03, G:0.06, T:0.15
Consensus pattern (27 bp):
AATAAAAGAAAAAGAAATAAACAAAAT
Found at i:41486230 original size:23 final size:22
Alignment explanation
Indices: 41486203--41486254 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
41486193 ATATCCATTA
41486203 GTTTATTCGATCTATCTTCTATTT
1 GTTTATTCGATC-AT-TTCTATTT
* *
41486227 -TTTATTCTATCATTTTTATTT
1 GTTTATTCGATCATTTCTATTT
41486248 GTTTATT
1 GTTTATT
41486255 ATGTTGAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 7 0.28
22 8 0.32
23 10 0.40
ACGTcount: A:0.17, C:0.12, G:0.06, T:0.65
Consensus pattern (22 bp):
GTTTATTCGATCATTTCTATTT
Found at i:41486490 original size:17 final size:19
Alignment explanation
Indices: 41486462--41486498 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
41486452 GAAAACAAGA
41486462 AAAATAAAGAAA-TTAAGT
1 AAAATAAAGAAATTTAAGT
41486480 AAAAT-AAGAAATTTAAGT
1 AAAATAAAGAAATTTAAGT
41486498 A
1 A
41486499 TAAAGAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.24
Consensus pattern (19 bp):
AAAATAAAGAAATTTAAGT
Found at i:41494299 original size:27 final size:27
Alignment explanation
Indices: 41494271--41494553 Score: 320
Period size: 27 Copynumber: 10.6 Consensus size: 27
41494261 ACATAGCGGT
* * * *
41494271 AAAACAGTCATCTTACCATAAAAGGGT
1 AAAACAGTCATTTTACCACATAAGGGC
*
41494298 AAAATAGTCATTTTACCACATAAGGG-
1 AAAACAGTCATTTTACCACATAAGGGC
* *
41494324 ATAAACAATCATTTTATCAC--AAGGGC
1 A-AAACAGTCATTTTACCACATAAGGGC
* **
41494350 AAAACAGTTATTTTACCTTATAAGGGC
1 AAAACAGTCATTTTACCACATAAGGGC
* ** *
41494377 AAAATAGTCATTTTACCATGTAAGAGC
1 AAAACAGTCATTTTACCACATAAGGGC
* * *
41494404 AAAATAATCATTTTACCACGTAAGGGC
1 AAAACAGTCATTTTACCACATAAGGGC
*
41494431 AAAACAGTCATTTTACCACGTAAGGGC
1 AAAACAGTCATTTTACCACATAAGGGC
* * **
41494458 AAAATAGTCATTTTACCATATAAGCAC
1 AAAACAGTCATTTTACCACATAAGGGC
*
41494485 AAAACAGTCATTTTACCACAAAAGGGC
1 AAAACAGTCATTTTACCACATAAGGGC
*
41494512 AAAATAGTCATTTTACCACATAAGGGC
1 AAAACAGTCATTTTACCACATAAGGGC
41494539 AAAACAGTCATTTTA
1 AAAACAGTCATTTTA
41494554 TCAATTAGGG
Statistics
Matches: 217, Mismatches: 35, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
25 18 0.08
26 2 0.01
27 197 0.91
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.27
Consensus pattern (27 bp):
AAAACAGTCATTTTACCACATAAGGGC
Found at i:41494456 original size:81 final size:79
Alignment explanation
Indices: 41494271--41494553 Score: 354
Period size: 81 Copynumber: 3.5 Consensus size: 79
41494261 ACATAGCGGT
* * * * * *
41494271 AAAACAGTCATCTTACCATAAAAGGGTAAAATAGTCATTTTACCACATAAG-GGATAAACAATCA
1 AAAACAGTCATTTTACCACATAAGGGCAAAATAGTCATTTTACCATATAAGAGCA-AAACAATCA
*
41494335 TTTTATCACAAGGGC
65 TTTTACCACAAGGGC
* ** * *
41494350 AAAACAGTTATTTTACCTTATAAGGGCAAAATAGTCATTTTACCATGTAAGAGCAAAATAATCAT
1 AAAACAGTCATTTTACCACATAAGGGCAAAATAGTCATTTTACCATATAAGAGCAAAACAATCAT
41494415 TTTACCACGTAAGGGC
66 TTTACCAC--AAGGGC
* *
41494431 AAAACAGTCATTTTACCACGTAAGGGCAAAATAGTCATTTTACCATATAAGCA-CAAAACAGTCA
1 AAAACAGTCATTTTACCACATAAGGGCAAAATAGTCATTTTACCATATAAG-AGCAAAACAATCA
41494495 TTTTACCACAAAAGGGC
65 TTTTACCAC--AAGGGC
* *
41494512 AAAATAGTCATTTTACCACATAAGGGCAAAACAGTCATTTTA
1 AAAACAGTCATTTTACCACATAAGGGCAAAATAGTCATTTTA
41494554 TCAATTAGGG
Statistics
Matches: 178, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
79 60 0.34
80 2 0.01
81 115 0.65
82 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.27
Consensus pattern (79 bp):
AAAACAGTCATTTTACCACATAAGGGCAAAATAGTCATTTTACCATATAAGAGCAAAACAATCAT
TTTACCACAAGGGC
Done.