Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold64
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: 7997333
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 95991 characters in sequence are not A, C, G, or T
File 29 of 45
Found at i:5130941 original size:21 final size:20
Alignment explanation
Indices: 5130912--5130960 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
5130902 CAAGGCCATA
*
5130912 TATCAATACAATCACACTAGG
1 TATCGATACAA-CACACTAGG
* *
5130933 TATCGATACCACACCCTAGG
1 TATCGATACAACACACTAGG
*
5130953 TATTGATA
1 TATCGATA
5130961 TTAAGCCTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (20 bp):
TATCGATACAACACACTAGG
Found at i:5131079 original size:112 final size:113
Alignment explanation
Indices: 5130879--5131089 Score: 291
Period size: 112 Copynumber: 1.9 Consensus size: 113
5130869 TCCTATCCAA
*
5130879 AAAAATTAAATTTTAGCTACTGCCAAGGCCATATATCAATACAATCACACTAGGTATCGATACCA
1 AAAAATCAAATTTTAGCTACTGCCAAGGCCATATATCAATACAATCACACTAGGTATCGATACCA
* ** *
5130944 CACCCTAGGTATTGATATTAAGCCTTCATGTATCAACACTTGCTGTCC
66 CACCCTAGGTATCGATACCAAGCCTCCATGTATCAACACTTGCTGTCC
* ** * *
5130992 AAAAATCAAATTTTAGCTATTGTTAAGG-CTTGTATCAATACAATCACACTAGGTATCGACT-CC
1 AAAAATCAAATTTTAGCTACTGCCAAGGCCATATATCAATACAATCACACTAGGTATCGA-TACC
* *
5131055 ACACCTTGGGTATCGATACCAAGCCTCCATGTATC
65 ACACCCTAGGTATCGATACCAAGCCTCCATGTATC
5131090 GATACATTGC
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
112 60 0.71
113 25 0.29
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (113 bp):
AAAAATCAAATTTTAGCTACTGCCAAGGCCATATATCAATACAATCACACTAGGTATCGATACCA
CACCCTAGGTATCGATACCAAGCCTCCATGTATCAACACTTGCTGTCC
Found at i:5131899 original size:71 final size:72
Alignment explanation
Indices: 5131745--5131900 Score: 215
Period size: 71 Copynumber: 2.2 Consensus size: 72
5131735 GAAGACTAAA
* * *
5131745 AAAGATAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAAAAAAAGAAAAAAGCATCCTACTCTT
1 AAAGATAAAGGTACCACCAACTTATATGGGCTTTG-AAAAAAAAAGAAAAAAGCATCCTACTCTT
*
5131810 TGAAGAGT
65 TAAAGAGT
* * * *
5131818 AAAGACAAAGGTACTACCAACTTATATGGGCTTTG-AAAAAAAAGAAAAAGGTATCCTACTCTTT
1 AAAGATAAAGGTACCACCAACTTATATGGGCTTTGAAAAAAAAAGAAAAAAGCATCCTACTCTTT
*
5131882 AAAGATT
66 AAAGAGT
5131889 AAAGATAAAGGT
1 AAAGATAAAGGT
5131901 GTGCTTTGAA
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
71 43 0.59
73 30 0.41
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (72 bp):
AAAGATAAAGGTACCACCAACTTATATGGGCTTTGAAAAAAAAAGAAAAAAGCATCCTACTCTTT
AAAGAGT
Found at i:5132195 original size:70 final size:71
Alignment explanation
Indices: 5132095--5132309 Score: 195
Period size: 73 Copynumber: 3.0 Consensus size: 71
5132085 AAAAACAAAA
* * * *
5132095 GTGCCACCAGCTTTTGTGGGCTTTG-AAAAAAGAAAAAGACGTTATGCTCTTTAAGGACT-AAAA
1 GTGCCACCAACTTGTATGGGCTTTGAAAAAAAG-AAAAGACGTCATGCTCTTTAAGGACTAAAAA
5132158 GATAAAG
65 GATAAAG
* ** * * * *
5132165 GTGCTACCAACTTGTATGGGCTTTTCAAAAAAGAAAAGATGTCCTGCTTTTTGAGGACTAAAAAA
1 GTGCCACCAACTTGTATGGGCTTTGAAAAAAAGAAAAGACGTCATGCTCTTTAAGGACT--AAAA
5132230 AGATAAAG
64 AGATAAAG
* * * * *
5132238 GTGCCATCAGCTTGTGTGGGCTTTGAAAAAAAAAGGAAAAG-CGTTC-TACTCTTTGAGGACTAA
1 GTGCCACCAACTTGTATGGGCTTTG--AAAAAAA-GAAAAGACG-TCATGCTCTTTAAGGACTAA
5132301 AAAGATAAA
62 AAAGATAAA
5132310 AAGTGGCCCT
Statistics
Matches: 118, Mismatches: 19, Indels: 13
0.79 0.13 0.09
Matches are distributed among these distances:
70 41 0.35
71 7 0.06
73 42 0.36
75 20 0.17
76 8 0.07
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (71 bp):
GTGCCACCAACTTGTATGGGCTTTGAAAAAAAGAAAAGACGTCATGCTCTTTAAGGACTAAAAAG
ATAAAG
Found at i:5132258 original size:73 final size:71
Alignment explanation
Indices: 5132091--5132343 Score: 244
Period size: 70 Copynumber: 3.5 Consensus size: 71
5132081 GAAAAAAAAC
* * * *
5132091 AAAAGTGCCACCAGCTTTTGTGGGC-TTTGAAAAAAGAAAAAGACGTTATGCTCTTTAAGGACT-
1 AAAAGTGCCACCAGCTTGTGTGGGCTTTTAAAAAAAG-AAAAGACGTTCTGCTCTTTGAGGACTA
5132154 AAAAGAT
65 AAAAGAT
* * * * * * * *
5132161 AAAGGTGCTACCAACTTGTATGGGCTTTTCAAAAAAGAAAAGATGTCCTGCTTTTTGAGGACTAA
1 AAAAGTGCCACCAGCTTGTGTGGGCTTTTAAAAAAAGAAAAGACGTTCTGCTCTTTGAGGACT--
5132226 AAAAAGAT
64 AAAAAGAT
* * * *
5132234 AAAGGTGCCATCAGCTTGTGTGGGCTTTGAAAAAAAAAGGAAAAG-CGTTCTACTCTTTGAGGAC
1 AAAAGTGCCACCAGCTTGTGTGGGCTTT--TAAAAAAA-GAAAAGACGTTCTGCTCTTTGAGGAC
5132298 TAAAAAGAT
63 TAAAAAGAT
* *
5132307 AAAAAGTGGCC-CTAGCTTGTGTGGGCTTTAAAAAAAA
1 -AAAAGT-GCCACCAGCTTGTGTGGGCTTTTAAAAAAA
5132344 TGTATCCCAC
Statistics
Matches: 150, Mismatches: 24, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
70 41 0.27
71 10 0.07
72 8 0.05
73 39 0.26
74 21 0.14
75 25 0.17
76 6 0.04
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.26
Consensus pattern (71 bp):
AAAAGTGCCACCAGCTTGTGTGGGCTTTTAAAAAAAGAAAAGACGTTCTGCTCTTTGAGGACTAA
AAAGAT
Found at i:5132833 original size:73 final size:72
Alignment explanation
Indices: 5132756--5132912 Score: 181
Period size: 72 Copynumber: 2.2 Consensus size: 72
5132746 CTTTGACAAG
* * *
5132756 AAAAAGGAAAAGCATCCTACTCTTTGAGGACT-AAAAAGAGAAAAAAAAAGCCACCAGCTTATGT
1 AAAAAGAAAAAACAGCCTACTCTTTGAGGACTGAAAAA-AG-AAAAAAAAGCCACCAGCTTATGT
*
5132820 GGGCTTTGA
64 GGGCTTTAA
* * * *** * *
5132829 AAAAAGAAAAAACAGCGTGCTCTTTGAGGACTGAAAAAAGACAAAGGTGCCATCAGCTTGTGTGG
1 AAAAAGAAAAAACAGCCTACTCTTTGAGGACTGAAAAAAGAAAAAAAAGCCACCAGCTTATGTGG
5132894 GCTTTAA
66 GCTTTAA
5132901 AAAAAGAAAAAA
1 AAAAAGAAAAAA
5132913 ATGTTCTTTT
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
72 37 0.52
73 29 0.41
74 5 0.07
ACGTcount: A:0.45, C:0.15, G:0.22, T:0.18
Consensus pattern (72 bp):
AAAAAGAAAAAACAGCCTACTCTTTGAGGACTGAAAAAAGAAAAAAAAGCCACCAGCTTATGTGG
GCTTTAA
Found at i:5149990 original size:62 final size:61
Alignment explanation
Indices: 5149827--5150081 Score: 359
Period size: 61 Copynumber: 4.2 Consensus size: 61
5149817 TGTCCTTTTT
* *
5149827 AGTCCTCAAAGAGCAGGACGTCTTTTTCTTTTTAAGGCCCACACAAGTTGGTGGCACCTTT-
1 AGTCCTCAAAGAGCAGGACGTC-TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
** * * * *
5149888 AGTCCTCAAAGAATAGGACGTCTTTTCCTTTTCAAGCCCACACGAGTTGGTGGCGCATTTC
1 AGTCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
5149949 AGTCCTCAAAGAGCAGGACGCTTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCCTCC
1 AGTCCTCAAAGAGCAGGACG-TCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
5150011 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCACTTTTC
1 AGTCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
5150072 AGTCCTCAAA
1 AGTCCTCAAA
5150082 AAATAGGACG
Statistics
Matches: 169, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
60 32 0.19
61 83 0.49
62 54 0.32
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (61 bp):
AGTCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:5150090 original size:123 final size:123
Alignment explanation
Indices: 5149821--5150095 Score: 383
Period size: 123 Copynumber: 2.2 Consensus size: 123
5149811 CCATTTTGTC
* * *
5149821 CTTTTTAGTCCTCAAAGAGCAGGACG-TCTTTTTCTTTTTAAGGCCCACACAAGTTGGTGGCACC
1 CTTTTCAGTCCTCAAAGAGCAGGACGCTCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
** * * * * * *
5149885 TTTAGTCCTCAAAGAATAGGACGTCTTTTCCTTTTCAAGCCCACACGAGTTGGTGGCG
66 TCCAGTCCTCAAAGAACAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCA
*
5149943 CATTTCAGTCCTCAAAGAGCAGGACGCT-TTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 CTTTTCAGTCCTCAAAGAGCAGGACGCTCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-C
*
5150007 CTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCA
65 CTCCAGTCCTCAAAGAACAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCA
* **
5150066 CTTTTCAGTCCTCAAAAAATAGGACGCTCT
1 CTTTTCAGTCCTCAAAGAGCAGGACGCTCT
5150096 CTCCTTTCAC
Statistics
Matches: 133, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
122 56 0.42
123 76 0.57
124 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (123 bp):
CTTTTCAGTCCTCAAAGAGCAGGACGCTCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
TCCAGTCCTCAAAGAACAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCA
Found at i:5150191 original size:99 final size:99
Alignment explanation
Indices: 5150011--5150200 Score: 285
Period size: 99 Copynumber: 1.9 Consensus size: 99
5150001 GGCACCCTCC
5150011 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCACTTTTCAGTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCACTTTTCAGTC
*
5150076 CTCAAAAAATAGGACG-CTCTCTCCTTTCACCTTT
66 CTCAAAAAACAGGACGCCT-TCTCCTTTCACCTTT
** *
5150110 AGTCCTCAAAGAGCAGGACGTTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT-AGT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCA-CTTTTCAGT
* * *
5150174 CCTCAAAGAGCATGACGCCTTCTCCTT
65 CCTCAAAAAACAGGACGCCTTCTCCTT
5150201 CAAAGCCCAC
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
99 75 0.91
100 7 0.09
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.29
Consensus pattern (99 bp):
AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCACTTTTCAGTC
CTCAAAAAACAGGACGCCTTCTCCTTTCACCTTT
Found at i:5150223 original size:60 final size:60
Alignment explanation
Indices: 5150103--5150380 Score: 326
Period size: 60 Copynumber: 4.5 Consensus size: 60
5150093 TCTCTCCTTT
**
5150103 CACCTTTAGTCCTCAAAGAGCAGGACGTTTTTTC-CTTTTAAAGCCCACACAAGTTGGTGG
1 CACCTTTAGTCCTCAAAGAGCAGGACGCCTTTTCTC-TTTAAAGCCCACACAAGTTGGTGG
* * * * *
5150163 CACCTTTTAGTCCTCAAAGAGCATGACGCCTTCTC-CTTCAAAGCCCACACGAGTTAGTGG
1 CACC-TTTAGTCCTCAAAGAGCAGGACGCCTTTTCTCTTTAAAGCCCACACAAGTTGGTGG
* ** *
5150223 CACCCTCTAGTCCTCAAAGAGCAGGACGTATTTTTTCTTTTTAAAGCCCACACAAGTTGGTGG
1 CA-CCTTTAGTCCTCAAAGAGCAGGACG--CCTTTTCTCTTTAAAGCCCACACAAGTTGGTGG
* * * * *
5150286 CACCTGTAGTCCTCGAACAGCAGGACACCTTTTCTTTTTAAAGCCCACACAAGTTGGTGG
1 CACCTTTAGTCCTCAAAGAGCAGGACGCCTTTTCTCTTTAAAGCCCACACAAGTTGGTGG
5150346 CACCCTCTTAGTCCTCAAAGAGCAGGACGCACTTT
1 CA-CCT-TTAGTCCTCAAAGAGCAGGACGC-CTTT
5150381 ATTTTCCTTT
Statistics
Matches: 184, Mismatches: 26, Indels: 13
0.83 0.12 0.06
Matches are distributed among these distances:
60 81 0.44
61 32 0.17
62 44 0.24
63 27 0.15
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.27
Consensus pattern (60 bp):
CACCTTTAGTCCTCAAAGAGCAGGACGCCTTTTCTCTTTAAAGCCCACACAAGTTGGTGG
Found at i:5150267 original size:222 final size:222
Alignment explanation
Indices: 5149881--5150760 Score: 637
Period size: 222 Copynumber: 3.9 Consensus size: 222
5149871 AAGTTGGTGG
* * * *
5149881 CACCTTTAGTCCTCAAAGAATAGGACGTCTTTTCCTTTTCAAGCCCACACGAGTTGGTGGCGCAT
1 CACCTTTAGTCCTCAAAGAACAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACAT
* * * *
5149946 TTCAGTCCTCAAAGAGCAGGACGCTTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCCTCC
66 TTCAGTCCTCAAAGAGCAGGACGCTCTTCTCCTTTCAAAGCCCACACAAGTTAGTGGCACCCTCC
5150011 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCACTTTTCAGTC
131 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCACTTTTCAGTC
5150076 CTCAAAAAATAGGACGCTCTCTCCTTT
196 CTCAAAAAATAGGACGCTCTCTCCTTT
* * *
5150103 CACCTTTAGTCCTCAAAGAGCAGGACGTTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCT
1 CACCTTTAGTCCTCAAAGAACAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACAT
* * * *
5150168 TTTAGTCCTCAAAGAGCATGACGC-CTTCTCC-TTCAAAGCCCACACGAGTTAGTGGCACCCTCT
66 TTCAGTCCTCAAAGAGCAGGACGCTCTTCTCCTTTCAAAGCCCACACAAGTTAGTGGCACCCTCC
** * * * *
5150231 AGTCCTCAAAGAGCAGGACGTATTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTGT-AG
131 AGTCCTCAAAGAGCAGGACG--CCTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCACTTTTCAG
* * ** * * *
5150295 TCCTCGAACAGCAGGACAC-CTTTTCTTT
194 TCCTCAAAAAATAGGACGCTCTCTCCTTT
* * * **** * * ** ** * ** **
5150323 ----TTAAAGCCCACACAAGTTGGTGGCACCCTCTTAGTCC-TCAAAGAGCAGGACGCACTTTAT
1 CACCTT-TAGTCCTCA-AAG-AACAGG-A-CGTCTT-TTCCTTTTAA-AGC-CCACACAAGTTGG
** * * *
5150383 TTTC-CTTTTCCCCTTTGTCCTCAAAGAGCAGGACGCACTTCATTTCCTTCTTTCTCTTTTAAAG
58 TGGCACATTT---C--AGTCCTCAAAGAGCAGGACG-----C---T-CTTC--TC-CTTTCAAAG
* ** * * *
5150447 CCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGAAAGACGCCTTTTCCTTTTAAAGCCC
106 CCCACACAAGTTAGTGGCAC-CCTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCC
* * * *
5150512 ACACAAGTTGGTGGCACTTCTCAGTCCTCAAAGAGTAGGACGCTCTCTCCTTT
170 ACACAAGTTAGTGGCACTTTTCAGTCCTCAAAAAATAGGACGCTCTCTCCTTT
* * * *
5150565 CGTCCTTTAGTCCTCAAAGAGCAGGACG------CCTTTCAAAGCCCACACAAGTTGGTGGCACT
1 C-ACCTTTAGTCCTCAAAGAACAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACA
* * ***
5150624 TTTCTAGTCCTCAAAGAGCAGGACG-TCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
65 TTTC-AGTCCTCAAAGAGCAGGACGCTCTTCTCCTTTCAAAGCCCACACAAGTTAGTGGCACCCT
* * * * * * *
5150688 TCAGTCTTCAAAGAGCAGGATG-C-TTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCC
129 CCAGTCCTCAAAGAGCAGGACGCCTTTTC-CTTT-TAAAGCCCACACAAGTTAGTGGCACTTTTC
*
5150751 AGTCTTCAAA
192 AGTCCTCAAA
5150761 GAGCAGGACG
Statistics
Matches: 514, Mismatches: 103, Indels: 87
0.73 0.15 0.12
Matches are distributed among these distances:
215 4 0.01
216 7 0.01
217 60 0.12
218 30 0.06
219 5 0.01
220 56 0.11
221 31 0.06
222 125 0.24
223 8 0.02
227 18 0.04
231 20 0.04
232 2 0.00
234 8 0.02
235 10 0.02
236 3 0.01
237 4 0.01
239 2 0.00
240 36 0.07
241 41 0.08
242 29 0.06
243 1 0.00
244 3 0.01
245 3 0.01
246 6 0.01
247 2 0.00
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.29
Consensus pattern (222 bp):
CACCTTTAGTCCTCAAAGAACAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACAT
TTCAGTCCTCAAAGAGCAGGACGCTCTTCTCCTTTCAAAGCCCACACAAGTTAGTGGCACCCTCC
AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCACTTTTCAGTC
CTCAAAAAATAGGACGCTCTCTCCTTT
Found at i:5150270 original size:123 final size:122
Alignment explanation
Indices: 5150108--5150374 Score: 394
Period size: 123 Copynumber: 2.2 Consensus size: 122
5150098 CCTTTCACCT
*
5150108 TTAGTCCTCAAAGAGCAGGACGTTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAG
1 TTAGTCCTCAAAGAGCAGGACGTTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC-TGTAG
* * * *
5150173 TCCTCAAAGAGCATGACGCCTTCTC-CTTCAAAGCCCACACGAGTTAGTGGCACCCTC
65 TCCTCAAACAGCAGGACACCTTCTCTCTTCAAAGCCCACACAAGTTAGTGGCACCCTC
*
5150230 -TAGTCCTCAAAGAGCAGGACGTATTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTGTA
1 TTAGTCCTCAAAGAGCAGGACG--TTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTGTA
* * * * *
5150294 GTCCTCGAACAGCAGGACACCTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCCTC
64 GTCCTCAAACAGCAGGACACCTTCTCTCTTCAAAGCCCACACAAGTTAGTGGCACCCTC
5150353 TTAGTCCTCAAAGAGCAGGACG
1 TTAGTCCTCAAAGAGCAGGACG
5150375 CACTTTATTT
Statistics
Matches: 130, Mismatches: 11, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
121 21 0.16
122 24 0.18
123 64 0.49
124 21 0.16
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (122 bp):
TTAGTCCTCAAAGAGCAGGACGTTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTGTAGT
CCTCAAACAGCAGGACACCTTCTCTCTTCAAAGCCCACACAAGTTAGTGGCACCCTC
Found at i:5150669 original size:62 final size:60
Alignment explanation
Indices: 5150572--5150829 Score: 332
Period size: 61 Copynumber: 4.3 Consensus size: 60
5150562 TTTCGTCCTT
5150572 TAGTCCTCAAAGAGCAGGACG----CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
1 TAGTCCTCAAAGAGCAGGACGCTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
*
5150628 TAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTC
1 TAGTCCTCAAAGAGCAGGACG-C-TTTCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
* * *
5150690 -AGTCTTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCAC-CTTC
1 TAGTCCTCAAAGAGCAGGACGCTTTC-CTTT-CAAAGCCCACACAAGTTGGTGGCACTTTTC
* * *
5150750 CAGTCTTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-
1 TAGTCCTCAAAGAGCAGGACG-CTTTCC-TTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
* *
5150811 TCGTCCTCAAAGAGTAGGA
1 TAGTCCTCAAAGAGCAGGA
5150830 TGCACTTTAT
Statistics
Matches: 178, Mismatches: 12, Indels: 19
0.85 0.06 0.09
Matches are distributed among these distances:
56 21 0.12
59 4 0.02
60 8 0.04
61 101 0.57
62 44 0.25
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (60 bp):
TAGTCCTCAAAGAGCAGGACGCTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
Found at i:5150790 original size:122 final size:122
Alignment explanation
Indices: 5150594--5150832 Score: 367
Period size: 122 Copynumber: 2.0 Consensus size: 122
5150584 AGCAGGACGC
* * *
5150594 CTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGTCTTTTCCTT
1 CTTTCAAAGCCCACACAAGTTGGTGGCACTCTTCCAGTCCTCAAAGAGCAGGACGTCCTTTCCTT
*
5150659 TCAAAGCCCACACAAGTTGGTGGCA-TTTTTCAGTCTTCAAAGAGCAGGATGCTTTCT
66 TCAAAGCCCACACAAGTTGGTGGCACTTTTTC-GTCCTCAAAGAGCAGGATGCTTTCT
*
5150716 CTTTGCAAAGCCCACACAAGTTGGTGGCAC-CTTCCAGTCTTCAAAGAGCAGGACG-CCTTTCCT
1 CTTT-CAAAGCCCACACAAGTTGGTGGCACTCTTCCAGTCCTCAAAGAGCAGGACGTCCTTTCC-
* *
5150779 TTTCAAAGCCCACACGAGTTGGTGGCACTTTTTCGTCCTCAAAGAGTAGGATGC
64 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTTCGTCCTCAAAGAGCAGGATGC
5150833 ACTTTATTTT
Statistics
Matches: 107, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
121 6 0.06
122 70 0.65
123 31 0.29
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (122 bp):
CTTTCAAAGCCCACACAAGTTGGTGGCACTCTTCCAGTCCTCAAAGAGCAGGACGTCCTTTCCTT
TCAAAGCCCACACAAGTTGGTGGCACTTTTTCGTCCTCAAAGAGCAGGATGCTTTCT
Found at i:5150878 original size:42 final size:42
Alignment explanation
Indices: 5150813--5151003 Score: 199
Period size: 42 Copynumber: 4.5 Consensus size: 42
5150803 GCACTTTTTC
* *
5150813 GTCCTCAAAGAGTAGGATGCACTTTATTTTCCTCTTTCCTTT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTTTCCTTT
* * *
5150855 GTCCTCAAAGAGCAGGACACACTTCATTCCTTTCT-TTTCTCTTTT
1 GTCCTCAAAGAGCAGGACGCACTTTATT--TTCCTCTTTC-C-TTT
* *
5150900 GTCCTCAAAGAGCAGGACGTACTTTATTTTCCTCTTTCTTTT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTTTCCTTT
* * *
5150942 GTCCTCAAAGAGCAGGACGCA-TTTCGTTTTTCGTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACGCACTTT--ATTTTCCTCTTTCCTTT
*
5150985 ATCCTCGAAA-AGCAGGACG
1 GTCCTC-AAAGAGCAGGACG
5151004 TACTCTTTTT
Statistics
Matches: 125, Mismatches: 16, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
41 3 0.02
42 47 0.38
43 35 0.28
44 12 0.10
45 28 0.22
ACGTcount: A:0.20, C:0.25, G:0.16, T:0.39
Consensus pattern (42 bp):
GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTTTCCTTT
Found at i:5150959 original size:87 final size:85
Alignment explanation
Indices: 5150808--5151007 Score: 260
Period size: 87 Copynumber: 2.3 Consensus size: 85
5150798 TGGTGGCACT
* * *
5150808 TTTTCGTCCTCAAAGAGTAGGATGCACTTTATTTTCCTCTTTCCTTTGTCCTCAAAGAGCAGGAC
1 TTTT-GTCCTCAAAGAGCAGGACGTACTTTATTTTCCTCTTTCCTTTGTCCTCAAAGAGCAGGAC
5150873 ACACTTCATTCCTTTC-TTTTCTC
65 ACACTTCATT--TTTCGTTTT-TC
* *
5150896 TTTTGTCCTCAAAGAGCAGGACGTACTTTATTTTCCTCTTTCTTTTGTCCTCAAAGAGCAGGACG
1 TTTTGTCCTCAAAGAGCAGGACGTACTTTATTTTCCTCTTTCCTTTGTCCTCAAAGAGCAGGACA
* *
5150961 CATTTCGTTTTTCGTTTTTC
66 CACTTCATTTTTCGTTTTTC
* *
5150981 CTTTATCCTCGAAA-AGCAGGACGTACT
1 TTTTGTCCTC-AAAGAGCAGGACGTACT
5151008 CTTTTTCACT
Statistics
Matches: 101, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
85 27 0.27
86 7 0.07
87 63 0.62
88 4 0.04
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (85 bp):
TTTTGTCCTCAAAGAGCAGGACGTACTTTATTTTCCTCTTTCCTTTGTCCTCAAAGAGCAGGACA
CACTTCATTTTTCGTTTTTC
Found at i:5158403 original size:28 final size:28
Alignment explanation
Indices: 5158371--5158438 Score: 102
Period size: 28 Copynumber: 2.4 Consensus size: 28
5158361 AATTGGGGAG
*
5158371 ACTCCAACCCCGTTATTTCAT-CGGAGAT
1 ACTCCAACCCCGTTATTT-ATGAGGAGAT
*
5158399 ACTCCAACCCCGTTATTTATGAGGGGAT
1 ACTCCAACCCCGTTATTTATGAGGAGAT
5158427 ACTCCAACCCCG
1 ACTCCAACCCCG
5158439 GCTTTATATC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 2 0.05
28 35 0.95
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (28 bp):
ACTCCAACCCCGTTATTTATGAGGAGAT
Found at i:5158603 original size:51 final size:52
Alignment explanation
Indices: 5158535--5158645 Score: 147
Period size: 51 Copynumber: 2.2 Consensus size: 52
5158525 TTCCGAGAGA
* *
5158535 ATACTCC-AACCCTGATTTTATTTCTAAAATACTAATTT-TCCACAATCAGGG
1 ATACTCCAAACCCTGATTTTATTTCTAAAACACCAATTTCT-CACAATCAGGG
* *
5158586 ATACTCCAAATCC-GATTTTATTTCTAAAACACCAATTTCTCATAATCAGGG
1 ATACTCCAAACCCTGATTTTATTTCTAAAACACCAATTTCTCACAATCAGGG
*
5158637 ATATTCCAA
1 ATACTCCAA
5158646 CCCCGTTATT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
51 48 0.91
52 5 0.09
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.34
Consensus pattern (52 bp):
ATACTCCAAACCCTGATTTTATTTCTAAAACACCAATTTCTCACAATCAGGG
Found at i:5158667 original size:79 final size:77
Alignment explanation
Indices: 5158584--5158801 Score: 215
Period size: 79 Copynumber: 2.7 Consensus size: 77
5158574 CCACAATCAG
* * *
5158584 GGATACTCCAAATCCGATTTTATTTCTAAAACACCAATTTCTCATAATCAGGGATATTCCAACCC
1 GGATACT-CAAACCCGATTTTATTTCTAAAACACCGATTT-TCATAATCAGGGATACTCCAACCC
* * *
5158649 CGTTATTTTTGCGA
64 CATTATTTTCGAGA
* * *
5158663 GGATACTTCAACCCCGATTTTATTT-TCAAAATACTGATTTTCTATAAAT-AGGGATACTCCAAC
1 GGATAC-TCAAACCCGATTTTATTTCT-AAAACACCGATTTTC-AT-AATCAGGGATACTCCAAC
* *
5158726 CCTATTATTTTCGAGG
62 CCCATTATTTTCGAGA
* * *
5158742 GGATACTCAAACCCCGATTTTTGTTTCTAGAACACCGATTTTCCATAATCGGGGATACTC
1 GGATACTCAAA-CCCGA-TTTTATTTCTAAAACACCGATTTT-CATAATCAGGGATACTC
5158802 TAGCCCCGTT
Statistics
Matches: 113, Mismatches: 17, Indels: 17
0.77 0.12 0.12
Matches are distributed among these distances:
78 7 0.06
79 71 0.63
80 33 0.29
81 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.34
Consensus pattern (77 bp):
GGATACTCAAACCCGATTTTATTTCTAAAACACCGATTTTCATAATCAGGGATACTCCAACCCCA
TTATTTTCGAGA
Found at i:5160677 original size:2 final size:2
Alignment explanation
Indices: 5160665--5160702 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
5160655 TTGATCTTCT
* *
5160665 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TT TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5160703 TAATCAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5161380 original size:2 final size:2
Alignment explanation
Indices: 5161373--5161398 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5161363 TATGTCATAA
5161373 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5161399 TCTGGTCAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5167089 original size:17 final size:16
Alignment explanation
Indices: 5167067--5167102 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
5167057 AAATAAAAAA
5167067 TTATTTTATTAATTATT
1 TTATTTTATT-ATTATT
*
5167084 TTATTTTATTTTTATT
1 TTATTTTATTATTATT
5167100 TTA
1 TTA
5167103 AATAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
TTATTTTATTATTATT
Found at i:5168047 original size:50 final size:50
Alignment explanation
Indices: 5167962--5168166 Score: 241
Period size: 50 Copynumber: 4.1 Consensus size: 50
5167952 TTTATTTCTA
** * *
5167962 TTGACTATTCTTCACTGACCTTTGACAATCGAGAGAGGTGACTGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCGTAATTG
* * * **
5168012 TT-AGCTATTCTTCACCAATCTTTGACAATAAAGAGAGGTGGCCAAAATTG
1 TTGA-CTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCGTAATTG
* * *
5168062 TTGACTATTCTTCACCAACCTTTGATAATCGAGAGAGGTGATCGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCGTAATTG
* * * * *
5168112 TTGACTATTTTTCATCATCCTCTGACAATAGAGAGAGGTGGCCGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCGTAATTG
5168162 TTGAC
1 TTGAC
5168167 CTTAAGCATC
Statistics
Matches: 128, Mismatches: 25, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
49 1 0.01
50 126 0.98
51 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (50 bp):
TTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCGTAATTG
Found at i:5168138 original size:100 final size:100
Alignment explanation
Indices: 5167962--5168166 Score: 281
Period size: 100 Copynumber: 2.0 Consensus size: 100
5167952 TTTATTTCTA
**
5167962 TTGACTATTCTTCACTGACCTTTGACAATCGAGAGAGGTGACTGTAATTGTTAGCTATTCTTCAC
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACTGTAATTGTTAGCTATTCTTCAC
*
5168027 CAATCTTTGACAATAAAGAGAGGTGGCCAAAATTG
66 CAATCTCTGACAATAAAGAGAGGTGGCCAAAATTG
* *
5168062 TTGACTATTCTTCACCAACCTTTGATAATCGAGAGAGGTGA-TCGTAATTGTT-GACTATTTTTC
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACT-GTAATTGTTAG-CTATTCTTC
* * **
5168125 ATC-ATCCTCTGACAATAGAGAGAGGTGGCCGTAATTG
64 ACCAAT-CTCTGACAATAAAGAGAGGTGGCCAAAATTG
5168162 TTGAC
1 TTGAC
5168167 CTTAAGCATC
Statistics
Matches: 93, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
99 4 0.04
100 89 0.96
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (100 bp):
TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACTGTAATTGTTAGCTATTCTTCAC
CAATCTCTGACAATAAAGAGAGGTGGCCAAAATTG
Found at i:5169840 original size:13 final size:13
Alignment explanation
Indices: 5169822--5169847 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5169812 TACACATAAG
5169822 ATGTATCGATACA
1 ATGTATCGATACA
5169835 ATGTATCGATACA
1 ATGTATCGATACA
5169848 TCCCAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5169864 original size:33 final size:32
Alignment explanation
Indices: 5169804--5169867 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
5169794 CTTAATTGTT
* *
5169804 TGTATCGATACACATAAGATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
5169836 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
5169868 TTGGCGTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:5176018 original size:13 final size:13
Alignment explanation
Indices: 5175999--5176037 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
5175989 ACAGCATTCT
5175999 CTGTATCGATACA
1 CTGTATCGATACA
*
5176012 TTGTATCGATACA
1 CTGTATCGATACA
5176025 CTGTATCGATACA
1 CTGTATCGATACA
5176038 AAGGGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (13 bp):
CTGTATCGATACA
Found at i:5178070 original size:33 final size:32
Alignment explanation
Indices: 5178023--5178090 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
5178013 CGTTACAAGC
* **
5178023 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCAATACATACTAT-GTGTATCGATA
*
5178056 CAATGTATCAATACATACTGTGTGTATCGATA
1 CAATGTATCAATACATACTATGTGTATCGATA
5178088 CAA
1 CAA
5178091 GTTTGGCTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 14 0.45
33 17 0.55
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (32 bp):
CAATGTATCAATACATACTATGTGTATCGATA
Found at i:5180503 original size:20 final size:21
Alignment explanation
Indices: 5180474--5180514 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
5180464 TGTTTTTGAT
5180474 GATGATTTT-GA-TGAAAAAC
1 GATGATTTTGGAGTGAAAAAC
5180493 GATGTATTTTGGAGTGAAAAAC
1 GATG-ATTTTGGAGTGAAAAAC
5180515 AAGAATTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 5 0.26
21 2 0.11
22 8 0.42
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (21 bp):
GATGATTTTGGAGTGAAAAAC
Found at i:5180664 original size:13 final size:13
Alignment explanation
Indices: 5180646--5180684 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
5180636 ATAATCCTCT
5180646 TGTATCGATACAG
1 TGTATCGATACAG
*
5180659 TGTATCGATACAA
1 TGTATCGATACAG
*
5180672 TGTATCAATACAG
1 TGTATCGATACAG
5180685 AAAATGCTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:5186978 original size:20 final size:21
Alignment explanation
Indices: 5186931--5186983 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
5186921 GCCAATGACC
**
5186931 TGTATCGATACATCTTTTTCA
1 TGTATCGATACATCTTGGTCA
*
5186952 AGTATCGATACAT-TTGGTCA
1 TGTATCGATACATCTTGGTCA
5186972 TGTATCGATACA
1 TGTATCGATACA
5186984 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATCTTGGTCA
Found at i:5186989 original size:13 final size:13
Alignment explanation
Indices: 5186971--5186995 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5186961 ACATTTGGTC
5186971 ATGTATCGATACA
1 ATGTATCGATACA
5186984 ATGTATCGATAC
1 ATGTATCGATAC
5186996 TATGCAACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5188495 original size:20 final size:19
Alignment explanation
Indices: 5188466--5188504 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
5188456 AGGTCAAAAC
5188466 CCTTAAATGTATCGATACA
1 CCTTAAATGTATCGATACA
5188485 CCTTCAAATGTATCGATACA
1 CCTT-AAATGTATCGATACA
5188505 TAATGCACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (19 bp):
CCTTAAATGTATCGATACA
Found at i:5188537 original size:20 final size:20
Alignment explanation
Indices: 5188470--5188565 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
5188460 CAAAACCCTT
****
5188470 AAATGTATCGATACACCTTC
1 AAATGTATCGATACATGAAC
5188490 AAATGTATCGATACAT-AATGC
1 AAATGTATCGATACATGAA--C
* *
5188511 ACA-GTATCGATACATGACC
1 AAATGTATCGATACATGAAC
* *
5188530 AAATGTATCGATACTTGTAAA
1 AAATGTATCGATACATG-AAC
5188551 AAATGTATCGATACA
1 AAATGTATCGATACA
5188566 GGTGATTGGT
Statistics
Matches: 61, Mismatches: 10, Indels: 9
0.76 0.12 0.11
Matches are distributed among these distances:
19 3 0.05
20 39 0.64
21 19 0.31
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.28
Consensus pattern (20 bp):
AAATGTATCGATACATGAAC
Found at i:5188643 original size:13 final size:13
Alignment explanation
Indices: 5188625--5188650 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5188615 TACACACAAG
5188625 ATGTATCGATACA
1 ATGTATCGATACA
5188638 ATGTATCGATACA
1 ATGTATCGATACA
5188651 TCCCAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5188667 original size:33 final size:32
Alignment explanation
Indices: 5188607--5188670 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
5188597 CTTAACTGTT
*
5188607 TGTATCGATACACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
5188639 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
5188671 TGGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:5192452 original size:50 final size:50
Alignment explanation
Indices: 5192390--5192650 Score: 396
Period size: 50 Copynumber: 5.2 Consensus size: 50
5192380 CAAGTGGGAG
* *
5192390 AATTATTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCGT
1 AATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGT
* * **
5192440 AACTGTTGACTATTCTTCACCAACCTTTGACAATCGTGAGAGGTGGTTGT
1 AATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGT
* * * *
5192490 AATTGTTGACTTTTCTTCACCAACCTTTGATAATAGAGGGAGGTGGCCGT
1 AATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGT
* *
5192540 AATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAAGTGACCGT
1 AATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGT
* *
5192590 AATTGTTGACTATTCTTCACCATCCTTTGACAATAGAGAGAGGTGGCCGT
1 AATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGT
5192640 AATTGTTGACT
1 AATTGTTGACT
5192651 TTAACCATCT
Statistics
Matches: 189, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 189 1.00
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (50 bp):
AATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGT
Found at i:5193691 original size:17 final size:17
Alignment explanation
Indices: 5193656--5193697 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
5193646 TTTACATTAA
* *
5193656 TTTTCTTAATTTTAATT
1 TTTTCTTTATTATAATT
5193673 TTTTCTTTATTAT-ATT
1 TTTTCTTTATTATAATT
5193689 TTTCTCTTT
1 TTT-TCTTT
5193698 TATCATCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTCTTTATTATAATT
Found at i:5193779 original size:18 final size:20
Alignment explanation
Indices: 5193758--5193797 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
5193748 TTAAATTATT
5193758 TTTATCAAAAAT-T-AATAA
1 TTTATCAAAAATATAAATAA
*
5193776 TTTATTAAAAATATAAATAA
1 TTTATCAAAAATATAAATAA
5193796 TT
1 TT
5193798 ATATTTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 1 0.05
20 7 0.37
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
TTTATCAAAAATATAAATAA
Found at i:5193794 original size:20 final size:18
Alignment explanation
Indices: 5193758--5193802 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 18
5193748 TTAAATTATT
*
5193758 TTTATCAAAAATTAATAA
1 TTTATTAAAAATTAATAA
5193776 TTTATTAAAAATATAAATAA
1 TTTATTAAAAAT-T-AATAA
5193796 TTATATT
1 TT-TATT
5193803 TATTAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 11 0.48
19 1 0.04
20 7 0.30
21 4 0.17
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTATTAAAAATTAATAA
Found at i:5193815 original size:25 final size:26
Alignment explanation
Indices: 5193752--5193819 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 26
5193742 TTTAATTTAA
*
5193752 ATTATTTTTATCAAAAATTAATAATTT
1 ATTAATTTTAT-AAAAATTAATAATTT
***
5193779 ATTAAAAATATAAATAATT-AT-ATTT
1 ATTAATTTTATAAA-AATTAATAATTT
5193804 ATTAATTTTATAAAAA
1 ATTAATTTTATAAAAA
5193820 AACTATTTGA
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
24 2 0.06
25 15 0.45
26 5 0.15
27 11 0.33
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (26 bp):
ATTAATTTTATAAAAATTAATAATTT
Found at i:5196817 original size:21 final size:21
Alignment explanation
Indices: 5196791--5196833 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
5196781 TATTAATGTG
5196791 TTTTATTATATTATA-ATTATA
1 TTTTA-TATATTATATATTATA
*
5196812 TTTTATATATTTTATATTATA
1 TTTTATATATTATATATTATA
5196833 T
1 T
5196834 AAATTTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTATATATTATATATTATA
Found at i:5196834 original size:7 final size:7
Alignment explanation
Indices: 5196797--5196834 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
5196787 TGTGTTTTAT
5196797 TATATTA
1 TATATTA
5196804 TA-ATTA
1 TATATTA
*
5196810 TATTTTA
1 TATATTA
*
5196817 TATATTT
1 TATATTA
5196824 TATATTA
1 TATATTA
5196831 TATA
1 TATA
5196835 AATTTTGATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
TATATTA
Found at i:5202246 original size:21 final size:21
Alignment explanation
Indices: 5202204--5202246 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
5202194 ATTAAAGATT
*
5202204 AAAATAAAAATATAAATTTAA
1 AAAATAAAAATATAAATATAA
5202225 AAAATAAAAA-ATATAATATAA
1 AAAATAAAAATATA-AATATAA
5202246 A
1 A
5202247 TGTGTCTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAATAAAAATATAAATATAA
Found at i:5204261 original size:111 final size:112
Alignment explanation
Indices: 5204143--5204366 Score: 333
Period size: 112 Copynumber: 2.0 Consensus size: 112
5204133 GCATCCAGCC
* * *
5204143 ATCCACGAGGTTTCCA-TTTGGAAAGAATTTTCTCTGAAAAAGAAAGGCGTGGAGAGAAAAGATG
1 ATCCACGAGATTTCCATTTTGGAAAGAATTTTCCCAGAAAAAGAAAGGCGTGGAGAGAAAAGATG
* **
5204207 TTTCCAATTCCCATAGAGGGGCCCAATCAATCATTCTCATGACAAAG
66 TTTCCAATTCCCATAGAGGCGCCCAATCAATCAAGCTCATGACAAAG
* *
5204254 ATCCACGAGATTTTCATTTTGGAAAGAATTTTCCCAGAAAAAGAAAGGCGTGGAGAGGAAAGATG
1 ATCCACGAGATTTCCATTTTGGAAAGAATTTTCCCAGAAAAAGAAAGGCGTGGAGAGAAAAGATG
* * * *
5204319 TTTCCAATTCCGATCGAGGCGTCCAATTAATCAAGCTCATGACAAAG
66 TTTCCAATTCCCATAGAGGCGCCCAATCAATCAAGCTCATGACAAAG
5204366 A
1 A
5204367 AATTTATATT
Statistics
Matches: 100, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
111 14 0.14
112 86 0.86
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (112 bp):
ATCCACGAGATTTCCATTTTGGAAAGAATTTTCCCAGAAAAAGAAAGGCGTGGAGAGAAAAGATG
TTTCCAATTCCCATAGAGGCGCCCAATCAATCAAGCTCATGACAAAG
Found at i:5205395 original size:17 final size:19
Alignment explanation
Indices: 5205373--5205408 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
5205363 GAGATATTGC
5205373 CTTGATTTT-T-GAAAAAT
1 CTTGATTTTATAGAAAAAT
5205390 CTTGATTTTATAGAAAAAT
1 CTTGATTTTATAGAAAAAT
5205409 AATAAAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 1 0.06
19 7 0.41
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (19 bp):
CTTGATTTTATAGAAAAAT
Found at i:5206554 original size:2 final size:2
Alignment explanation
Indices: 5206547--5206592 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
5206537 TAGATCATCA
5206547 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5206589 AT AT
1 AT AT
5206593 TACTTAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5207401 original size:13 final size:14
Alignment explanation
Indices: 5207370--5207403 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5207360 GCAAAAAGAA
*
5207370 AAAAAATTTCAATT
1 AAAAAACTTCAATT
*
5207384 AAAAAACTTCATTT
1 AAAAAACTTCAATT
5207398 AAAAAA
1 AAAAAA
5207404 GGTGATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAAAACTTCAATT
Found at i:5209914 original size:16 final size:16
Alignment explanation
Indices: 5209895--5209932 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5209885 ACCTAACCCA
5209895 AAATGACCCGAAAC-TG
1 AAATGACCCG-AACTTG
*
5209911 AAATTACCCGAACTTG
1 AAATGACCCGAACTTG
5209927 AAATGA
1 AAATGA
5209933 TCCAAACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.45, C:0.21, G:0.16, T:0.18
Consensus pattern (16 bp):
AAATGACCCGAACTTG
Found at i:5211402 original size:28 final size:28
Alignment explanation
Indices: 5211342--5211415 Score: 114
Period size: 28 Copynumber: 2.7 Consensus size: 28
5211332 AAAATAAAAT
5211342 CAGGGTTGGAGTATCCCC-CAAAAATAA
1 CAGGGTTGGAGTATCCCCGCAAAAATAA
* **
5211369 CGGGGTTGGAGTATCCCCGTGAAAATAA
1 CAGGGTTGGAGTATCCCCGCAAAAATAA
5211397 CAGGGTTGGAGTATCCCCG
1 CAGGGTTGGAGTATCCCCG
5211416 ATTGTGAGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 17 0.40
28 25 0.60
ACGTcount: A:0.28, C:0.22, G:0.30, T:0.20
Consensus pattern (28 bp):
CAGGGTTGGAGTATCCCCGCAAAAATAA
Found at i:5211402 original size:106 final size:107
Alignment explanation
Indices: 5211265--5211494 Score: 259
Period size: 106 Copynumber: 2.2 Consensus size: 107
5211255 AATAAAATCA
** * * * ** *
5211265 GGGTTGGAGTATCCCATTGGAAATAATAGGGTCGGAGTATCCCTAATTAT-AGAAAATTGGAGCT
1 GGGTTGGAGTATCCCCGTGAAAATAACAGGGTCGGAGTATCCCCAATTATGAG-AAA-TCAAGAT
*
5211329 TTGA-AAATAAAATCAGGGTTGGAGTATCCC-CCAAAAATAACG
64 TTGAGAAATAAAACCAGGGTTGGAGTATCCCTCCAAAAATAACG
* * * *
5211371 GGGTTGGAGTATCCCCGTGAAAATAACAGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTT
1 GGGTTGGAGTATCCCCGTGAAAATAACAGGGTCGGAGTATCCCCAATTATGAGAAATCAAGATTT
* * * **
5211436 TAGGAATAAAACCAGGGTTGGAGTATCCCTTCGGAAATAACG
66 GAGAAATAAAACCAGGGTTGGAGTATCCCTCCAAAAATAACG
5211478 GGGTTGGAGTATCCCCG
1 GGGTTGGAGTATCCCCG
5211495 ATTATGAGAA
Statistics
Matches: 103, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
105 6 0.06
106 69 0.67
107 28 0.27
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.25
Consensus pattern (107 bp):
GGGTTGGAGTATCCCCGTGAAAATAACAGGGTCGGAGTATCCCCAATTATGAGAAATCAAGATTT
GAGAAATAAAACCAGGGTTGGAGTATCCCTCCAAAAATAACG
Found at i:5211459 original size:79 final size:77
Alignment explanation
Indices: 5211371--5211545 Score: 260
Period size: 79 Copynumber: 2.2 Consensus size: 77
5211361 AAAAATAACG
*
5211371 GGGTTGGAGTATCCCCGTGAAAATAACAGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTT
1 GGGTTGGAGTATCCCCG-G-AAATAACAGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTT
5211436 TAGGAATAAAACCA
64 TAGGAATAAAACCA
*
5211450 GGGTTGGAGTATCCCTTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTT
1 GGGTTGGAGTATCCC--CGGAAATAACAGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTT
* **
5211515 TAGGAATAAAGCTG
64 TAGGAATAAAACCA
*
5211529 GGGTTGGAGTACCCCCG
1 GGGTTGGAGTATCCCCG
5211546 ATTATGAAAA
Statistics
Matches: 88, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
77 2 0.02
79 83 0.94
80 1 0.01
81 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (77 bp):
GGGTTGGAGTATCCCCGGAAATAACAGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTA
GGAATAAAACCA
Found at i:5213871 original size:20 final size:20
Alignment explanation
Indices: 5213846--5213885 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5213836 AATGCCTGAA
5213846 TGTAAAATGTATCGATACAT
1 TGTAAAATGTATCGATACAT
5213866 TGTAAAATGTATCGATACAT
1 TGTAAAATGTATCGATACAT
5213886 CTGGGTAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (20 bp):
TGTAAAATGTATCGATACAT
Found at i:5213921 original size:13 final size:13
Alignment explanation
Indices: 5213903--5213928 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5213893 AACTTCCTAG
5213903 ATGTATCGATACA
1 ATGTATCGATACA
5213916 ATGTATCGATACA
1 ATGTATCGATACA
5213929 TTTCCTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5215859 original size:79 final size:78
Alignment explanation
Indices: 5215779--5216139 Score: 535
Period size: 79 Copynumber: 4.6 Consensus size: 78
5215769 AAAATAGAAT
* *
5215779 CGGGGTTGGAGTATCCCCGTGAAAATAATGGGGTTGGAGTATCCCCAATTATGAGAAATTAATAT
1 CGGGGTTGGAGTATCCCC-TGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
*
5215844 TTTAGGAATAAAAT
65 TTTAGGAATAAAAC
* *
5215858 CGGGGTTGGAGTATCCCCTCTG-AAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATA
1 CGGGGTTGGAGTAT-CCC-CTGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATA
5215922 TTTTAGGAATAAAAC
64 TTTTAGGAATAAAAC
* * * *
5215937 CGGAGTTGAAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTGTGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCT-GAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
5216002 TTTAGGAATAAAAC
65 TTTAGGAATAAAAC
* * *
5216016 CGGGGTTGGAGTATCCCTTGGAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATT
1 CGGGGTTGGAGTATCCCCTGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATT
*
5216081 TTAGGAATAAAGC
66 TTAGGAATAAAAC
* *
5216094 CAGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCCT-GAAAATAACGGGGTTGGAGTATCCCC
5216140 GATGATTAAC
Statistics
Matches: 259, Mismatches: 18, Indels: 10
0.90 0.06 0.03
Matches are distributed among these distances:
77 2 0.01
78 77 0.30
79 174 0.67
80 5 0.02
81 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCCTGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATT
TTAGGAATAAAAC
Found at i:5216120 original size:157 final size:157
Alignment explanation
Indices: 5215781--5216139 Score: 580
Period size: 157 Copynumber: 2.3 Consensus size: 157
5215771 AATAGAATCG
* *
5215781 GGGTTGGAGTATCCCCGT-GAAAATAATGGGGTTGGAGTATCCCCAATTATGAGAAATTAATATT
1 GGGTTGGAGTATCCCC-TCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATT
* *
5215845 TTAGGAATAAAATCGGGGTTGGAGTATCCCCTCTGAAATAACGGGGTTGGAGTATCCCCGATTGT
65 TTAGGAATAAAACCGGGGTTGGAGTATCCCCTCTGAAATAACGGGGTTGGAGTATCCCCGATTAT
5215910 GAGAAATCAATATTTTAGGAATAAAACC
130 GAGAAATCAATATTTTAGGAATAAAACC
* * *
5215938 GGAGTTGAAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTGTGAGAAATCAATATT
1 GG-GTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATT
5216003 TTAGGAATAAAACCGGGGTTGGAGTAT-CCCT-TGGAAATAACGGGGTTGGAGTATCCCCGATTA
65 TTAGGAATAAAACCGGGGTTGGAGTATCCCCTCT-GAAATAACGGGGTTGGAGTATCCCCGATTA
*
5216066 TGAGAAATCAATATTTTAGGAATAAAGCC
129 TGAGAAATCAATATTTTAGGAATAAAACC
*
5216095 AGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCC
1 -GGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCC
5216140 GATGATTAAC
Statistics
Matches: 187, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
156 1 0.01
157 103 0.55
158 83 0.44
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (157 bp):
GGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTT
TAGGAATAAAACCGGGGTTGGAGTATCCCCTCTGAAATAACGGGGTTGGAGTATCCCCGATTATG
AGAAATCAATATTTTAGGAATAAAACC
Found at i:5216129 original size:28 final size:28
Alignment explanation
Indices: 5216094--5216170 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
5216084 GGAATAAAGC
5216094 CAGGGTTGGAGTATCCCCTCGA-AAATAA
1 CAGGGTTGGAGTATCCCC-CGATAAATAA
* *
5216122 CAGGGTTGGAGTAT-CCCCGATGATTAA
1 CAGGGTTGGAGTATCCCCCGATAAATAA
*
5216149 CGGGGTTGGAGTATCCCCCGAT
1 CAGGGTTGGAGTATCCCCCGAT
5216171 TGTGAAAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 3 0.07
27 20 0.45
28 21 0.48
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (28 bp):
CAGGGTTGGAGTATCCCCCGATAAATAA
Found at i:5216157 original size:27 final size:26
Alignment explanation
Indices: 5216094--5216166 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 26
5216084 GGAATAAAGC
5216094 CAGGGTTGGAGTATCCCCTCGAAAATAA
1 CAGGGTTGGAGTAT-CCC-CGAAAATAA
* *
5216122 CAGGGTTGGAGTATCCCCGATGATTAA
1 CAGGGTTGGAGTATCCCCGA-AAATAA
*
5216149 CGGGGTTGGAGTATCCCC
1 CAGGGTTGGAGTATCCCC
5216167 CGATTGTGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
26 3 0.07
27 24 0.59
28 14 0.34
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (26 bp):
CAGGGTTGGAGTATCCCCGAAAATAA
Found at i:5218630 original size:21 final size:21
Alignment explanation
Indices: 5218604--5218645 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
5218594 GTATCGATAC
*
5218604 AATGTATCAATACATTTCCTT
1 AATGTACCAATACATTTCCTT
5218625 AATGTACCAATACATTTCCTT
1 AATGTACCAATACATTTCCTT
5218646 GACAGTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.40
Consensus pattern (21 bp):
AATGTACCAATACATTTCCTT
Found at i:5218703 original size:32 final size:32
Alignment explanation
Indices: 5218662--5218734 Score: 110
Period size: 32 Copynumber: 2.3 Consensus size: 32
5218652 AGCTTCGTAG
* *
5218662 CGATACATTGTATCAATATAAAACTTATGTAT
1 CGATACATTGTATCAATACAAAACTTATGCAT
* *
5218694 CGATACATTGTATCGATACAACACTTATGCAT
1 CGATACATTGTATCAATACAAAACTTATGCAT
5218726 CGATACATT
1 CGATACATT
5218735 TTCTGTTTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCAATACAAAACTTATGCAT
Found at i:5218707 original size:13 final size:13
Alignment explanation
Indices: 5218689--5218713 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5218679 ATAAAACTTA
5218689 TGTATCGATACAT
1 TGTATCGATACAT
5218702 TGTATCGATACA
1 TGTATCGATACA
5218714 ACACTTATGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5218761 original size:19 final size:19
Alignment explanation
Indices: 5218701--5218762 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
5218691 TATCGATACA
5218701 TTGTATCGATACAACACT-T
1 TTGTATCGATACAA-ACTGT
* * **
5218720 ATGCATCGATACATTTTCTGT
1 TTGTATCGATACA--AACTGT
5218741 TTGTATCGATACAAACTGT
1 TTGTATCGATACAAACTGT
5218760 TTG
1 TTG
5218763 AAATTCAAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
19 18 0.56
20 2 0.06
21 12 0.38
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (19 bp):
TTGTATCGATACAAACTGT
Found at i:5223013 original size:10 final size:9
Alignment explanation
Indices: 5222998--5223062 Score: 56
Period size: 8 Copynumber: 8.0 Consensus size: 9
5222988 GATAATTAAA
5222998 ATATAATAT
1 ATATAATAT
*
5223007 GATATAA-AA
1 -ATATAATAT
5223016 AT-TAAT--
1 ATATAATAT
5223022 ATA-AATAT
1 ATATAATAT
5223030 AT-TAATAT
1 ATATAATAT
5223038 AT-TAATAT
1 ATATAATAT
5223046 ATAT-ATAT
1 ATATAATAT
5223054 ATATAATAT
1 ATATAATAT
5223063 GAATTATTAA
Statistics
Matches: 47, Mismatches: 1, Indels: 15
0.75 0.02 0.24
Matches are distributed among these distances:
6 5 0.11
7 3 0.06
8 27 0.57
9 6 0.13
10 6 0.13
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (9 bp):
ATATAATAT
Found at i:5223025 original size:12 final size:14
Alignment explanation
Indices: 5223008--5223076 Score: 55
Period size: 14 Copynumber: 5.4 Consensus size: 14
5222998 ATATAATATG
5223008 ATATAAA-A-ATTA
1 ATATAAATATATTA
5223020 ATATAAATATATTA
1 ATATAAATATATTA
5223034 ATATATTAATATA-T-
1 ATATA--AATATATTA
5223048 ATAT--ATATA-TA
1 ATATAAATATATTA
*
5223059 ATATGAAT-TATTA
1 ATATAAATATATTA
5223072 ATATA
1 ATATA
5223077 TTAAAATTTA
Statistics
Matches: 48, Mismatches: 1, Indels: 15
0.75 0.02 0.23
Matches are distributed among these distances:
10 6 0.12
11 4 0.08
12 9 0.19
13 9 0.19
14 13 0.27
15 1 0.02
16 6 0.12
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (14 bp):
ATATAAATATATTA
Found at i:5223025 original size:22 final size:22
Alignment explanation
Indices: 5222997--5223056 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
5222987 AGATAATTAA
5222997 AATATAATATGATATAA-AAATT
1 AATATAATAT-ATATAATAAATT
*
5223019 AATATAA-ATATATTAATATATT
1 AATATAATATATA-TAATAAATT
5223041 AATATATATATATATA
1 AATATA-ATATATATA
5223057 TAATATGAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
20 3 0.09
21 5 0.15
22 17 0.52
23 3 0.09
24 5 0.15
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
AATATAATATATATAATAAATT
Found at i:5223036 original size:8 final size:8
Alignment explanation
Indices: 5223016--5223080 Score: 61
Period size: 8 Copynumber: 8.6 Consensus size: 8
5223006 TGATATAAAA
5223016 ATTAATAT
1 ATTAATAT
5223024 A--AATAT
1 ATTAATAT
5223030 ATTAATAT
1 ATTAATAT
5223038 ATTAATAT
1 ATTAATAT
5223046 A-T-ATAT
1 ATTAATAT
5223052 A-TATATAAT
1 ATTA-AT-AT
*
5223061 ATGAAT-T
1 ATTAATAT
5223068 ATTAATAT
1 ATTAATAT
5223076 ATTAA
1 ATTAA
5223081 AATTTATAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
6 12 0.25
7 7 0.15
8 23 0.48
9 5 0.10
10 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (8 bp):
ATTAATAT
Found at i:5223078 original size:38 final size:39
Alignment explanation
Indices: 5222992--5223093 Score: 113
Period size: 38 Copynumber: 2.7 Consensus size: 39
5222982 GTAAAAGATA
*
5222992 ATTAAAATA-TAATATGATATAAAAATTAATATAAATAT
1 ATTAATATATTAATATGATATAAAAATTAATATAAATAT
* * *
5223030 ATTAATATATTAATAT-ATATATATATATAATATGAAT-T
1 ATTAATATATTAATATGATATAAAAAT-TAATATAAATAT
* *
5223068 ATTAATATATTAAAAT-TTATAAAAAT
1 ATTAATATATTAATATGATATAAAAAT
5223094 AAAAATATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
38 39 0.72
39 15 0.28
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (39 bp):
ATTAATATATTAATATGATATAAAAATTAATATAAATAT
Found at i:5223409 original size:14 final size:15
Alignment explanation
Indices: 5223387--5223419 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5223377 AATGCAAATT
*
5223387 AAGGGAAAA-AAAAA
1 AAGGAAAAAGAAAAA
5223401 AAGGAAAAAGAAAAA
1 AAGGAAAAAGAAAAA
5223416 AAGG
1 AAGG
5223420 GCTTTAGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AAGGAAAAAGAAAAA
Found at i:5225645 original size:21 final size:21
Alignment explanation
Indices: 5225604--5225646 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
5225594 GTTGGGAAAG
* *
5225604 AAAAAAAAAAAATCTAGGAGA
1 AAAAAAAAAAAAACGAGGAGA
5225625 AAAAAAAAAAAAGACGA-GAGA
1 AAAAAAAAAAAA-ACGAGGAGA
5225646 A
1 A
5225647 TAAGGCCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.74, C:0.05, G:0.16, T:0.05
Consensus pattern (21 bp):
AAAAAAAAAAAAACGAGGAGA
Found at i:5226446 original size:19 final size:19
Alignment explanation
Indices: 5226422--5226459 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5226412 TATATAAATT
*
5226422 TAATTTAACGTTTTTTAAA
1 TAATTTAAAGTTTTTTAAA
*
5226441 TAATTTAAATTTTTTTAAA
1 TAATTTAAAGTTTTTTAAA
5226460 GTATGATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (19 bp):
TAATTTAAAGTTTTTTAAA
Found at i:5226500 original size:24 final size:23
Alignment explanation
Indices: 5226468--5226513 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
5226458 AAGTATGATT
5226468 TTTTATTTATAAAATTAATTTTA
1 TTTTATTTATAAAATTAATTTTA
* *
5226491 TTTTATTTTATTAAATTTATTTT
1 TTTTA-TTTATAAAATTAATTTT
5226514 TACATGTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTATTTATAAAATTAATTTTA
Found at i:5226769 original size:17 final size:18
Alignment explanation
Indices: 5226734--5226778 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 18
5226724 TTTAATTTAA
*
5226734 TTTTTTTAAGTAATTTAAT
1 TTTTTTTAAG-AATCTAAT
5226753 TTTTTTTAA-AATCTAAT
1 TTTTTTTAAGAATCTAAT
5226770 TTATTTTTA
1 TT-TTTTTA
5226779 TTTATAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 9 0.38
18 6 0.25
19 9 0.38
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTTTTTAAGAATCTAAT
Found at i:5226804 original size:23 final size:23
Alignment explanation
Indices: 5226722--5226818 Score: 81
Period size: 24 Copynumber: 4.2 Consensus size: 23
5226712 TAATTATACA
* ** *
5226722 AATTTAATTTAATTTTTTTAAGT
1 AATTTAATTTAATTTATAAAATT
*
5226745 AATTTAATTT--TTTTTAAAATCT
1 AATTTAATTTAATTTATAAAAT-T
* *
5226767 AATTTATTTTTATTTATAAAATT
1 AATTTAATTTAATTTATAAAATT
*
5226790 AATTTAATTTAATTTTATGAAATT
1 AATTTAATTTAA-TTTATAAAATT
*
5226814 TATTT
1 AATTT
5226819 TTATTTTATT
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
21 7 0.11
22 10 0.16
23 21 0.34
24 23 0.38
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (23 bp):
AATTTAATTTAATTTATAAAATT
Found at i:5226815 original size:20 final size:20
Alignment explanation
Indices: 5226790--5226827 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5226780 TTATAAAATT
5226790 AATTTAATTTAATTTTATGA
1 AATTTAATTTAATTTTATGA
* *
5226810 AATTTATTTTTATTTTAT
1 AATTTAATTTAATTTTAT
5226828 TATATATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (20 bp):
AATTTAATTTAATTTTATGA
Found at i:5230250 original size:13 final size:14
Alignment explanation
Indices: 5230232--5230263 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
5230222 AGAAAATTAA
5230232 TAAAATTTTAA-TT
1 TAAAATTTTAATTT
5230245 TAAAATTTTAATTT
1 TAAAATTTTAATTT
5230259 TAAAA
1 TAAAA
5230264 AACATAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAAAATTTTAATTT
Found at i:5230414 original size:131 final size:130
Alignment explanation
Indices: 5230237--5230482 Score: 390
Period size: 131 Copynumber: 1.9 Consensus size: 130
5230227 ATTAATAAAA
* *
5230237 TTTTAATTTAAAATTTTAATTTTAAAAAACATAATAATTAATATTTTAATTTGTTAATGTAAATT
1 TTTTAATTTAAAATTTTAATTTTAAAAAACATAATAACTAATATTTTAATTTGTTAATAT-AATT
*
5230302 -TTTTAAACTTAATTAAATATT-TTTTT-ATTTTATTAAAAATTATAATAAATATCCTTTTTTAT
65 GTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAATAATAATAAATATCCTTTTTTAT
5230364 T
130 T
* *
5230365 TTTTATTTTAAAATTTTTTATTTTTATAAAAACATAATAACTAATATTTTAATTTGTTAATATAA
1 TTTTAATTTAAAA--TTTTAATTTTA-AAAAACATAATAACTAATATTTTAATTTGTTAATATAA
5230430 TTGTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAATAATAATAA
63 TTGTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAATAATAATAA
5230483 TAAACCCTTT
Statistics
Matches: 107, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
128 12 0.11
130 14 0.13
131 55 0.51
132 5 0.05
133 21 0.20
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (130 bp):
TTTTAATTTAAAATTTTAATTTTAAAAAACATAATAACTAATATTTTAATTTGTTAATATAATTG
TTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAATAATAATAAATATCCTTTTTTATT
Found at i:5230512 original size:131 final size:128
Alignment explanation
Indices: 5230250--5230577 Score: 369
Period size: 131 Copynumber: 2.6 Consensus size: 128
5230240 TAATTTAAAA
* *
5230250 TTTTAATTTTAAAAAACATAATAATTAATATTTTAATTTGTTAATGTAAATTTTTTAAACTTAAT
1 TTTTAATTTTAAAAAACATAATAACTAATATTTTAATTTGTTAATATAAATTTTTTAAACTTAAT
* * * * *
5230315 TAAATATTTTTTTATTTTATTAAAAATTATAATAAATATCCTTTTTTATTTTTTATTTTAAAATT
66 TAAATATTTTTTTATTTTATTAAAAATAATAATAAAAACCCTTTTTAATTTATTATTTT--AATT
*
5230380 TTTTATTTTTATAAAAACATAATAACTAATATTTTAATTTGTTAATAT-AATTGTTTTAAACTTA
1 TTTTAATTTTA-AAAAACATAATAACTAATATTTTAATTTGTTAATATAAATT-TTTTAAACTTA
5230444 ATTAAATATTATTTTTAATTTTATTAAAAATAATAATAATAAACCC---TT--TTTA--A-TTTA
64 ATTAAATATT-TTTTT-ATTTTATTAAAAATAATAATAA-AAACCCTTTTTAATTTATTATTTTA
5230501 ATT
126 ATT
* * * *
5230504 TTTT-ATTTT--TAAA-A-AATAACTAATATTTTAATTTATTAATGTAAATTTTTTTAAAGTTAA
1 TTTTAATTTTAAAAAACATAATAACTAATATTTTAATTTGTTAATATAAA-TTTTTTAAACTTAA
*
5230564 TTAAATATTATTTT
65 TTAAATATTTTTTT
5230578 CATTAAAAAA
Statistics
Matches: 178, Mismatches: 13, Indels: 26
0.82 0.06 0.12
Matches are distributed among these distances:
118 30 0.17
119 23 0.13
120 5 0.03
123 4 0.02
124 8 0.04
126 3 0.02
127 1 0.01
129 3 0.02
130 14 0.08
131 57 0.32
132 5 0.03
133 21 0.12
134 4 0.02
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (128 bp):
TTTTAATTTTAAAAAACATAATAACTAATATTTTAATTTGTTAATATAAATTTTTTAAACTTAAT
TAAATATTTTTTTATTTTATTAAAAATAATAATAAAAACCCTTTTTAATTTATTATTTTAATT
Found at i:5232573 original size:34 final size:34
Alignment explanation
Indices: 5232518--5232734 Score: 276
Period size: 34 Copynumber: 6.4 Consensus size: 34
5232508 TGGTATAAAA
* *
5232518 TGTTGATTAAAT-GGTGATTTGGTAGTTTACAAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * *
5232551 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* *
5232585 TGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* **
5232619 TGTTGATTAAATGAGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* *
5232653 TATTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * *
5232687 TGTTGACTAAAT-GGTAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGT-GATTTGGTAGCTTACCAT
5232721 TGTTGATTAAATGG
1 TGTTGATTAAATGG
5232735 TGGTTTTTAC
Statistics
Matches: 159, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
33 15 0.09
34 143 0.90
35 1 0.01
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.41
Consensus pattern (34 bp):
TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
Found at i:5232710 original size:102 final size:101
Alignment explanation
Indices: 5232518--5232734 Score: 335
Period size: 102 Copynumber: 2.1 Consensus size: 101
5232508 TGGTATAAAA
** * * * *
5232518 TGTTGATTAAATGGTGATTTGGTAGTTTACAATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGAAATTTGGTAGCTTACAATTATTGATTAAATGGGTGATTTGGTGGCTTACC
5232583 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
66 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
*
5232619 TGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
1 TGTTGATTAAATG-GAAATTTGGTAGCTTACAATTATTGATTAAATGGGTGATTTGGTGGCTTAC
* * *
5232684 CATTGTTGACTAAATGGTAGATTTGGTAGGTTGCCAT
65 CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
5232721 TGTTGATTAAATGG
1 TGTTGATTAAATGG
5232735 TGGTTTTTAC
Statistics
Matches: 105, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
101 14 0.13
102 91 0.87
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.41
Consensus pattern (101 bp):
TGTTGATTAAATGGAAATTTGGTAGCTTACAATTATTGATTAAATGGGTGATTTGGTGGCTTACC
ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:5233270 original size:29 final size:28
Alignment explanation
Indices: 5233238--5233310 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 28
5233228 GTTATGAATA
*
5233238 TTTAATTTTATTAAATTATATTATTGAT
1 TTTAATTTTATTAAATTAGATTATTGAT
* *
5233266 TTTTATTATT-TATAAATTAGATTATTTAT
1 TTTAATT-TTAT-TAAATTAGATTATTGAT
*
5233295 ATTAATTTTATTAAAT
1 TTTAATTTTATTAAAT
5233311 AATTTTAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
28 14 0.38
29 23 0.62
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (28 bp):
TTTAATTTTATTAAATTAGATTATTGAT
Found at i:5234946 original size:22 final size:20
Alignment explanation
Indices: 5234917--5234969 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
5234907 ATTTGATATG
*
5234917 AATATAAAATATAATTTTTAA
1 AATATAAAATAT-ATTTATAA
*
5234938 ATATATAAAAAATATTTATAA
1 A-ATATAAAATATATTTATAA
*
5234959 AATAAAAAATA
1 AATATAAAATA
5234970 ATCATATCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 8 0.30
21 9 0.33
22 10 0.37
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AATATAAAATATATTTATAA
Found at i:5235292 original size:2 final size:2
Alignment explanation
Indices: 5235280--5235320 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
5235270 TATAGTCATC
*
5235280 TA TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5235321 TGATAAGCTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5235534 original size:11 final size:11
Alignment explanation
Indices: 5235499--5235543 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
5235489 TTATCAATTC
*
5235499 AAATAAAA-AC
1 AAATAAAATAA
5235509 AAATAAAAT--
1 AAATAAAATAA
*
5235518 AAATAAATTAA
1 AAATAAAATAA
5235529 AAATAAAATAA
1 AAATAAAATAA
5235540 AAAT
1 AAAT
5235544 TACTGATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
9 8 0.27
10 8 0.27
11 14 0.47
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:5237223 original size:16 final size:16
Alignment explanation
Indices: 5237204--5237244 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
5237194 TTTTTTTCAT
*
5237204 TTTTTTTTCAATTTTC
1 TTTTTTTTCAATTTTA
*
5237220 TTTTTTTTTAATTTTA
1 TTTTTTTTCAATTTTA
*
5237236 ATTTTTTTC
1 TTTTTTTTC
5237245 TTCTTTTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTTTTCAATTTTA
Found at i:5237240 original size:17 final size:17
Alignment explanation
Indices: 5237197--5237243 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
5237187 TTCACTTTTT
5237197 TTTTCATTTTTTTTTCAA
1 TTTT-ATTTTTTTTTCAA
*
5237215 TTTTCTTTTTTTTT-AA
1 TTTTATTTTTTTTTCAA
5237231 TTTTAATTTTTTT
1 TTTT-ATTTTTTT
5237244 CTTCTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 6 0.23
17 16 0.62
18 4 0.15
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTATTTTTTTTTCAA
Found at i:5238298 original size:41 final size:41
Alignment explanation
Indices: 5238226--5238341 Score: 171
Period size: 41 Copynumber: 2.8 Consensus size: 41
5238216 GAAACTTTTT
*
5238226 TTTTGATAAGGCGTGGGCACGCTAA-GAAAACAGAAGCTCTC
1 TTTTGATAAGGCGTGGGCACGTTAATG-AAACAGAAGCTCTC
* *
5238267 TTTTGATAAGGCGTGGACACGTTAATGAAACATAAGCTCTC
1 TTTTGATAAGGCGTGGGCACGTTAATGAAACAGAAGCTCTC
* *
5238308 GTTTGATAAGGCGTGGGCACGTTAATAAAACAGA
1 TTTTGATAAGGCGTGGGCACGTTAATGAAACAGA
5238342 GTTTCTGTTT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 66 0.99
42 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (41 bp):
TTTTGATAAGGCGTGGGCACGTTAATGAAACAGAAGCTCTC
Found at i:5243139 original size:167 final size:164
Alignment explanation
Indices: 5242943--5243272 Score: 430
Period size: 166 Copynumber: 2.0 Consensus size: 164
5242933 TAATCAAACC
* * *
5242943 AATCAAAAATTTTACTTTATTAGTTATTTTAATTTTAAATGATTTATTTAAAAAAGTTGGACTGT
1 AATCAAAAATTTTACTTTATTAATTATTTTAACTTTAAATGATTTATTTAAAAAAGTT--A-TCT
* * * * ** *
5243008 AC-GTTAACATACAAG-TCAATTTAAGATTTCTACTTGGCTTGTATGAAAAAATTTTAAAAATAA
63 ACAGTTAACATA-AAGATCAATTTAAAATTTATACCTGACTCATATGAAAAAAATTTAAAAATAA
5243071 TTTTTTATTAATTATTTTTATTATATTTTAAAATGATTT
127 TTTTTTATTAATTATTTTTATTA-ATTTTAAAATGATTT
* *
5243110 AATCTAAAATTTTACTTTATTAATTATTTTAACTTTAAATGATTTATTTAAATAAGTTATCTACA
1 AATCAAAAATTTTACTTTATTAATTATTTTAACTTTAAATGATTTATTTAAAAAAGTTATCTACA
* ** ** *
5243175 TGTTAACTTATTGATTGATTTAAAATTTATACCTGACTCATTTGAAAAAAATTTAAAAATAATTT
66 -GTTAACATAAAGATCAATTTAAAATTTATACCTGACTCATATGAAAAAAATTTAAAAATAATTT
5243240 TTTATTAATTATTTTTATTAATTTTAAAATGAT
130 TTTATTAATTATTTTTATTAATTTTAAAATGAT
5243273 ATATTTAAAG
Statistics
Matches: 142, Mismatches: 18, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
164 4 0.03
165 15 0.11
166 69 0.49
167 54 0.38
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.48
Consensus pattern (164 bp):
AATCAAAAATTTTACTTTATTAATTATTTTAACTTTAAATGATTTATTTAAAAAAGTTATCTACA
GTTAACATAAAGATCAATTTAAAATTTATACCTGACTCATATGAAAAAAATTTAAAAATAATTTT
TTATTAATTATTTTTATTAATTTTAAAATGATTT
Found at i:5243256 original size:13 final size:13
Alignment explanation
Indices: 5243238--5243262 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5243228 TAAAAATAAT
5243238 TTTTTATTAATTA
1 TTTTTATTAATTA
5243251 TTTTTATTAATT
1 TTTTTATTAATT
5243263 TTAAAATGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTATTAATTA
Found at i:5245737 original size:21 final size:20
Alignment explanation
Indices: 5245694--5245738 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
5245684 GATACATTAG
**
5245694 TTTAATGAAAAAATATATTT
1 TTTAATGAAAAAATATAACT
*
5245714 TTTAGATGAAAAAATGTAACT
1 TTTA-ATGAAAAAATATAACT
5245735 TTTA
1 TTTA
5245739 TAACCAAAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (20 bp):
TTTAATGAAAAAATATAACT
Found at i:5250705 original size:21 final size:21
Alignment explanation
Indices: 5250666--5250706 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5250656 CATTGGTTGA
* **
5250666 ATGAAATAATGCATTTTTTAG
1 ATGAAAAAATGCAACTTTTAG
5250687 ATGAAAAAATGCAACTTTTA
1 ATGAAAAAATGCAACTTTTA
5250707 TAACCAAAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (21 bp):
ATGAAAAAATGCAACTTTTAG
Found at i:5251211 original size:20 final size:21
Alignment explanation
Indices: 5251186--5251227 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
5251176 CTCAACTACC
*
5251186 AAAGAAAAAAAA-TAAAGAAA
1 AAAGAAAAAAAAGGAAAGAAA
5251206 AAAGAAAAAAAAGGAAAGAAA
1 AAAGAAAAAAAAGGAAAGAAA
5251227 A
1 A
5251228 GATAGTAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (21 bp):
AAAGAAAAAAAAGGAAAGAAA
Found at i:5251909 original size:21 final size:21
Alignment explanation
Indices: 5251861--5251911 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
5251851 CTGACATGCA
* *
5251861 TAAAGTATCGATACTTTAGCT
1 TAAAGTATCGATACATGAGCT
* * *
5251882 CAGAGTATCGATACATGAGGT
1 TAAAGTATCGATACATGAGCT
5251903 TAAAGTATC
1 TAAAGTATC
5251912 AAAACTTTGA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (21 bp):
TAAAGTATCGATACATGAGCT
Found at i:5253212 original size:30 final size:30
Alignment explanation
Indices: 5253178--5253273 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
5253168 ATTTTAAGGT
5253178 CATTTAGGTTATTCTCCATAATCTGAGGAC
1 CATTTAGGTTATTCTCCATAATCTGAGGAC
** * * * **
5253208 CATTTA-GCAATTCT-TATGCATTTGAGGGT
1 CATTTAGGTTATTCTCCAT-AATCTGAGGAC
*
5253237 CATTTAAGTTATTCTCCATAATCT-AGGGAC
1 CATTTAGGTTATTCTCCATAATCTGA-GGAC
5253267 CATTTAG
1 CATTTAG
5253274 TAACTTCACT
Statistics
Matches: 47, Mismatches: 15, Indels: 8
0.67 0.21 0.11
Matches are distributed among these distances:
28 2 0.04
29 20 0.43
30 23 0.49
31 2 0.04
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.39
Consensus pattern (30 bp):
CATTTAGGTTATTCTCCATAATCTGAGGAC
Found at i:5253264 original size:29 final size:30
Alignment explanation
Indices: 5253175--5253264 Score: 78
Period size: 29 Copynumber: 3.1 Consensus size: 30
5253165 TGCATTTTAA
*
5253175 GGTCATTTAGGTTATTCTCCATAATCTGAG
1 GGTCATTTAAGTTATTCTCCATAATCTGAG
** ** * * *
5253205 GACCATTT-AGCAATTCT-TATGCATTTGAG
1 GGTCATTTAAGTTATTCTCCAT-AATCTGAG
5253234 GGTCATTTAAGTTATTCTCCATAATCT-AG
1 GGTCATTTAAGTTATTCTCCATAATCTGAG
5253263 GG
1 GG
5253265 ACCATTTAGT
Statistics
Matches: 42, Mismatches: 15, Indels: 7
0.66 0.23 0.11
Matches are distributed among these distances:
28 2 0.05
29 22 0.52
30 16 0.38
31 2 0.05
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (30 bp):
GGTCATTTAAGTTATTCTCCATAATCTGAG
Found at i:5253345 original size:118 final size:117
Alignment explanation
Indices: 5253086--5253368 Score: 299
Period size: 118 Copynumber: 2.4 Consensus size: 117
5253076 GCAAAATATA
* * * * * *
5253086 AGGATCATTAAGCAATTTTCATGCATCTTAAGGTCATTTAAATTATTTCCCATAGTCTAGGGACC
1 AGGACCATTTAGCATTTTTCATGCATCTTAGGGTCATTTAAGTTATTTCCCATAATCTAGGGACC
* * *
5253151 ATTAGCAACTTCAATGCATTTTAAGGTCATTTAGGTTATTCTCCATAATCTG
66 ATTAGCAACTTCAATACAATTTAAGGTCAGTTAGGTTATTCTCCATAATCTG
*
5253203 AGGACCATTTAGCAATTCTT-ATGCAT-TTGAGGGTCATTTAAGTTA-TTCTCCATAATCTAGGG
1 AGGACCATTTAGC-ATTTTTCATGCATCTT-AGGGTCATTTAAGTTATTTC-CCATAATCTAGGG
* * * *
5253265 ACCATTTAGTAACTTCACTACAATTTAGGGAT-AGTTAGGTTGCTTC-CCATAATCT-
63 ACCA-TTAGCAACTTCAATACAATTTAAGG-TCAGTTAGGTT-ATTCTCCATAATCTG
* * * *
5253320 AGGGGCCATTTAGCATTTTTCATGCATGTTAGGGCCATTTAGGTTATTT
1 A-GGACCATTTAGCATTTTTCATGCATCTTAGGGTCATTTAAGTTATTT
5253369 TATATACTCT
Statistics
Matches: 138, Mismatches: 18, Indels: 18
0.79 0.10 0.10
Matches are distributed among these distances:
116 5 0.04
117 53 0.38
118 72 0.52
119 8 0.06
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (117 bp):
AGGACCATTTAGCATTTTTCATGCATCTTAGGGTCATTTAAGTTATTTCCCATAATCTAGGGACC
ATTAGCAACTTCAATACAATTTAAGGTCAGTTAGGTTATTCTCCATAATCTG
Found at i:5253362 original size:59 final size:57
Alignment explanation
Indices: 5253103--5253367 Score: 227
Period size: 59 Copynumber: 4.5 Consensus size: 57
5253093 TTAAGCAATT
* ** * *
5253103 TTCATGCATCTTAAGGTCATTTAAATTATT-TCCCATAGTCTAGGGACCA-TTAGCAAC
1 TTCATGCAT-TTAGGGTCATTTAGGTTATTCT-CCATAATCTAGGGACCATTTAGCATC
*
5253160 TTCAATGCATTTTAAGGTCATTTAGGTTATTCTCCATAATCT-GAGGACCATTTAGCAATTC
1 TTC-ATGCA-TTTAGGGTCATTTAGGTTATTCTCCATAATCTAG-GGACCATTTAGC-A-TC
* * *
5253221 TT-ATGCATTTGAGGGTCATTTAAGTTATTCTCCATAATCTAGGGACCATTTAGTAAC
1 TTCATGCATTT-AGGGTCATTTAGGTTATTCTCCATAATCTAGGGACCATTTAGCATC
* * * * *
5253278 TTCACTACAATTTAGGGAT-AGTTAGGTTGCTTC-CCATAATCTAGGGGCCATTTAGCATTT
1 TTCA-TGC-ATTTAGGG-TCATTTAGGTT-ATTCTCCATAATCTAGGGACCATTTAGCA-TC
*
5253338 TTCATGCATGTTAGGGCCATTTAGGTTATT
1 TTCATGCAT-TTAGGGTCATTTAGGTTATT
5253368 TTATATACTC
Statistics
Matches: 171, Mismatches: 20, Indels: 33
0.76 0.09 0.15
Matches are distributed among these distances:
57 7 0.04
58 46 0.27
59 101 0.59
60 14 0.08
61 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (57 bp):
TTCATGCATTTAGGGTCATTTAGGTTATTCTCCATAATCTAGGGACCATTTAGCATC
Found at i:5253398 original size:59 final size:60
Alignment explanation
Indices: 5253335--5253509 Score: 174
Period size: 60 Copynumber: 2.9 Consensus size: 60
5253325 CCATTTAGCA
* * * * *
5253335 TTTTTCATGCATGTTAGGGCCATTTAGGTTATTTTATATACTCTAAGG-TAGCTTTA-GTT
1 TTTTTCATGCATTTTAGGGCCATTTAGGTTATTTTACATAATATAAGGTTA-CTTTACATT
* * ** * * *
5253394 TTTTTCTTACATTTTAGGAACATGTAGGCTATTTTACATAATATAGGGTTACTTTACATT
1 TTTTTCATGCATTTTAGGGCCATTTAGGTTATTTTACATAATATAAGGTTACTTTACATT
** * * *
5253454 TTTTTCATGCATTTTAAAGCCATTTAGATTATTTTACATAATTTAAGGTTATTTTA
1 TTTTTCATGCATTTTAGGGCCATTTAGGTTATTTTACATAATATAAGGTTACTTTA
5253510 GAAATTTTCA
Statistics
Matches: 90, Mismatches: 24, Indels: 3
0.77 0.21 0.03
Matches are distributed among these distances:
59 42 0.47
60 48 0.53
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.49
Consensus pattern (60 bp):
TTTTTCATGCATTTTAGGGCCATTTAGGTTATTTTACATAATATAAGGTTACTTTACATT
Found at i:5255007 original size:13 final size:13
Alignment explanation
Indices: 5254991--5255022 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
5254981 CATTTTTTTC
5254991 TTTTTTTTTTGTT
1 TTTTTTTTTTGTT
*
5255004 TTTTTGTTTTGTT
1 TTTTTTTTTTGTT
5255017 TTTTTT
1 TTTTTT
5255023 AAAAGTCCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (13 bp):
TTTTTTTTTTGTT
Found at i:5255726 original size:13 final size:13
Alignment explanation
Indices: 5255710--5255740 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5255700 CATTTTTTTC
5255710 TTTTTTTTTGTTT
1 TTTTTTTTTGTTT
*
5255723 TTTTGTTTTGTTT
1 TTTTTTTTTGTTT
5255736 TTTTT
1 TTTTT
5255741 AAAAGTCCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (13 bp):
TTTTTTTTTGTTT
Found at i:5256444 original size:13 final size:13
Alignment explanation
Indices: 5256428--5256458 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5256418 CATTTTTTTC
5256428 TTTTTTTTTGTTT
1 TTTTTTTTTGTTT
*
5256441 TTTTGTTTTGTTT
1 TTTTTTTTTGTTT
5256454 TTTTT
1 TTTTT
5256459 AAAAGTCCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (13 bp):
TTTTTTTTTGTTT
Found at i:5256942 original size:717 final size:719
Alignment explanation
Indices: 5254914--5257660 Score: 5457
Period size: 718 Copynumber: 3.8 Consensus size: 719
5254904 ACTTATAGAA
5254914 TAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGAGTAATCTCCTAGGAAGTGCTCGTATTGCACC
1 TAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGAGTAATCTCCTAGGAAGTGCTCGTATTGCACC
5254979 CCCATTTTTTTCTTTTTTTTTTGTTTTTTTGTTTTGTTTTTTTTAAAAGTCCAAATTAAAAGAAA
66 CCCATTTTTTTCTTTTTTTTTTGTTTTTTTGTTTTGTTTTTTTTAAAAGTCCAAATTAAAAGAAA
5255044 GAAAAAAAAACCCAACTAATCCGAATCTTACAAATCTAAATCAAAGATGGCCTGATTAATTAAAA
131 GAAAAAAAAACCCAACTAATCCGAATCTTACAAATCTAAATCAAAGATGGCCTGATTAATTAAAA
5255109 ACAAGTGTGCCAAAAATGGCAAGACAAAATTTGGTATCTACAGATAATAAGTAATATAGTACTAG
196 ACAAGTGTGCCAAAAATGGCAAGACAAAATTTGGTATCTACAGATAATAAGTAATATAGTACTAG
5255174 CATATTAGAATTGTACTTAAACCATAAATTTGAGTTAAGATAAATATTCATTAAAATATACGCTA
261 CATATTAGAATTGTACTTAAACCATAAATTTGAGTTAAGATAAATATTCATTAAAATATACGCTA
5255239 AATTAAGCTTCATCATCATCATCATCGTTGTTTTTGTCATCTTGAACATCATCATCGAGTTGTCC
326 AATTAAGCTTCATCATCATCATCATCGTTGTTTTTGTCATCTTGAACATCATCATCGAGTTGTCC
5255304 ATGAGCTACTAGTGGAACCTCTGATGGTGGGTTCAGAACCTGAATTCCCATACCTCTTAATGCAT
391 ATGAGCTACTAGTGGAACCTCTGATGGTGGGTTCAGAACCTGAATTCCCATACCTCTTAATGCAT
5255369 CCTGGAGGCGAGCTAGTAGAATATCATCCAATCGTTGCATTACTTGATTTAAAATCTGATCCACG
456 CCTGGAGGCGAGCTAGTAGAATATCATCCAATCGTTGCATTACTTGATTTAAAATCTGATCCACG
5255434 TGTTCAGTCGAAATTGGAGGACATCTAGAAGTAGCAAAAATATATGAAGATGACCTTGAATAAGA
521 TGTTCAGTCGAAATTGGAGGACATCTAGAAGTAGCAAAAATATATGAAGATGACCTTGAATAAGA
*
5255499 AACAATGCTTTAAGGTGGTTAAGATTGGTCCAAACAAAATAAGAAATAATTGCATTTGTAGTTTG
586 AACAATGCCTTAAGGTGGTTAAGATTGGTCCAAACAAAATAAGAAATAATTGCATTTGTAGTTTG
5255564 TTGTTGCATCAAAGGATGGATGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCTG
651 TTGTTGCATCAAAGGATGGATGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCTG
5255629 CAGT
716 CAGT
5255633 TAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGAGTAATCTCCTAGGAAGTGCTCGTATTGCACC
1 TAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGAGTAATCTCCTAGGAAGTGCTCGTATTGCACC
5255698 CCCATTTTTTTC-TTTTTTTTTGTTTTTTTGTTTTGTTTTTTTTAAAAGTCCAAATTAAAAGAAA
66 CCCATTTTTTTCTTTTTTTTTTGTTTTTTTGTTTTGTTTTTTTTAAAAGTCCAAATTAAAAGAAA
5255762 GAAAAAAAAACCCAACTAATCCGAATCTTACAAATCTAAATCAAAGATGGCCTGATTAATTAAAA
131 GAAAAAAAAACCCAACTAATCCGAATCTTACAAATCTAAATCAAAGATGGCCTGATTAATTAAAA
5255827 ACAAGTGTGCCAAAAATGGCAAGACAAAATTTGGTATCTACAGATAATAAGTAATATAGTACTAG
196 ACAAGTGTGCCAAAAATGGCAAGACAAAATTTGGTATCTACAGATAATAAGTAATATAGTACTAG
5255892 CATATTAGAATTGTACTTAAACCATAAATTTGAGTTAAGATAAATATTCATTAAAATATACGCTA
261 CATATTAGAATTGTACTTAAACCATAAATTTGAGTTAAGATAAATATTCATTAAAATATACGCTA
5255957 AATTAAGCTTCATCATCATCATCATCGTTGTTTTTGTCATCTTGAACATCATCATCGAGTTGTCC
326 AATTAAGCTTCATCATCATCATCATCGTTGTTTTTGTCATCTTGAACATCATCATCGAGTTGTCC
5256022 ATGAGCTACTAGTGGAACCTCTGATGGTGGGTTCAGAACCTGAATTCCCATACCTCTTAATGCAT
391 ATGAGCTACTAGTGGAACCTCTGATGGTGGGTTCAGAACCTGAATTCCCATACCTCTTAATGCAT
5256087 CCTGGAGGCGAGCTAGTAGAATATCATCCAATCGTTGCATTACTTGATTTAAAATCTGATCCACG
456 CCTGGAGGCGAGCTAGTAGAATATCATCCAATCGTTGCATTACTTGATTTAAAATCTGATCCACG
5256152 TGTTCAGTCGAAATTGGAGGACATCTAGAAGTAGCAAAAATATATGAAGATGACCTTGAATAAGA
521 TGTTCAGTCGAAATTGGAGGACATCTAGAAGTAGCAAAAATATATGAAGATGACCTTGAATAAGA
5256217 AACAATGCCTTAAGGTGGTTAAGATTGGTCCAAACAAAATAAGAAATAATTGCATTTGTAGTTTG
586 AACAATGCCTTAAGGTGGTTAAGATTGGTCCAAACAAAATAAGAAATAATTGCATTTGTAGTTTG
5256282 TTGTTGCATCAAAGGATGGATGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCTG
651 TTGTTGCATCAAAGGATGGATGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCTG
5256347 CAGT
716 CAGT
5256351 TAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGAGTAATCTCCTAGGAAGTGCTCGTATTGCACC
1 TAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGAGTAATCTCCTAGGAAGTGCTCGTATTGCACC
5256416 CCCATTTTTTTC-TTTTTTTTTGTTTTTTTGTTTTGTTTTTTTTAAAAGTCCAAATTAAAAGAAA
66 CCCATTTTTTTCTTTTTTTTTTGTTTTTTTGTTTTGTTTTTTTTAAAAGTCCAAATTAAAAGAAA
5256480 G-AAAAAAAACCCAACTAATCCGAATCTTACAAATCTAAATCAAAGATGGCCTGATTAATTAAAA
131 GAAAAAAAAACCCAACTAATCCGAATCTTACAAATCTAAATCAAAGATGGCCTGATTAATTAAAA
5256544 ACAAGTGTGCCAAAAATGGCAAGACAAAATTTGGTATCTACAGATAATAAGTAATATAGTACTAG
196 ACAAGTGTGCCAAAAATGGCAAGACAAAATTTGGTATCTACAGATAATAAGTAATATAGTACTAG
5256609 CATATTAGAATTGTACTTAAACCATAAATTTGAGTTAAGATAAATATTCATTAAAATATACGCTA
261 CATATTAGAATTGTACTTAAACCATAAATTTGAGTTAAGATAAATATTCATTAAAATATACGCTA
5256674 AATTAAGCTTCATCATCATCATCATCGTTGTTTTTGTCATCTTGAACATCATCATCGAGTTGTCC
326 AATTAAGCTTCATCATCATCATCATCGTTGTTTTTGTCATCTTGAACATCATCATCGAGTTGTCC
5256739 ATGAGCTACTAGTGGAACCTCTGATGGTGGGTTCAGAACCTGAATTCCCATACCTCTTAATGCAT
391 ATGAGCTACTAGTGGAACCTCTGATGGTGGGTTCAGAACCTGAATTCCCATACCTCTTAATGCAT
5256804 CCTGGAGGCGAGCTAGTAGAATATCATCCAATCGTTGCATTACTTGATTTAAAATCTGATCCACG
456 CCTGGAGGCGAGCTAGTAGAATATCATCCAATCGTTGCATTACTTGATTTAAAATCTGATCCACG
5256869 TGTTCAGTCGAAATTGGAGGACATCTAGAAGTAGCAAAAATATATGAAGATGACCTTGAATAAGA
521 TGTTCAGTCGAAATTGGAGGACATCTAGAAGTAGCAAAAATATATGAAGATGACCTTGAATAAGA
5256934 AACAATGCCTTAAGGTGGTTAAGATTGGTCCAAACAAAATAAGAAATAATTGCATTTGTAGTTTG
586 AACAATGCCTTAAGGTGGTTAAGATTGGTCCAAACAAAATAAGAAATAATTGCATTTGTAGTTTG
5256999 TTGTTGCATCAAAGGATGGATGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCTG
651 TTGTTGCATCAAAGGATGGATGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCTG
5257064 CAGT
716 CAGT
5257068 TAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGAGTAATCTCCTAGGAAGTGCTCGTATTGCACC
1 TAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGAGTAATCTCCTAGGAAGTGCTCGTATTGCACC
5257133 CCCATTTTTTTCTTTTTTTTTTGTTTTTTTGTTTTGTTTTTTTTAAAAGTCCAAATTAAAAGAAA
66 CCCATTTTTTTCTTTTTTTTTTGTTTTTTTGTTTTGTTTTTTTTAAAAGTCCAAATTAAAAGAAA
5257198 -AAAAAAAAACCCAACTAATCCGAATCTTACAAATCTAAATCAAAGATGGCCTGATTAATTAAAA
131 GAAAAAAAAACCCAACTAATCCGAATCTTACAAATCTAAATCAAAGATGGCCTGATTAATTAAAA
5257262 ACAAGTGTGCCAAAAATGGCAAGACAAAATTTGGTATCTACAGATAATAAGTAATATAGTACTAG
196 ACAAGTGTGCCAAAAATGGCAAGACAAAATTTGGTATCTACAGATAATAAGTAATATAGTACTAG
5257327 CATATTAGAATTGTACTTAAACCATAAATTTGAGTTAAGATAAATATTCATTAAAATATACGCTA
261 CATATTAGAATTGTACTTAAACCATAAATTTGAGTTAAGATAAATATTCATTAAAATATACGCTA
5257392 AATTAAGCTTCATCATCATCATCATCGTTGTTTTTGTCATCTTGAACATCATCATCGAGTTGTCC
326 AATTAAGCTTCATCATCATCATCATCGTTGTTTTTGTCATCTTGAACATCATCATCGAGTTGTCC
5257457 ATGAGCTACTAGTGGAACCTCTGATGGTGGGTTCAGAACCTGAATTCCCATACCTCTTAATGCAT
391 ATGAGCTACTAGTGGAACCTCTGATGGTGGGTTCAGAACCTGAATTCCCATACCTCTTAATGCAT
5257522 CCTGGAGGCGAGCTAGTAGAATATCATCCAATCGTTGCATTACTTGATTTAAAATCTGATCCACG
456 CCTGGAGGCGAGCTAGTAGAATATCATCCAATCGTTGCATTACTTGATTTAAAATCTGATCCACG
5257587 TGTTCAGTCGAAATTGGAGGACATCTAGAAGTAGCAAAAATATATGAAGATGACCTTGAATAAGA
521 TGTTCAGTCGAAATTGGAGGACATCTAGAAGTAGCAAAAATATATGAAGATGACCTTGAATAAGA
5257652 AACAATGCC
586 AACAATGCC
5257661 AAGTATATCT
Statistics
Matches: 2025, Mismatches: 1, Indels: 5
1.00 0.00 0.00
Matches are distributed among these distances:
717 664 0.33
718 1284 0.63
719 77 0.04
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (719 bp):
TAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGAGTAATCTCCTAGGAAGTGCTCGTATTGCACC
CCCATTTTTTTCTTTTTTTTTTGTTTTTTTGTTTTGTTTTTTTTAAAAGTCCAAATTAAAAGAAA
GAAAAAAAAACCCAACTAATCCGAATCTTACAAATCTAAATCAAAGATGGCCTGATTAATTAAAA
ACAAGTGTGCCAAAAATGGCAAGACAAAATTTGGTATCTACAGATAATAAGTAATATAGTACTAG
CATATTAGAATTGTACTTAAACCATAAATTTGAGTTAAGATAAATATTCATTAAAATATACGCTA
AATTAAGCTTCATCATCATCATCATCGTTGTTTTTGTCATCTTGAACATCATCATCGAGTTGTCC
ATGAGCTACTAGTGGAACCTCTGATGGTGGGTTCAGAACCTGAATTCCCATACCTCTTAATGCAT
CCTGGAGGCGAGCTAGTAGAATATCATCCAATCGTTGCATTACTTGATTTAAAATCTGATCCACG
TGTTCAGTCGAAATTGGAGGACATCTAGAAGTAGCAAAAATATATGAAGATGACCTTGAATAAGA
AACAATGCCTTAAGGTGGTTAAGATTGGTCCAAACAAAATAAGAAATAATTGCATTTGTAGTTTG
TTGTTGCATCAAAGGATGGATGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCTG
CAGT
Found at i:5257161 original size:13 final size:13
Alignment explanation
Indices: 5257145--5257176 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
5257135 CATTTTTTTC
5257145 TTTTTTTTTTGTT
1 TTTTTTTTTTGTT
*
5257158 TTTTTGTTTTGTT
1 TTTTTTTTTTGTT
5257171 TTTTTT
1 TTTTTT
5257177 AAAAGTCCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (13 bp):
TTTTTTTTTTGTT
Found at i:5258919 original size:27 final size:27
Alignment explanation
Indices: 5258881--5258953 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
5258871 CTATATTAAC
*
5258881 TGGTTCAGTAGGCTCGATAGCAGTGGG
1 TGGTTCAGTAGGCTCGACAGCAGTGGG
* **
5258908 TGGTTTAGTAGGCTTAACAGCAGTGGG
1 TGGTTCAGTAGGCTCGACAGCAGTGGG
* *
5258935 TTGTTCAATAGGCTCGACA
1 TGGTTCAGTAGGCTCGACA
5258954 ACTGAAGGGT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.22, C:0.15, G:0.34, T:0.29
Consensus pattern (27 bp):
TGGTTCAGTAGGCTCGACAGCAGTGGG
Found at i:5259499 original size:18 final size:18
Alignment explanation
Indices: 5259456--5259503 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
5259446 CAAATAAATG
* *
5259456 ATCATCATTTTCATCATC
1 ATCATCATCTTCATAATC
5259474 ATCATCATCTTCATAATC
1 ATCATCATCTTCATAATC
5259492 AT-ATTCATCTTC
1 ATCA-TCATCTTC
5259504 TTCATCACCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 1 0.04
18 26 0.96
ACGTcount: A:0.29, C:0.27, G:0.00, T:0.44
Consensus pattern (18 bp):
ATCATCATCTTCATAATC
Found at i:5265439 original size:26 final size:26
Alignment explanation
Indices: 5265404--5265462 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
5265394 TATATTGACA
5265404 TAAAAATTTTAATAAAAATAAAT-AAT
1 TAAAAATTTTAA-AAAAATAAATAAAT
* * *
5265430 TAAAATTTTTCAAATAATAAATAAAT
1 TAAAAATTTTAAAAAAATAAATAAAT
5265456 TAAAAAT
1 TAAAAAT
5265463 CACTTACCTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 9 0.32
26 19 0.68
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36
Consensus pattern (26 bp):
TAAAAATTTTAAAAAAATAAATAAAT
Found at i:5269330 original size:24 final size:24
Alignment explanation
Indices: 5269303--5269354 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
5269293 ACAGGATGTG
*
5269303 ACATGCCATGTCAGCAAACAATTA
1 ACATGCCATATCAGCAAACAATTA
5269327 ACATGCCATATCAGCAAACAATTA
1 ACATGCCATATCAGCAAACAATTA
5269351 ACAT
1 ACAT
5269355 TTAACAGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.44, C:0.25, G:0.10, T:0.21
Consensus pattern (24 bp):
ACATGCCATATCAGCAAACAATTA
Found at i:5272018 original size:17 final size:18
Alignment explanation
Indices: 5271989--5272028 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
5271979 AAAAATAAAT
*
5271989 ATATTATTTTTATTTTTA
1 ATATTATTTTTATATTTA
*
5272007 TTATTA-TTTTATATTTA
1 ATATTATTTTTATATTTA
5272024 ATATT
1 ATATT
5272029 TTAATAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
ATATTATTTTTATATTTA
Found at i:5273683 original size:26 final size:28
Alignment explanation
Indices: 5273632--5273685 Score: 85
Period size: 26 Copynumber: 2.0 Consensus size: 28
5273622 AAATCGATAA
5273632 AATTTTTAAAATATTATAAAAATAAATAT
1 AATTTTTAAAATA-TATAAAAATAAATAT
5273661 AATTTTTAAAA-A-ATAAAAATAAATA
1 AATTTTTAAAATATATAAAAATAAATA
5273686 AATATAACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 13 0.52
28 1 0.04
29 11 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (28 bp):
AATTTTTAAAATATATAAAAATAAATAT
Found at i:5273687 original size:30 final size:29
Alignment explanation
Indices: 5273632--5273692 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
5273622 AAATCGATAA
* * *
5273632 AATTTTTAAAATATTATAAAAATAAATAT
1 AATTTTTAAAAAATAAAAAAAATAAATAT
5273661 AATTTTTAAAAAATAAAAATAAATAAATAT
1 AATTTTTAAAAAATAAAAA-AAATAAATAT
5273691 AA
1 AA
5273693 CTCAATCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (29 bp):
AATTTTTAAAAAATAAAAAAAATAAATAT
Found at i:5273740 original size:36 final size:36
Alignment explanation
Indices: 5273638--5273740 Score: 88
Period size: 36 Copynumber: 2.9 Consensus size: 36
5273628 ATAAAATTTT
* **
5273638 TAAAATATT-ATAAAAATAAAT-ATAATTTTTAAAAAA
1 TAAAATATTAATAAAAATTAATAATAA--TAAAAAAAA
* * *
5273674 TAAAA-ATAAATAAATA-TAACTCAATCATAAAAAAAA
1 TAAAATATTAATAAAAATTAA-T-AATAATAAAAAAAA
5273710 TAAAATATTAATAAAAATTAATAATAATAAA
1 TAAAATATTAATAAAAATTAATAATAATAAA
5273741 TACTTCTCTT
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
35 4 0.08
36 32 0.62
37 10 0.19
38 6 0.12
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (36 bp):
TAAAATATTAATAAAAATTAATAATAATAAAAAAAA
Found at i:5275651 original size:14 final size:13
Alignment explanation
Indices: 5275607--5275653 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
5275597 ATAAAAGAAG
5275607 TATTTTAATTTT-
1 TATTTTAATTTTA
*
5275619 TATTATTAAATTTA
1 TATT-TTAATTTTA
5275633 GTATTTTAATTTCTA
1 -TATTTTAATTT-TA
5275648 TATTTT
1 TATTTT
5275654 TTAAATTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 4 0.14
13 7 0.24
14 12 0.41
15 6 0.21
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (13 bp):
TATTTTAATTTTA
Found at i:5277363 original size:22 final size:23
Alignment explanation
Indices: 5277337--5277383 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
5277327 GGCATGACCT
*
5277337 AAATACAATATCAAAATAAT-TA
1 AAATACAATATAAAAATAATATA
*
5277359 AAATATAATATAAAAATAATATA
1 AAATACAATATAAAAATAATATA
5277382 AA
1 AA
5277384 CATGATAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (23 bp):
AAATACAATATAAAAATAATATA
Found at i:5277377 original size:11 final size:11
Alignment explanation
Indices: 5277343--5277383 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
5277333 ACCTAAATAC
*
5277343 AATATCAAAAT
1 AATATAAAAAT
5277354 AAT-TAAAATAT
1 AATATAAAA-AT
5277365 AATATAAAAAT
1 AATATAAAAAT
5277376 AATATAAA
1 AATATAAA
5277384 CATGATAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 4 0.15
11 18 0.67
12 5 0.19
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (11 bp):
AATATAAAAAT
Found at i:5277677 original size:2 final size:2
Alignment explanation
Indices: 5277670--5277732 Score: 85
Period size: 2 Copynumber: 31.5 Consensus size: 2
5277660 TAAGTATTGT
*
5277670 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TGA T- TA TA GTG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA -TA TA
5277712 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
5277733 TGATTATAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
1 2 0.04
2 51 0.93
3 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5279194 original size:19 final size:18
Alignment explanation
Indices: 5279170--5279207 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5279160 TGATTCGATT
5279170 TAAATTATTATTTAATTAA
1 TAAATTATT-TTTAATTAA
*
5279189 TAAATTATTTTTATTTAA
1 TAAATTATTTTTAATTAA
5279207 T
1 T
5279208 TTTAAAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TAAATTATTTTTAATTAA
Found at i:5279215 original size:22 final size:23
Alignment explanation
Indices: 5279177--5279221 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
5279167 ATTTAAATTA
5279177 TTATTTAATTAATAAAT-TATTT
1 TTATTTAATTAATAAATGTATTT
*
5279199 TTATTTAATT-TTAAAATGTATTT
1 TTATTTAATTAAT-AAATGTATTT
5279222 AAAATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 1 0.05
22 14 0.70
23 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
TTATTTAATTAATAAATGTATTT
Found at i:5279234 original size:26 final size:26
Alignment explanation
Indices: 5279200--5279252 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
5279190 AAATTATTTT
*
5279200 TATTTAATTTTAAAATGTATTTAAAA
1 TATTAAATTTTAAAATGTATTTAAAA
* * *
5279226 TATTAAATTTTTAAATTTTTTTAAAA
1 TATTAAATTTTAAAATGTATTTAAAA
5279252 T
1 T
5279253 TGAATTTCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (26 bp):
TATTAAATTTTAAAATGTATTTAAAA
Found at i:5281595 original size:31 final size:31
Alignment explanation
Indices: 5281554--5281625 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
5281544 ATTTTTGACT
*
5281554 ATTTACAAATTACCACATGTATTTTGAAAAA
1 ATTTTCAAATTACCACATGTATTTTGAAAAA
5281585 ATTTTCAAATTACCACATGTATTTTGAAAAA
1 ATTTTCAAATTACCACATGTATTTTGAAAAA
*
5281616 AATTTCAAAT
1 ATTTTCAAAT
5281626 AAGGAATTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (31 bp):
ATTTTCAAATTACCACATGTATTTTGAAAAA
Found at i:5286904 original size:17 final size:17
Alignment explanation
Indices: 5286863--5286916 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
5286853 AATTATAAAT
*
5286863 TATAAATTAAATTATATAA
1 TATAAAATAAA-TAT-TAA
5286882 -AT-AAATAAATATTAA
1 TATAAAATAAATATTAA
5286897 TATAAAAT-AATATTTAA
1 TATAAAATAAATA-TTAA
5286914 TAT
1 TAT
5286917 TATTATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
15 3 0.10
16 9 0.29
17 17 0.55
18 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TATAAAATAAATATTAA
Found at i:5287146 original size:18 final size:19
Alignment explanation
Indices: 5287123--5287168 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
5287113 TATACTTTTT
5287123 AAATTATAACAA-ATAAAA
1 AAATTATAACAAGATAAAA
*
5287141 AAATTATTAACAATGTTAAAA
1 AAATTA-TAACAA-GATAAAA
5287162 AAATTAT
1 AAATTAT
5287169 TTGAATGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.25
19 6 0.25
20 1 0.04
21 11 0.46
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.30
Consensus pattern (19 bp):
AAATTATAACAAGATAAAA
Done.