Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 125 of 185
Found at i:39098270 original size:6 final size:6
Alignment explanation
Indices: 39098259--39098293 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
39098249 GTGTGTTGAA
* *
39098259 TACTGT TACTGT TACTGT TACTGC TACCGT TACTG
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG
39098294 ATTATTGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.43
Consensus pattern (6 bp):
TACTGT
Found at i:39110576 original size:44 final size:45
Alignment explanation
Indices: 39110444--39110742 Score: 182
Period size: 45 Copynumber: 6.6 Consensus size: 45
39110434 AAGTTACAAA
* * * *
39110444 TCTTATCTCTCTGAAATTGCAGTAGAGCAGACTAAAGAAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAG
* *
39110489 TCTTATCTCCCTGAAGTTGCAGTGGAGCTGACTTAAGAAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAG
* * * * *
39110534 TCTTATC-CCCTGAAGTTGTAGTGGGGCAGACTGAGGATAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAG
* ** * * * *
39110578 TGTTA-CTTCCCTGAAGCCGCAGTGGAACAGATTAAAGCTATAAATCATAG
1 TCTTATC-TCCCTGAAGTTGCAGTGGAGCAGACTGAAG----AAAGCA-AG
* * * * * * *
39110628 ATCTTATCTCTCTTAAGTTACAGTAGAGCAGA-TCATG---GCAAA
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAG
* * * **
39110670 TCTGATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGCCA-CTAA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGC-AAG
*
39110714 TCCTATCTCCCTGAAGTTGCAAGTGGAGC
1 TCTTATCTCCCTGAAGTTGC-AGTGGAGC
39110743 GGATTAAAAC
Statistics
Matches: 194, Mismatches: 45, Indels: 30
0.72 0.17 0.11
Matches are distributed among these distances:
41 27 0.14
42 4 0.02
43 3 0.02
44 52 0.27
45 78 0.40
49 4 0.02
50 4 0.02
51 21 0.11
52 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (45 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAG
Found at i:39110943 original size:44 final size:44
Alignment explanation
Indices: 39110849--39110932 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 44
39110839 GATCATGGCA
* * *
39110849 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACC
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACC
* *
39110893 AATCCTATTTCCCTGAAGTTGCAGTGGAGCGGATTAAAAC
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAC
39110933 GATGAATCCT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (44 bp):
AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACC
Found at i:39110953 original size:44 final size:44
Alignment explanation
Indices: 39110859--39110961 Score: 118
Period size: 44 Copynumber: 2.3 Consensus size: 44
39110849 AATCTTATCT
* * **
39110859 CCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAATCCTATTT
1 CCCTGAAGTTGCAGTGGAGCAGATTAAAACCACCAATCCTATGA
* * **
39110903 CCCTGAAGTTGCAGTGGAGCGGATTAAAACGATGAATCCTA-GA
1 CCCTGAAGTTGCAGTGGAGCAGATTAAAACCACCAATCCTATGA
39110946 CCTCTGAAGTTGCAGT
1 CC-CTGAAGTTGCAGT
39110962 AGGTCAGATC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
43 2 0.04
44 48 0.96
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.24
Consensus pattern (44 bp):
CCCTGAAGTTGCAGTGGAGCAGATTAAAACCACCAATCCTATGA
Found at i:39111006 original size:180 final size:180
Alignment explanation
Indices: 39110626--39111106 Score: 657
Period size: 181 Copynumber: 2.6 Consensus size: 180
39110616 TATAAATCAT
* * * * *
39110626 AGATCTTATCTCTCTTAAGTTACAGTAGAGCAGATCATGGCAAATCTGATCTCTCTGAAGTTGCA
1 AGATCTTATCTCTCTAAAGTTGCAGTAGAACAGATCATGGCAAATCTTATCTCCCTGAAGTTGCA
*
39110691 GTGGAGCAGATTGAAGCCACTAATCCTATCTCCCTGAAGTTGCAAGTGGAGCGGATTAAAACGAT
66 GTGGAGCAGATTGAAGCCACCAATCCTATCTCCCTGAAGTTGC-AGTGGAGCGGATTAAAACGAT
*
39110756 GAATCATATACCTCTGAAGTTGCAGTAGGTCGAATCAAATTCACCAAAGAC
130 GAATCATAGACCTCTGAAGTTGCAGTAGGTCGAATCAAATTCACCAAAGAC
39110807 AGATCTTATCTCTCTAAAGTTGCAGTAGAACAGATCATGGCAAATCTTATCTCCCTGAAGTTGCA
1 AGATCTTATCTCTCTAAAGTTGCAGTAGAACAGATCATGGCAAATCTTATCTCCCTGAAGTTGCA
*
39110872 GTGGAGCAGATTGAAGCCACCAATCCTATTTCCCTGAAGTTGCAGTGGAGCGGATTAAAACGATG
66 GTGGAGCAGATTGAAGCCACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACGATG
*
39110937 AATCCTAGACCTCTGAAGTTGCAGTAGGTC-AGATCAAATTCACCAAAGAC
131 AATCATAGACCTCTGAAGTTGCAGTAGGTCGA-ATCAAATTCACCAAAGAC
* * * * *
39110987 A-AGTCTTATCTCCCTAAAGTTGCACT-GAACCAGACTAAAGATAGCAAATCTTA-CTTTCCTGA
1 AGA-TCTTATCTCTCTAAAGTTGCAGTAGAA-CAGA-T---CATGGCAAATCTTATC-TCCCTGA
* * * * * *
39111049 AGTTGCAGTAGAGTAGATTGAAGCCATC-AGCCTTATCTCTCTGAAGTTGCAATGGAGC
59 AGTTGCAGTGGAGCAGATTGAAGCCACCAATCC-TATCTCCCTGAAGTTGCAGTGGAGC
39111107 AGACTGAAGA
Statistics
Matches: 270, Mismatches: 21, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
179 5 0.02
180 94 0.35
181 102 0.38
183 4 0.01
184 65 0.24
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (180 bp):
AGATCTTATCTCTCTAAAGTTGCAGTAGAACAGATCATGGCAAATCTTATCTCCCTGAAGTTGCA
GTGGAGCAGATTGAAGCCACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACGATG
AATCATAGACCTCTGAAGTTGCAGTAGGTCGAATCAAATTCACCAAAGAC
Found at i:39111143 original size:89 final size:89
Alignment explanation
Indices: 39110991--39111161 Score: 236
Period size: 89 Copynumber: 1.9 Consensus size: 89
39110981 AAAGACAAGT
* * *
39110991 CTTATCTCCCTAAAGTTGCACTGAACCAGACTAAAGATAGCAAATCTTACTTTCCTGAAGTTGCA
1 CTTATCTCCCTAAAGTTGCAATGAACCAGACTAAAGACAGAAAATCTTACTTTCCTGAAGTTGCA
39111056 GTAGAGTAGATTGAAGCCATCAGC
66 GTAGAGTAGATTGAAGCCATCAGC
* * * * * *
39111080 CTTATCTCTCTGAAGTTGCAATGGAGCAGACTGAAGACAGAAAATCTTA-TTTCCTTGATGTTGC
1 CTTATCTCCCTAAAGTTGCAATGAACCAGACTAAAGACAGAAAATCTTACTTTCC-TGAAGTTGC
*
39111144 AGTGGAGTAGATTGAAGC
65 AGTAGAGTAGATTGAAGC
39111162 GACAAATTCC
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
88 5 0.07
89 66 0.93
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (89 bp):
CTTATCTCCCTAAAGTTGCAATGAACCAGACTAAAGACAGAAAATCTTACTTTCCTGAAGTTGCA
GTAGAGTAGATTGAAGCCATCAGC
Found at i:39116000 original size:24 final size:22
Alignment explanation
Indices: 39115968--39116046 Score: 81
Period size: 22 Copynumber: 3.5 Consensus size: 22
39115958 ATAAATGTTG
*
39115968 TTTAAATTTATCACATATTATTAT
1 TTTAAATTTAT--CATATAATTAT
39115992 TTTAAATTTATCATATAATTAT
1 TTTAAATTTATCATATAATTAT
* *
39116014 TTTAAGTTT-TCATGT-ATTAT
1 TTTAAATTTATCATATAATTAT
39116034 TCTTCAAATTTAT
1 T-TT-AAATTTAT
39116047 TATGTATTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
20 6 0.12
21 7 0.15
22 23 0.48
23 1 0.02
24 11 0.23
ACGTcount: A:0.34, C:0.08, G:0.03, T:0.56
Consensus pattern (22 bp):
TTTAAATTTATCATATAATTAT
Found at i:39116012 original size:22 final size:21
Alignment explanation
Indices: 39115968--39116060 Score: 80
Period size: 22 Copynumber: 4.2 Consensus size: 21
39115958 ATAAATGTTG
39115968 TTTAAATTTATCACATATTATTAT
1 TTTAAATTTAT--CATA-TATTAT
39115992 TTTAAATTTATCATATAATTAT
1 TTTAAATTTATCATAT-ATTAT
* *
39116014 TTTAAGTTT-TCATGTATTAT
1 TTTAAATTTATCATATATTAT
* * *
39116034 TCTTCAAATTTATTATGTATTGT
1 T-TT-AAATTTATCATATATTAT
39116057 TTTA
1 TTTA
39116061 TATATTTTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
20 6 0.10
21 9 0.15
22 24 0.40
23 10 0.17
24 11 0.18
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.57
Consensus pattern (21 bp):
TTTAAATTTATCATATATTAT
Found at i:39116087 original size:41 final size:41
Alignment explanation
Indices: 39116039--39116122 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
39116029 ATTATTCTTC
* *
39116039 AAATTTATTATGTATTGTTTTATATATTTTTATGTAAATTT
1 AAATTTATTACGTATTGTTTTATATATTTTTATGCAAATTT
39116080 AAATTTATTACGTATTGTTTTATATATTTTTATGCAAATTT
1 AAATTTATTACGTATTGTTTTATATATTTTTATGCAAATTT
39116121 AA
1 AA
39116123 TATCATTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.57
Consensus pattern (41 bp):
AAATTTATTACGTATTGTTTTATATATTTTTATGCAAATTT
Found at i:39120215 original size:43 final size:42
Alignment explanation
Indices: 39120168--39120307 Score: 129
Period size: 42 Copynumber: 3.3 Consensus size: 42
39120158 TCCTAGGCAT
* * * *
39120168 GGTCTTACATGTAATCAAACAATGATGCCACTGTCCCAGATAG
1 GGTCTTACATGTAATCAAA-AACGACGCCAATGTCCCAGACAG
* * * *
39120211 GGTCTTACATGTAATCATATACGACGCCAATGTTCCAGACAT
1 GGTCTTACATGTAATCAAAAACGACGCCAATGTCCCAGACAG
* * * *
39120253 GGTCTTACATGTAATTCTCAAATCGAGGCCAACGTCCCAGAC-G
1 GGTCTTACATGTAA-TC-AAAAACGACGCCAATGTCCCAGACAG
39120296 TGGTCTTACATG
1 -GGTCTTACATG
39120308 ATGTCATGTT
Statistics
Matches: 78, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
42 30 0.38
43 20 0.26
44 28 0.36
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.27
Consensus pattern (42 bp):
GGTCTTACATGTAATCAAAAACGACGCCAATGTCCCAGACAG
Found at i:39120262 original size:42 final size:42
Alignment explanation
Indices: 39120151--39120307 Score: 145
Period size: 43 Copynumber: 3.7 Consensus size: 42
39120141 CTCGTACAAT
* * * * * *
39120151 GCCAACGTCCTAGGCATGGTCTTACATGTAATCAAACAATGAT
1 GCCAATGTCCCAGACATGGTCTTACATGTAATCATA-AACGAC
* * * *
39120194 GCCACTGTCCCAGATAGGGTCTTACATGTAATCATATACGAC
1 GCCAATGTCCCAGACATGGTCTTACATGTAATCATAAACGAC
* *
39120236 GCCAATGTTCCAGACATGGTCTTACATGTAATTC-TCAAATCGAG
1 GCCAATGTCCCAGACATGGTCTTACATGTAA-TCAT-AAA-CGAC
* *
39120280 GCCAACGTCCCAGACGTGGTCTTACATG
1 GCCAATGTCCCAGACATGGTCTTACATG
39120308 ATGTCATGTT
Statistics
Matches: 92, Mismatches: 19, Indels: 5
0.79 0.16 0.04
Matches are distributed among these distances:
42 31 0.34
43 33 0.36
44 28 0.30
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (42 bp):
GCCAATGTCCCAGACATGGTCTTACATGTAATCATAAACGAC
Found at i:39124644 original size:155 final size:157
Alignment explanation
Indices: 39124448--39124770 Score: 440
Period size: 155 Copynumber: 2.1 Consensus size: 157
39124438 AGAAATTAAA
* *
39124448 AGTAAAATAAAAATCATTTCGGGATTGATTCTTGCCATTCAACGATTTTATTCCAAAATTGTTTT
1 AGTAATATAAAAATCATTTCGGGATTGATTCTCGCCATTCAACGATTTTATTCCAAAATTGTTTT
* * *
39124513 ATTTCC-AAAAACGAGTAAAAT-AAAATCGTTTCAGG-ATCGATTCCCGCCG-TTCATTGATTTT
66 ATTTCCAAAAAACGAGTAAAATAAAAATCGTTTC-GGAATCGATTCCCACCGCTT-AATGATTTC
*
39124574 ATTCCAAATTTGTTTTATTTCCAAAAACG
129 ATTCCAAATTTGGTTTATTTCCAAAAACG
* * * * *
39124603 AGTAATATAAAAATCGTTTCGGGATTGTTTCTCGTCGTTCAACGATTTTATTCCAAATTTGTTTT
1 AGTAATATAAAAATCATTTCGGGATTGATTCTCGCCATTCAACGATTTTATTCCAAAATTGTTTT
* * * *
39124668 ATTTCCAAAAAAATGAGTTAAATAAAAATCGTTTCGGAATTGATTCCTACCGCTTAATGATTTCA
66 ATTTCC-AAAAAACGAGTAAAATAAAAATCGTTTCGGAATCGATTCCCACCGCTTAATGATTTCA
39124733 TTCCAAATTTGGTTTATTTCCAAAAACG
130 TTCCAAATTTGGTTTATTTCCAAAAACG
*
39124761 AGAAAT-TAAA
1 AGTAATATAAA
39124771 TTAAATAAAA
Statistics
Matches: 147, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
155 64 0.44
157 19 0.13
158 62 0.42
159 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (157 bp):
AGTAATATAAAAATCATTTCGGGATTGATTCTCGCCATTCAACGATTTTATTCCAAAATTGTTTT
ATTTCCAAAAAACGAGTAAAATAAAAATCGTTTCGGAATCGATTCCCACCGCTTAATGATTTCAT
TCCAAATTTGGTTTATTTCCAAAAACG
Found at i:39124659 original size:78 final size:78
Alignment explanation
Indices: 39124448--39124770 Score: 402
Period size: 77 Copynumber: 4.1 Consensus size: 78
39124438 AGAAATTAAA
* * * *
39124448 AGTAAAATAAAAATCATTTCGGGATTGATTCTTGCCATTCAACGATTTTATTCCAAAATTGTTTT
1 AGTAAAATAAAAATCGTTTCGGGATTGATTCTCGCCGTTCAACGATTTTATTCCAAATTTGTTTT
39124513 ATTTCCAAAAACG
66 ATTTCCAAAAACG
* * * **
39124526 AGTAAAAT-AAAATCGTTTCAGGATCGATTCCCGCCGTTCATTGATTTTATTCCAAATTTGTTTT
1 AGTAAAATAAAAATCGTTTCGGGATTGATTCTCGCCGTTCAACGATTTTATTCCAAATTTGTTTT
39124590 ATTTCCAAAAACG
66 ATTTCCAAAAACG
* * *
39124603 AGTAATATAAAAATCGTTTCGGGATTGTTTCTCGTCGTTCAACGATTTTATTCCAAATTTGTTTT
1 AGTAAAATAAAAATCGTTTCGGGATTGATTCTCGCCGTTCAACGATTTTATTCCAAATTTGTTTT
*
39124668 ATTTCCAAAAAAATG
66 ATTTCC--AAAAACG
* * * * * *
39124683 AGTTAAATAAAAATCGTTTCGGAATTGATTC-CTACCGCTT-AATGATTTCATTCCAAATTTGGT
1 AGTAAAATAAAAATCGTTTCGGGATTGATTCTC-GCCG-TTCAACGATTTTATTCCAAATTTGTT
39124746 TTATTTCCAAAAACG
64 TTATTTCCAAAAACG
*
39124761 AG-AAATTAAA
1 AGTAAAATAAA
39124771 TTAAATAAAA
Statistics
Matches: 210, Mismatches: 30, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
77 73 0.35
78 71 0.34
79 1 0.00
80 63 0.30
81 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (78 bp):
AGTAAAATAAAAATCGTTTCGGGATTGATTCTCGCCGTTCAACGATTTTATTCCAAATTTGTTTT
ATTTCCAAAAACG
Found at i:39124917 original size:85 final size:84
Alignment explanation
Indices: 39124767--39125012 Score: 329
Period size: 85 Copynumber: 2.9 Consensus size: 84
39124757 AACGAGAAAT
* * *
39124767 TAAATTAAATAAAATCTGTTTCGGGATTT-ATTCCGTTGTTTAACAGGATTTTATTTGATTTTAT
1 TAAATTAAATAAAATCTGTTTCGGGATTTAACTCCGTCGTTTAACAAGATTTTATTTGATTTTAT
39124831 TTTGTTTCCAAATT-AGAA-
66 TTTGTTTCCAAATTCA-AAC
* * *
39124849 TATAATTAAATAAAATCTGTTTTGGGATTTAACCTCCGCCGTTTAACAATATTTTATTTGATTTT
1 TA-AATTAAATAAAATCTGTTTCGGGATTTAA-CTCCGTCGTTTAACAAGATTTTATTTGATTTT
*
39124914 ATTTTGTTTCTAAATTCAAAC
64 ATTTTGTTTCCAAATTCAAAC
* * * *
39124935 TAAATTAAATAAAATATGTTTCGGGATTT-ATTCCCGTCGTTTAACAAGATTTTATTTGATATTG
1 TAAATTAAATAAAATCTGTTTCGGGATTTAACT-CCGTCGTTTAACAAGATTTTATTTGATTTTA
39124999 TTTTGTTTCCAAAT
65 TTTTGTTTCCAAAT
39125013 AAAGATGTAA
Statistics
Matches: 143, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
82 2 0.01
83 27 0.19
84 42 0.29
85 69 0.48
86 3 0.02
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.47
Consensus pattern (84 bp):
TAAATTAAATAAAATCTGTTTCGGGATTTAACTCCGTCGTTTAACAAGATTTTATTTGATTTTAT
TTTGTTTCCAAATTCAAAC
Found at i:39125029 original size:84 final size:83
Alignment explanation
Indices: 39124769--39125049 Score: 311
Period size: 85 Copynumber: 3.4 Consensus size: 83
39124759 CGAGAAATTA
* * *
39124769 AATTAAATAAAATCTGTTTCGGGATTTATT-CCGTTGTTTAACAGGATTTTATTTGATTTTATTT
1 AATTAAATAAAATATGTTTCGGGATTTATTCCCGTCGTTTAACAAGATTTTATTTGATTTTATTT
*
39124833 TGTTTCCAAAT-TAGAATAT
66 TGTTTCCAAATAAAG-AT-T
* * ** * *
39124852 AATTAAATAAAATCTGTTTTGGGATTTAACCTCCGCCGTTTAACAATATTTTATTTGATTTTATT
1 AATTAAATAAAATATGTTTCGGGATTTATTC-CCGTCGTTTAACAAGATTTTATTTGATTTTATT
* * *
39124917 TTGTTTCTAAATTCAAA-CTA
65 TTGTTTCCAAA-T-AAAGATT
* *
39124937 AATTAAATAAAATATGTTTCGGGATTTATTCCCGTCGTTTAACAAGATTTTATTTGATATTGTTT
1 AATTAAATAAAATATGTTTCGGGATTTATTCCCGTCGTTTAACAAGATTTTATTTGATTTTATTT
39125002 TGTTTCCAAATAAAGATGT
66 TGTTTCCAAATAAAGAT-T
* *
39125021 AATCAAATAATTATAT-TTT-GGGATTTATT
1 AATTAAATAA-AATATGTTTCGGGATTTATT
39125050 TTTGCCGTTG
Statistics
Matches: 166, Mismatches: 24, Indels: 16
0.81 0.12 0.08
Matches are distributed among these distances:
82 3 0.02
83 39 0.23
84 51 0.31
85 70 0.42
86 2 0.01
88 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (83 bp):
AATTAAATAAAATATGTTTCGGGATTTATTCCCGTCGTTTAACAAGATTTTATTTGATTTTATTT
TGTTTCCAAATAAAGATT
Found at i:39125185 original size:46 final size:47
Alignment explanation
Indices: 39125088--39125185 Score: 112
Period size: 46 Copynumber: 2.1 Consensus size: 47
39125078 TTAATGATAT
* * ***
39125088 AATTTTGTTTCAGGATTTAATCCTGCCGTTTAACAAAATTAATTTTG
1 AATTTTGTTTCAGAATTTAATCCTGCCGTTTAACAAAATCAATAGGG
*
39125135 -ATTTTGTTTCAGAATTTTATCCTGCCGTTTAAC-AAATCAA-AGGG
1 AATTTTGTTTCAGAATTTAATCCTGCCGTTTAACAAAATCAATAGGG
39125179 AAATTTT
1 -AATTTT
39125186 TCTATTTATG
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
44 1 0.02
45 6 0.14
46 36 0.84
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (47 bp):
AATTTTGTTTCAGAATTTAATCCTGCCGTTTAACAAAATCAATAGGG
Found at i:39131407 original size:23 final size:22
Alignment explanation
Indices: 39131381--39131426 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
39131371 AATTAGAAAA
*
39131381 TCATATACTCCACCAAATAAATT
1 TCATATAC-CCAACAAATAAATT
* *
39131404 TCATCTACCCAACAACTAAATT
1 TCATATACCCAACAAATAAATT
39131426 T
1 T
39131427 GCTTTATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.41, C:0.28, G:0.00, T:0.30
Consensus pattern (22 bp):
TCATATACCCAACAAATAAATT
Found at i:39134940 original size:20 final size:20
Alignment explanation
Indices: 39134912--39134971 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
39134902 CAGCTGAAGG
* *
39134912 AGAAGAAAGAAAAGGAAAGC
1 AGAAAAAAGAAAAAGAAAGC
*
39134932 AGAAAAAAGAAAAAGAAAGAAAA
1 AGAAAAAAGAAAAAGAAAG---C
39134955 AGAAAAAAGAAAAAGAA
1 AGAAAAAAGAAAAAGAA
39134972 GGAGAAGGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 17 0.50
23 17 0.50
ACGTcount: A:0.77, C:0.02, G:0.22, T:0.00
Consensus pattern (20 bp):
AGAAAAAAGAAAAAGAAAGC
Found at i:39134944 original size:6 final size:6
Alignment explanation
Indices: 39134912--39134971 Score: 52
Period size: 6 Copynumber: 9.7 Consensus size: 6
39134902 CAGCTGAAGG
* *
39134912 AGAAGAA AGAAAA GGAAAGC AGAAAAA AGAAAA AG--AA AGAAAA AGAAAAA
1 AGAA-AA AGAAAA AGAAA-A AG-AAAA AGAAAA AGAAAA AGAAAA AG-AAAA
39134962 AGAAAA AGAA
1 AGAAAA AGAA
39134972 GGAGAAGGTG
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
4 4 0.09
6 24 0.55
7 13 0.30
8 3 0.07
ACGTcount: A:0.77, C:0.02, G:0.22, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:39134948 original size:13 final size:13
Alignment explanation
Indices: 39134932--39134971 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
39134922 AAAGGAAAGC
39134932 AGAAAAAAGAAAA
1 AGAAAAAAGAAAA
39134945 AG---AAAGAAAA
1 AGAAAAAAGAAAA
39134955 AGAAAAAAGAAAA
1 AGAAAAAAGAAAA
39134968 AGAA
1 AGAA
39134972 GGAGAAGGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
10 10 0.42
13 14 0.58
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AGAAAAAAGAAAA
Found at i:39134952 original size:17 final size:17
Alignment explanation
Indices: 39134935--39134966 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
39134925 GGAAAGCAGA
39134935 AAAAAG-AAAAAGAAAG
1 AAAAAGAAAAAAGAAAG
39134951 AAAAAGAAAAAAGAAA
1 AAAAAGAAAAAAGAAA
39134967 AAGAAGGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAAGAAAG
Found at i:39134992 original size:38 final size:38
Alignment explanation
Indices: 39134950--39135050 Score: 98
Period size: 41 Copynumber: 2.6 Consensus size: 38
39134940 GAAAAAGAAA
* * *
39134950 GAAAAAGAAA-AAAGAAAAAGAAGGAGAAGGTGGCGTAG
1 GAAAAAGAAAGAAAGAAAAAGAAGAAGAAGGAGG-GAAG
* * *
39134988 GAAAAGAGAAAGAGAAGGAGAAGAAGAAGAGGGAGGGAAG
1 GAAAA-AGAAAGA-AAGAAAAAGAAGAAGAAGGAGGGAAG
39135028 GAAAAAGAAAGAAA-AATAAAGAA
1 GAAAAAGAAAGAAAGAA-AAAGAA
39135051 AGAAAGATAA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
37 1 0.02
38 12 0.24
39 12 0.24
40 9 0.18
41 17 0.33
ACGTcount: A:0.61, C:0.01, G:0.35, T:0.03
Consensus pattern (38 bp):
GAAAAAGAAAGAAAGAAAAAGAAGAAGAAGGAGGGAAG
Found at i:39135050 original size:14 final size:14
Alignment explanation
Indices: 39135031--39135060 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39135021 AGGGAAGGAA
39135031 AAAGAAAGAAAAAT
1 AAAGAAAGAAAAAT
*
39135045 AAAGAAAGAAAGAT
1 AAAGAAAGAAAAAT
39135059 AA
1 AA
39135061 TTTTTTTGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAGAAAGAAAAAT
Found at i:39135083 original size:20 final size:19
Alignment explanation
Indices: 39135058--39135096 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
39135048 GAAAGAAAGA
39135058 TAATTTTTTTGGTATTATTT
1 TAATTTTTTT-GTATTATTT
39135078 TAATTTTTTTGTATTATTT
1 TAATTTTTTTGTATTATTT
39135097 GTGTAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.72
Consensus pattern (19 bp):
TAATTTTTTTGTATTATTT
Found at i:39135996 original size:160 final size:159
Alignment explanation
Indices: 39135280--39136806 Score: 2271
Period size: 158 Copynumber: 9.7 Consensus size: 159
39135270 ATGAAAAAAA
* * * * *
39135280 TAAAATAAGA-AAAA-AATAAAAAACAAAAATAGTATATTTATTGAAAGTAATAAAATCCG---G
1 TAAAATAATATAAAATAATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAA
*
39135340 AAA-AAAAATACGAACAAAGGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAACACAC
66 AAAGAAAAATACGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAACACAC
* *
39135404 TAAATTAATTCATTTCAAATATAATGTAC
131 TAAATTAATACATTTCAAACATAATGTAC
39135433 TAAAATAATATAAAATAATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAA
1 TAAAATAATATAAAATAATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAA
* *
39135498 AAAGAAAGATACGAACAAATGGCCAAAATAAGAGTTTTTTACTAAATTTATAT-AAAAAA-ACAC
66 AAAGAAAAATACGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAACACAC
39135561 TAAATTAATACATTTCAAACATAATGTAC
131 TAAATTAATACATTTCAAACATAATGTAC
* *
39135590 TAAAATAATATAAAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATCTGAAAA
1 TAAAATAATATAAAATAATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAA
* *
39135655 AAA-AAAGATACGAACAAATGGCCAAAATAAGAGTTTTTTACTAAATTTATATAAAAAAACACAC
66 AAAGAAAAATACGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAACACAC
39135719 TAAATTAATACATTTCAAACATAATGTAC
131 TAAATTAATACATTTCAAACATAATGTAC
*
39135748 TAAAATAATATAAAATAATAAAATACGAAAATAGTATATTTTTTGAAAGTAGTAAAATCC-----
1 TAAAATAATATAAAATAATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAA
* *
39135808 AAA-AAAAATATGAACAAATGACCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAACACAC
66 AAAGAAAAATACGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAACACAC
*
39135872 TAAATTAATACATTTCAAACATTATGTAC
131 TAAATTAATACATTTCAAACATAATGTAC
*
39135901 TAAAATAATATAAAATAATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCCAAAAA
1 TAAAATAATATAAAATAATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCC-GAAA
*
39135966 AAAAGAAAAATAGGAACAAATGGCCAAAATAAGGG-TTTTTACTAAATTTATAT-AAAAAACACA
65 AAAAGAAAAATACGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAACACA
* * *
39136029 CTAAATTAATAAATTTTAAACATTATGTAC
130 CTAAATTAATACATTTCAAACATAATGTAC
*
39136059 TAAAATAATATAAAATAATAAAATACGAAAATAG--TATTTTTTGAAAGTAATAAAATCTGAAAA
1 TAAAATAATATAAAATAATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCCG----
* *
39136122 AAAAAAAGAAAAATACGGACAAAGGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAAC
62 AAAAAAAGAAAAATACGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAAC
* *
39136187 ACACTAAATTACTACATTTGAAACATAATGTAC
127 ACACTAAATTAATACATTTCAAACATAATGTAC
* * **
39136220 TAAAATAATATAAAATAATAAAATACGAAAAATAGTATATTATTTGAAAGTAATAAAATTCGGGA
1 TAAAATAATATAAAATAATAAAATACG-AAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAA
* * *
39136285 AAAAGAAAAATACGAACAAAGGGACAAAATAAGGGTTTTTTACTAAATTTATAT-AAAAAATACA
65 AAAAGAAAAATACGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAACACA
* * *
39136349 CTAAATTAATATATTTGAAACGTAATGTAC
130 CTAAATTAATACATTTCAAACATAATGTAC
* *
39136379 TAAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTTGAAAGTAATAAAATTCGACAA
1 TAAAATAATATAAAATAATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCCGA-AA
* *
39136444 AAAGAGAAAAATACGAACAAAGGGCCAAAATAAGGGTTTCTTACTAAATTTATATAAAAAAAACA
65 AAA-AGAAAAATACGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATAT-AAAAAAACA
*
39136509 CACTAAATTAATACATTTCAAACATTATGTAC
128 CACTAAATTAATACATTTCAAACATAATGTAC
* * * *
39136541 CAAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTTGTAAGTAATAAAATCTGAAAA
1 TAAAATAATATAAAATAATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAA
* * *
39136606 TAAGAAAAATCCGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATAT-AAAAAATACAC
66 AAAGAAAAATACGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAACACAC
*
39136670 TAAATTAATACATTTCAAACATTATGTAC
131 TAAATTAATACATTTCAAACATAATGTAC
* *
39136699 TAAAATAATATAAAATAATAAAATACGAAAATAGTAT-TTTTTTGAAAGTAATGAAATTC----A
1 TAAAATAATATAAAATAATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAA
* * * *
39136759 GAA-AAAAATACGAACAAAAGGCTAAAATAAAGGTTTTTTACTAAATTT
66 AAAGAAAAATACGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTT
39136807 GTTTTGAAGT
Statistics
Matches: 1270, Mismatches: 76, Indels: 57
0.91 0.05 0.04
Matches are distributed among these distances:
152 41 0.03
153 159 0.13
154 4 0.00
155 42 0.03
156 72 0.06
157 121 0.10
158 277 0.22
159 169 0.13
160 196 0.15
161 67 0.05
162 100 0.08
164 22 0.02
ACGTcount: A:0.54, C:0.08, G:0.09, T:0.28
Consensus pattern (159 bp):
TAAAATAATATAAAATAATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAA
AAAGAAAAATACGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAACACAC
TAAATTAATACATTTCAAACATAATGTAC
Found at i:39136471 original size:320 final size:317
Alignment explanation
Indices: 39135280--39136806 Score: 2241
Period size: 320 Copynumber: 4.9 Consensus size: 317
39135270 ATGAAAAAAA
* * *
39135280 TAAAATAAGA-AAAA-AATAAAAAAC-AAAAATAGTATATTTATTGAAAGTAATAAAATCCGG--
1 TAAAATAATATAAAATAATAAAATACGAAAAATAGTATATTTTTTGAAAGTAATAAAAT-CGGAA
*
39135340 AAA-AAAAATACGAACAAAGGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAACACAC
65 AAAGAAAAATACGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATAT-AAAAAACACAC
* *
39135404 TAAATTAATTCATTTCAAATATAATGTACTAAAATAATATAAAATAATAAAATACGAAAATAGTA
129 TAAATTAATACATTTCAAACATAATGTACTAAAATAATATAAAATAATAAAATACGAAAATAGTA
* * * *
39135469 TATTTTTTGAAAGTAATAAAATCCGA-AAAAAAGAAAGATACGAACAAATGGCCAAAATAAGAGT
194 TATTTTTTGAAAGTAATAAAATTCGACAAAAAAGAAAAATACGAACAAAGGGCCAAAATAAGGGT
39135533 TTTTTACTAAATTTATAT-AAAAAA-ACACTAAATTAATACATTTCAAACATAATGTAC
259 TTTTTACTAAATTTATATAAAAAAACACACTAAATTAATACATTTCAAACATAATGTAC
*
39135590 TAAAATAATATAAAATAATAAAATAC-AAAAATAGTATATTTTTTGAAAGTAATAAAATCTGAAA
1 TAAAATAATATAAAATAATAAAATACGAAAAATAGTATATTTTTTGAAAGTAATAAAATCGGAAA
* *
39135654 AAAAAAAGATACGAACAAATGGCCAAAATAAGAGTTTTTTACTAAATTTATATAAAAAAACACAC
66 AAGAAAA-ATACGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATAT-AAAAAACACAC
39135719 TAAATTAATACATTTCAAACATAATGTACTAAAATAATATAAAATAATAAAATACGAAAATAGTA
129 TAAATTAATACATTTCAAACATAATGTACTAAAATAATATAAAATAATAAAATACGAAAATAGTA
* * * *
39135784 TATTTTTTGAAAGTAGTAAAA-TC--C---AAA-AAAAATATGAACAAATGACCAAAATAAGGGT
194 TATTTTTTGAAAGTAATAAAATTCGACAAAAAAGAAAAATACGAACAAAGGGCCAAAATAAGGGT
*
39135842 TTTTTACTAAATTTATATAAAAAAACACACTAAATTAATACATTTCAAACATTATGTAC
259 TTTTTACTAAATTTATATAAAAAAACACACTAAATTAATACATTTCAAACATAATGTAC
**
39135901 TAAAATAATATAAAATAATAAAATACG-AAAATAGTATATTTTTTGAAAGTAATAAAATCCAAAA
1 TAAAATAATATAAAATAATAAAATACGAAAAATAGTATATTTTTTGAAAGTAATAAAAT-C--GG
*
39135965 AAAAAGAAAAATAGGAACAAATGGCCAAAATAAGGG-TTTTTACTAAATTTATATAAAAAACACA
63 AAAAAGAAAAATACGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACA
* * *
39136029 CTAAATTAATAAATTTTAAACATTATGTACTAAAATAATATAAAATAATAAAATACGAAAATAG-
128 CTAAATTAATACATTTCAAACATAATGTACTAAAATAATATAAAATAATAAAATACGAAAATAGT
* *
39136093 -TATTTTTTGAAAGTAATAAAA-TCTGAAAAAAAAAAAGAAAAATACGGACAAAGGGCCAAAATA
193 ATATTTTTTGAAAGTAATAAAATTC-G---ACAAAAAAGAAAAATACGAACAAAGGGCCAAAATA
* *
39136156 AGGGTTTTTTACTAAATTTATATAAAAAAACACACTAAATTACTACATTTGAAACATAATGTAC
254 AGGGTTTTTTACTAAATTTATATAAAAAAACACACTAAATTAATACATTTCAAACATAATGTAC
*
39136220 TAAAATAATATAAAATAATAAAATACGAAAAATAGTATATTATTTGAAAGTAATAAAATTCGGGA
1 TAAAATAATATAAAATAATAAAATACGAAAAATAGTATATTTTTTGAAAGTAATAAAA-TC-GGA
* * *
39136285 AAAAGAAAAATACGAACAAAGGGACAAAATAAGGGTTTTTTACTAAATTTATATAAAAAATACAC
64 AAAAGAAAAATACGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACAC
* * * *
39136350 TAAATTAATATATTTGAAACGTAATGTACTAAAATAATATAAAATAATAAAATACGAAAATAATA
129 TAAATTAATACATTTCAAACATAATGTACTAAAATAATATAAAATAATAAAATACGAAAATAGTA
39136415 TATTTTTTGAAAGTAATAAAATTCGACAAAAAGAGAAAAATACGAACAAAGGGCCAAAATAAGGG
194 TATTTTTTGAAAGTAATAAAATTCGACAAAAA-AGAAAAATACGAACAAAGGGCCAAAATAAGGG
* *
39136480 TTTCTTACTAAATTTATATAAAAAAAACACACTAAATTAATACATTTCAAACATTATGTAC
258 TTTTTTACTAAATTTATAT-AAAAAAACACACTAAATTAATACATTTCAAACATAATGTAC
* * * *
39136541 CAAAATAATATAAAATAATAAAATACG-AAAATAATATATTTTTTGTAAGTAATAAAATCTGAAA
1 TAAAATAATATAAAATAATAAAATACGAAAAATAGTATATTTTTTGAAAGTAATAAAATC-GGAA
* *
39136605 ATAAGAAAAATCCGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAATACAC
65 A-AAGAAAAATACGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACAC
*
39136670 TAAATTAATACATTTCAAACATTATGTACTAAAATAATATAAAATAATAAAATACGAAAATAGTA
129 TAAATTAATACATTTCAAACATAATGTACTAAAATAATATAAAATAATAAAATACGAAAATAGTA
* * * * *
39136735 T-TTTTTTGAAAGTAATGAAATT---C--AGAA-AAAAATACGAACAAAAGGCTAAAATAAAGGT
194 TATTTTTTGAAAGTAATAAAATTCGACAAAAAAGAAAAATACGAACAAAGGGCCAAAATAAGGGT
39136793 TTTTTACTAAATTT
259 TTTTTACTAAATTT
39136807 GTTTTGAAGT
Statistics
Matches: 1114, Mismatches: 71, Indels: 62
0.89 0.06 0.05
Matches are distributed among these distances:
309 67 0.06
310 18 0.02
311 166 0.15
312 100 0.09
313 28 0.03
314 16 0.01
315 138 0.12
316 1 0.00
318 3 0.00
319 175 0.16
320 313 0.28
321 65 0.06
322 22 0.02
323 2 0.00
ACGTcount: A:0.54, C:0.08, G:0.09, T:0.28
Consensus pattern (317 bp):
TAAAATAATATAAAATAATAAAATACGAAAAATAGTATATTTTTTGAAAGTAATAAAATCGGAAA
AAGAAAAATACGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACTA
AATTAATACATTTCAAACATAATGTACTAAAATAATATAAAATAATAAAATACGAAAATAGTATA
TTTTTTGAAAGTAATAAAATTCGACAAAAAAGAAAAATACGAACAAAGGGCCAAAATAAGGGTTT
TTTACTAAATTTATATAAAAAAACACACTAAATTAATACATTTCAAACATAATGTAC
Found at i:39139113 original size:8 final size:8
Alignment explanation
Indices: 39139100--39139141 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
39139090 GGGTGTTACA
39139100 ACAACATT
1 ACAACATT
39139108 ACAACATT
1 ACAACATT
*
39139116 ACAATATT
1 ACAACATT
*
39139124 AC-ACATA
1 ACAACATT
*
39139131 ACAACTTT
1 ACAACATT
39139139 ACA
1 ACA
39139142 GCATAAGCTC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
7 5 0.18
8 23 0.82
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (8 bp):
ACAACATT
Found at i:39140629 original size:32 final size:32
Alignment explanation
Indices: 39140588--39140651 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
39140578 ATAGCCAAGT
39140588 CCCATCCACCTGCACAAACAGCTTGCAGTAGG
1 CCCATCCACCTGCACAAACAGCTTGCAGTAGG
39140620 CCCATCCACCTGCACAAACAGCTTGCAGTAGG
1 CCCATCCACCTGCACAAACAGCTTGCAGTAGG
39140652 GAAATACTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.38, G:0.19, T:0.16
Consensus pattern (32 bp):
CCCATCCACCTGCACAAACAGCTTGCAGTAGG
Found at i:39141172 original size:29 final size:29
Alignment explanation
Indices: 39141130--39141192 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
39141120 CTGCCTTCCA
*
39141130 ACACTCTCCAATATATACTGTCGGTTTAG
1 ACACTCCCCAATATATACTGTCGGTTTAG
39141159 ACACTCCCCAATATATACTGTCGGTTTAG
1 ACACTCCCCAATATATACTGTCGGTTTAG
39141188 ACACT
1 ACACT
39141193 GCGACTTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.32
Consensus pattern (29 bp):
ACACTCCCCAATATATACTGTCGGTTTAG
Found at i:39142781 original size:3 final size:3
Alignment explanation
Indices: 39142773--39142809 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
39142763 TTTTTAATCC
39142773 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
39142810 CCTTCTTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:39143282 original size:25 final size:25
Alignment explanation
Indices: 39143249--39143337 Score: 70
Period size: 25 Copynumber: 3.4 Consensus size: 25
39143239 TAATGTTTGA
*
39143249 TATTATTATGTTTATAAATTTCAAG
1 TATTTTTATGTTTATAAATTTCAAG
* * ** * *
39143274 TATTTTTATATCTATATTTTTGATG
1 TATTTTTATGTTTATAAATTTCAAG
39143299 TTTGATATTATTATGTTTATAAATTTCAAG
1 --T-AT-TT-TTATGTTTATAAATTTCAAG
39143329 TATTTTTAT
1 TATTTTTAT
39143338 ATCTATATAT
Statistics
Matches: 46, Mismatches: 13, Indels: 10
0.67 0.19 0.14
Matches are distributed among these distances:
25 22 0.48
26 2 0.04
27 3 0.07
28 3 0.07
29 2 0.04
30 14 0.30
ACGTcount: A:0.30, C:0.03, G:0.08, T:0.58
Consensus pattern (25 bp):
TATTTTTATGTTTATAAATTTCAAG
Found at i:39143301 original size:55 final size:55
Alignment explanation
Indices: 39143236--39143345 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
39143226 TATATTATTG
39143236 TTTTAATGTTTGATATTATTATGTTTATAAATTTCAAGTATTTTTATATCTATAT
1 TTTTAATGTTTGATATTATTATGTTTATAAATTTCAAGTATTTTTATATCTATAT
*
39143291 TTTTGATGTTTGATATTATTATGTTTATAAATTTCAAGTATTTTTATATCTATAT
1 TTTTAATGTTTGATATTATTATGTTTATAAATTTCAAGTATTTTTATATCTATAT
39143346 ATGTATTTTA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.30, C:0.04, G:0.08, T:0.58
Consensus pattern (55 bp):
TTTTAATGTTTGATATTATTATGTTTATAAATTTCAAGTATTTTTATATCTATAT
Found at i:39145078 original size:14 final size:15
Alignment explanation
Indices: 39145054--39145114 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 15
39145044 AATCTGTTAA
39145054 AAAATAAAAAAATTC
1 AAAATAAAAAAATTC
*
39145069 AAAA-AAAAAAATTG
1 AAAATAAAAAAATTC
* *
39145083 AACAGTAAATAAATTAC
1 AA-AATAAAAAAATT-C
*
39145100 TTAAATAAAAAAATT
1 -AAAATAAAAAAATT
39145115 TAATGTTTCA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
14 11 0.31
15 5 0.14
16 8 0.23
17 10 0.29
18 1 0.03
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (15 bp):
AAAATAAAAAAATTC
Found at i:39145225 original size:15 final size:15
Alignment explanation
Indices: 39145205--39145255 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
39145195 CCACTAATCC
39145205 TAATAACTAAC-ACAA
1 TAATAAC-AACAACAA
39145220 TAATAACAACAACAA
1 TAATAACAACAACAA
* * *
39145235 TAATAATAATAATAA
1 TAATAACAACAACAA
39145250 TAATAA
1 TAATAA
39145256 TAGTTTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
14 3 0.09
15 29 0.91
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.24
Consensus pattern (15 bp):
TAATAACAACAACAA
Found at i:39145239 original size:3 final size:3
Alignment explanation
Indices: 39145218--39145257 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
39145208 TAACTAACAC
* * *
39145218 AAT AAT AAC AAC AAC AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
39145258 GTTTTTTTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:39145325 original size:37 final size:37
Alignment explanation
Indices: 39145236--39145336 Score: 109
Period size: 40 Copynumber: 2.7 Consensus size: 37
39145226 CAACAACAAT
* **
39145236 AATAATAA-TAATAATAATAATAGTTTTTTTACTAAA
1 AATAATAACTAACAATAATAATAGTGGTTTTACTAAA
39145272 AATAATACTAACTAACAATAATAATTAG-GGTTTTACTAAA
1 AAT-A-A-TAACTAACAATAATAA-TAGTGGTTTTACTAAA
*
39145312 AATAATAACTAACAATGAT-ATAGTG
1 AATAATAACTAACAATAATAATAGTG
39145337 TAAAAACTAA
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
35 3 0.05
36 5 0.09
37 14 0.25
38 2 0.04
39 4 0.07
40 24 0.44
41 3 0.05
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.35
Consensus pattern (37 bp):
AATAATAACTAACAATAATAATAGTGGTTTTACTAAA
Found at i:39145669 original size:24 final size:21
Alignment explanation
Indices: 39145642--39145695 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 21
39145632 ATTTTTTTCC
39145642 TTCTCTTTCTTTCTCATTTCTCTA
1 TTCTCTTTC--TCTCATTT-TCTA
*
39145666 TTCTCTTTCTCTCATTTTCTT
1 TTCTCTTTCTCTCATTTTCTA
*
39145687 TTCTTTTTC
1 TTCTCTTTC
39145696 CAGCACCGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 11 0.39
22 8 0.29
24 9 0.32
ACGTcount: A:0.06, C:0.28, G:0.00, T:0.67
Consensus pattern (21 bp):
TTCTCTTTCTCTCATTTTCTA
Found at i:39145722 original size:3 final size:3
Alignment explanation
Indices: 39145708--39145748 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
39145698 GCACCGCCCT
*
39145708 CTC CTT CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CT
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CT
39145749 TCTTCTTCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (3 bp):
CTC
Found at i:39145886 original size:40 final size:40
Alignment explanation
Indices: 39145810--39145906 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 40
39145800 CGTTTGGACA
* *
39145810 AAAAACGCCGGTAAAAATAGAGCATTAGCGGCTTTTTTTG
1 AAAAACGCCGCTAAAAATAGAGCATTACCGGCTTTTTTTG
* **
39145850 AAAATCGCCGCTAAAAAT-GAGCATTACCGG-TGTTTTTCCA
1 AAAAACGCCGCTAAAAATAGAGCATTACCGGCT-TTTTT-TG
*
39145890 AAAAACGCCGCAAAAAA
1 AAAAACGCCGCTAAAAA
39145907 CCTAAGCCCA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
38 1 0.02
39 16 0.33
40 31 0.65
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.23
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATAGAGCATTACCGGCTTTTTTTG
Found at i:39146402 original size:14 final size:15
Alignment explanation
Indices: 39146363--39146409 Score: 62
Period size: 14 Copynumber: 3.3 Consensus size: 15
39146353 TATTTTAAGG
*
39146363 TTTAGGGAGTATGGA
1 TTTAGGGATTATGGA
*
39146378 TTTAGGAATTATGGA
1 TTTAGGGATTATGGA
39146393 -TTAGGGATTATGG-
1 TTTAGGGATTATGGA
39146406 TTTA
1 TTTA
39146410 AGGGTTGGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 15 0.54
15 13 0.46
ACGTcount: A:0.28, C:0.00, G:0.32, T:0.40
Consensus pattern (15 bp):
TTTAGGGATTATGGA
Found at i:39146430 original size:21 final size:21
Alignment explanation
Indices: 39146396--39146451 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
39146386 TTATGGATTA
*
39146396 GGGA-TTATGGTTTAAGGGTT
1 GGGATTTAAGGTTTAAGGGTT
*
39146416 GGGATTTAAGGTTTAGGGGTT
1 GGGATTTAAGGTTTAAGGGTT
*
39146437 AGGAGTTTAGAGGTT
1 GGGA-TTTA-AGGTT
39146452 AGACGTTAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.13
21 17 0.57
22 4 0.13
23 5 0.17
ACGTcount: A:0.21, C:0.00, G:0.41, T:0.38
Consensus pattern (21 bp):
GGGATTTAAGGTTTAAGGGTT
Found at i:39146446 original size:15 final size:15
Alignment explanation
Indices: 39146426--39146491 Score: 50
Period size: 15 Copynumber: 4.5 Consensus size: 15
39146416 GGGATTTAAG
39146426 GTTTAGGGGTTAGGA
1 GTTTAGGGGTTAGGA
*
39146441 GTTTAGAGGTTA-GA
1 GTTTAGGGGTTAGGA
* *
39146455 CG-TTAGGGATTAAGA
1 -GTTTAGGGGTTAGGA
*
39146470 G-TTAGGGATTTAGGA
1 GTTTAGGG-GTTAGGA
39146485 -TTTAGGG
1 GTTTAGGG
39146492 ATTCAGGGGT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
14 17 0.40
15 25 0.60
ACGTcount: A:0.26, C:0.02, G:0.39, T:0.33
Consensus pattern (15 bp):
GTTTAGGGGTTAGGA
Found at i:39146492 original size:15 final size:15
Alignment explanation
Indices: 39146456--39146494 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
39146446 GAGGTTAGAC
39146456 GTTAGGGA-TTAAGA
1 GTTAGGGATTTAAGA
*
39146470 GTTAGGGATTTAGGA
1 GTTAGGGATTTAAGA
*
39146485 TTTAGGGATT
1 GTTAGGGATT
39146495 CAGGGGTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.28, C:0.00, G:0.36, T:0.36
Consensus pattern (15 bp):
GTTAGGGATTTAAGA
Found at i:39146736 original size:7 final size:7
Alignment explanation
Indices: 39146726--39146773 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
39146716 GATTTAAGGT
*
39146726 TTAGAGG
1 TTAGGGG
39146733 TTAGGGG
1 TTAGGGG
39146740 TTAGGGG
1 TTAGGGG
**
39146747 TTAGACG
1 TTAGGGG
39146754 TTAGGGG
1 TTAGGGG
* *
39146761 TTAAGAG
1 TTAGGGG
39146768 TTAGGG
1 TTAGGG
39146774 ATTTAAGGTT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.23, C:0.02, G:0.46, T:0.29
Consensus pattern (7 bp):
TTAGGGG
Found at i:39146770 original size:21 final size:21
Alignment explanation
Indices: 39146726--39146771 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
39146716 GATTTAAGGT
* * *
39146726 TTAGAGGTTAGGGGTTAGGGG
1 TTAGACGTTAGGGGTTAAGAG
39146747 TTAGACGTTAGGGGTTAAGAG
1 TTAGACGTTAGGGGTTAAGAG
39146768 TTAG
1 TTAG
39146772 GGATTTAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.24, C:0.02, G:0.43, T:0.30
Consensus pattern (21 bp):
TTAGACGTTAGGGGTTAAGAG
Found at i:39147050 original size:23 final size:24
Alignment explanation
Indices: 39147019--39147104 Score: 97
Period size: 23 Copynumber: 3.6 Consensus size: 24
39147009 AAACCATTTG
39147019 ATATA-TTTAAATAGAATTAATAA
1 ATATAGTTTAAATAGAATTAATAA
* * *
39147042 ATA-AGTTTAATTAAAATATATTTAA
1 ATATAGTTTAAATAGAAT-TA-ATAA
39147067 ATATTAGTTTAAATAGAATTAATAA
1 ATA-TAGTTTAAATAGAATTAATAA
39147092 ATATA-TTTAAATA
1 ATATAGTTTAAATA
39147105 TTAGTTTAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
22 1 0.02
23 21 0.40
24 4 0.08
25 12 0.23
26 2 0.04
27 12 0.23
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (24 bp):
ATATAGTTTAAATAGAATTAATAA
Found at i:39147079 original size:12 final size:11
Alignment explanation
Indices: 39147055--39147116 Score: 56
Period size: 12 Copynumber: 5.5 Consensus size: 11
39147045 AGTTTAATTA
39147055 AAATATA-TTT
1 AAATATAGTTT
39147065 AAATATTAGTTT
1 AAATA-TAGTTT
* *
39147077 AAATAGAATTAAT
1 AAATATAGTT--T
39147090 AAATATA-TTT
1 AAATATAGTTT
39147100 AAATATTAGTTT
1 AAATA-TAGTTT
39147112 AAATA
1 AAATA
39147117 AAATAATTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
10 11 0.26
11 7 0.16
12 18 0.42
13 7 0.16
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.44
Consensus pattern (11 bp):
AAATATAGTTT
Found at i:39152191 original size:43 final size:40
Alignment explanation
Indices: 39152094--39152210 Score: 119
Period size: 43 Copynumber: 2.8 Consensus size: 40
39152084 AAGTCATGTT
* *
39152094 TTTAGCGGCGTTTGTA-AATAAGTGCCGCTAAAAGTAACTT
1 TTTAGCGGCGTTTGTATAA-AAGCGCCGCTAAAAGTAACTC
* * *
39152134 TTATAGCGGCGTTTGTATTAGAAGCGCCGCTAAAGGTCACGATC
1 TT-TAGCGGCGTTTGTA-TAAAAGCGCCGCTAAAAGTAAC--TC
*
39152178 TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAA
1 TTTAGCGGCGTTTGT-ATAAAAGCGCCGCTAAA
39152211 TACCATAATG
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
40 2 0.03
41 14 0.22
42 16 0.25
43 29 0.45
44 3 0.05
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (40 bp):
TTTAGCGGCGTTTGTATAAAAGCGCCGCTAAAAGTAACTC
Found at i:39153021 original size:19 final size:19
Alignment explanation
Indices: 39152990--39153028 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
39152980 TTATATGGAT
39152990 ATAATTATATAAAATAAAA
1 ATAATTATATAAAATAAAA
*
39153009 ATAATGTAT-TAAATTAAAA
1 ATAAT-TATATAAAATAAAA
39153028 A
1 A
39153029 GTTGGTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
ATAATTATATAAAATAAAA
Found at i:39154822 original size:3 final size:3
Alignment explanation
Indices: 39154816--39154843 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
39154806 CATGTTGTTT
39154816 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
39154844 GAATGATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:39156668 original size:13 final size:13
Alignment explanation
Indices: 39156650--39156674 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39156640 ACAAACAATA
39156650 AAATTTTCACACG
1 AAATTTTCACACG
39156663 AAATTTTCACAC
1 AAATTTTCACAC
39156675 ATATAAATTA
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:39159606 original size:25 final size:24
Alignment explanation
Indices: 39159578--39159631 Score: 58
Period size: 23 Copynumber: 2.2 Consensus size: 24
39159568 AAAAAAACCT
*
39159578 AAAAAGCGTGCTATA-TAAGCAGAGG
1 AAAAA-CGAGCTATAGT-AGCAGAGG
*
39159603 -AAAATGAGCTATAGTAGCAGAGG
1 AAAAACGAGCTATAGTAGCAGAGG
39159626 AAAAAC
1 AAAAAC
39159632 TCTCAAAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.48, C:0.11, G:0.26, T:0.15
Consensus pattern (24 bp):
AAAAACGAGCTATAGTAGCAGAGG
Found at i:39159659 original size:20 final size:20
Alignment explanation
Indices: 39159621--39159659 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
39159611 CTATAGTAGC
* * *
39159621 AGAGGAAAAACTCTCAAAGA
1 AGAGAAAAAACCCTAAAAGA
39159641 AGAGAAAAAACCCTAAAAG
1 AGAGAAAAAACCCTAAAAG
39159660 CTAATCCAGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.59, C:0.15, G:0.18, T:0.08
Consensus pattern (20 bp):
AGAGAAAAAACCCTAAAAGA
Found at i:39160061 original size:94 final size:94
Alignment explanation
Indices: 39159952--39160137 Score: 241
Period size: 95 Copynumber: 2.0 Consensus size: 94
39159942 TATTGTTAAA
* * * *
39159952 TCAATGTGAGATT-AAAATGAATTTTTTAATAAAAATAATAAAGAAA-TTATCACTTATTTATAA
1 TCAACGTGAGATTAAAAATGAACTATTTAATAAAAATAATAAAGAAATTTA-CACTGATTTATAA
*
39160015 AGTAAATGTGATATATGAGAGTGTTCTCTAG
65 AGTAAATGT-ATACATGAGAGTGTTCTCTAG
* * * *
39160046 TCAACGTGTGATTAAAAATTAACTATTTAATAAAAATAATGAAGAAATTTACACTGATTTATAAG
1 TCAACGTGAGATTAAAAATGAACTATTTAATAAAAATAATAAAGAAATTTACACTGATTTATAAA
* *
39160111 GTAAGTGTATGCATGAGAGTGTTCTCT
66 GTAAATGTATACATGAGAGTGTTCTCT
39160138 CACCAAGGTG
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
94 28 0.35
95 48 0.61
96 3 0.04
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.36
Consensus pattern (94 bp):
TCAACGTGAGATTAAAAATGAACTATTTAATAAAAATAATAAAGAAATTTACACTGATTTATAAA
GTAAATGTATACATGAGAGTGTTCTCTAG
Found at i:39160337 original size:94 final size:94
Alignment explanation
Indices: 39160215--39160398 Score: 255
Period size: 94 Copynumber: 2.0 Consensus size: 94
39160205 AGAAGTAAGT
* * *
39160215 TATAAGAGAATTTTCTATTCAATGTGGGATAAAAATTAACTTTTTAATGAAAATAGTGAAGAAAT
1 TATAAGAGAATTTTCTAGTCAATGTGGGATAAAAATTAACTTTTTAATGAAAATAGTAAACAAAT
39160280 TATCACTTAATTAT-AAGATAAATGTCAGA
66 TATCACTTAATTATAAAG-TAAATGTCAGA
* * * *
39160309 TATAAGAGTA-TTTCTTAGTCAATGTGGGATTAAAGTTAACTTTTTAATGAAAATAGTAAACAAG
1 TATAAGAGAATTTTC-TAGTCAATGTGGGATAAAAATTAACTTTTTAATGAAAATAGTAAACAAA
* *
39160373 TTGTCACTTATTTATAAAGTAAATGT
65 TTATCACTTAATTATAAAGTAAATGT
39160399 GAGACGAGAC
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
93 4 0.05
94 72 0.91
95 3 0.04
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.37
Consensus pattern (94 bp):
TATAAGAGAATTTTCTAGTCAATGTGGGATAAAAATTAACTTTTTAATGAAAATAGTAAACAAAT
TATCACTTAATTATAAAGTAAATGTCAGA
Found at i:39161213 original size:21 final size:22
Alignment explanation
Indices: 39161172--39161223 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
39161162 TATAAATTAT
*
39161172 TAATATATTT-ATGAATCTTTA
1 TAATATTTTTAATGAATCTTTA
*
39161193 TAATATTTTTAATG-ATGTTTA
1 TAATATTTTTAATGAATCTTTA
*
39161214 TTA-ATTTTTA
1 TAATATTTTTA
39161224 TATTTATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.26
21 17 0.63
22 3 0.11
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.58
Consensus pattern (22 bp):
TAATATTTTTAATGAATCTTTA
Found at i:39161224 original size:31 final size:29
Alignment explanation
Indices: 39161159--39161234 Score: 82
Period size: 31 Copynumber: 2.6 Consensus size: 29
39161149 TTATTTTTTA
39161159 TTTTATAAATTATTAATATATTTATGAAT
1 TTTTATAAATTATTAATATATTTATGAAT
* * * *
39161188 CTTTATAATATTTTTAATGATGTTTATTAAT
1 TTTTATAA-ATTATTAAT-ATATTTATGAAT
*
39161219 TTTTAT-ATTTATTAAT
1 TTTTATAAATTATTAAT
39161235 TTTTTTTATA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
29 14 0.37
30 9 0.24
31 15 0.39
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.59
Consensus pattern (29 bp):
TTTTATAAATTATTAATATATTTATGAAT
Found at i:39161321 original size:14 final size:15
Alignment explanation
Indices: 39161304--39161332 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39161294 TTTATAGTTT
39161304 TTAA-TTTATTTTTA
1 TTAATTTTATTTTTA
39161318 TTAATTTTATTTTTA
1 TTAATTTTATTTTTA
39161333 AAAAATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTAATTTTATTTTTA
Found at i:39164548 original size:13 final size:13
Alignment explanation
Indices: 39164530--39164573 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
39164520 TAAGTATTGA
39164530 AATTATATTATAT
1 AATTATATTATAT
*
39164543 AATTATATTATAC
1 AATTATATTATAT
39164556 AATTAT-TTA-AT
1 AATTATATTATAT
39164567 ATATTAT
1 A-ATTAT
39164574 TAAAAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 2 0.07
12 8 0.29
13 18 0.64
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (13 bp):
AATTATATTATAT
Found at i:39174101 original size:19 final size:19
Alignment explanation
Indices: 39174069--39174107 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
39174059 TGTTTTAAAG
* *
39174069 TAAAATAGTGTTATATTAT
1 TAAAATAATATTATATTAT
*
39174088 TAAAATAATATTATTTTAT
1 TAAAATAATATTATATTAT
39174107 T
1 T
39174108 TTAATTTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
TAAAATAATATTATATTAT
Found at i:39175031 original size:21 final size:21
Alignment explanation
Indices: 39175007--39175054 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
39174997 ATAAGTAAAT
*
39175007 TTTGTAATATACTATGAATGA
1 TTTGTAAAATACTATGAATGA
* * * *
39175028 TTTGAAAAATATTGTGTATGA
1 TTTGTAAAATACTATGAATGA
39175049 TTTGTA
1 TTTGTA
39175055 TCTATTATGA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.02, G:0.17, T:0.46
Consensus pattern (21 bp):
TTTGTAAAATACTATGAATGA
Found at i:39185463 original size:19 final size:19
Alignment explanation
Indices: 39185435--39185473 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
39185425 TATATGTTGA
39185435 AAATATTTTGAT-TATTGC
1 AAATATTTTGATATATTGC
*
39185453 AAATGATTTTGGTATATTGC
1 AAAT-ATTTTGATATATTGC
39185473 A
1 A
39185474 TGAGACAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 7 0.39
20 7 0.39
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.46
Consensus pattern (19 bp):
AAATATTTTGATATATTGC
Found at i:39187853 original size:18 final size:18
Alignment explanation
Indices: 39187830--39187867 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
39187820 TCAAACAAAA
39187830 TCTTATGGCGTGTTTAGT
1 TCTTATGGCGTGTTTAGT
39187848 TCTTATGGCGTGTTTAGT
1 TCTTATGGCGTGTTTAGT
39187866 TC
1 TC
39187868 GCTGTAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.11, C:0.13, G:0.26, T:0.50
Consensus pattern (18 bp):
TCTTATGGCGTGTTTAGT
Found at i:39188244 original size:36 final size:36
Alignment explanation
Indices: 39188199--39188270 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
39188189 TTAGCTATCC
39188199 TATATAAAGACCTCTTCATTGTTCATTAAAATTTTA
1 TATATAAAGACCTCTTCATTGTTCATTAAAATTTTA
39188235 TATATAAAGACCTCTTCATTGTTCATTAAAATTTTA
1 TATATAAAGACCTCTTCATTGTTCATTAAAATTTTA
39188271 ACTCTGGAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (36 bp):
TATATAAAGACCTCTTCATTGTTCATTAAAATTTTA
Found at i:39188548 original size:20 final size:20
Alignment explanation
Indices: 39188525--39188575 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
39188515 TTTGTTTATT
*
39188525 TATTTATTTTTTGT-TTTGAA
1 TATTTATTTTTTGTCCTT-AA
*
39188545 TATTTATTCTTTGTCCTTAA
1 TATTTATTTTTTGTCCTTAA
39188565 -ATTTATTTTTT
1 TATTTATTTTTT
39188576 TAGTTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 10 0.37
20 15 0.56
21 2 0.07
ACGTcount: A:0.20, C:0.06, G:0.06, T:0.69
Consensus pattern (20 bp):
TATTTATTTTTTGTCCTTAA
Found at i:39188875 original size:20 final size:23
Alignment explanation
Indices: 39188831--39188881 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
39188821 AAATTATGAC
*
39188831 TTTAAAGATATATATATTTATAT
1 TTTATAGATATATATATTTATAT
*
39188854 TTT-TAGATATAT-TTTTTA-AT
1 TTTATAGATATATATATTTATAT
39188874 TTTATAGA
1 TTTATAGA
39188882 ATTATTGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 5 0.20
21 9 0.36
22 8 0.32
23 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (23 bp):
TTTATAGATATATATATTTATAT
Found at i:39190015 original size:27 final size:27
Alignment explanation
Indices: 39189984--39190066 Score: 80
Period size: 27 Copynumber: 3.0 Consensus size: 27
39189974 GTTTATCTAT
39189984 TAATATATATTAAATTATTTTTTAAAA
1 TAATATATATTAAATTATTTTTTAAAA
* *
39190011 TAATATGT-TTAAATGATTTGTTTTAAAA
1 TAATATATATTAAATTA-TT-TTTTAAAA
* * *
39190039 -AATAAATATGTAAAATATTTTTTCAAA
1 TAATATATAT-TAAATTATTTTTTAAAA
39190066 T
1 T
39190067 TTTATTTATT
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
26 7 0.16
27 21 0.48
28 11 0.25
29 5 0.11
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (27 bp):
TAATATATATTAAATTATTTTTTAAAA
Found at i:39197839 original size:11 final size:11
Alignment explanation
Indices: 39197823--39197849 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
39197813 TCACAAACGG
39197823 ATTCAGAATTA
1 ATTCAGAATTA
39197834 ATTCAGAATTA
1 ATTCAGAATTA
39197845 ATTCA
1 ATTCA
39197850 TCTTGGGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.37
Consensus pattern (11 bp):
ATTCAGAATTA
Found at i:39198124 original size:15 final size:15
Alignment explanation
Indices: 39198100--39198131 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
39198090 CATGCATGCA
*
39198100 AAATATAAAAGACAT
1 AAATACAAAAGACAT
39198115 AAATACAAAAGACAT
1 AAATACAAAAGACAT
39198130 AA
1 AA
39198132 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:39201496 original size:13 final size:13
Alignment explanation
Indices: 39201478--39201504 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39201468 GCCCGCTCAT
39201478 ATAAGCCTGCCAA
1 ATAAGCCTGCCAA
39201491 ATAAGCCTGCCAA
1 ATAAGCCTGCCAA
39201504 A
1 A
39201505 CTCTTGACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.30, G:0.15, T:0.15
Consensus pattern (13 bp):
ATAAGCCTGCCAA
Found at i:39209603 original size:22 final size:22
Alignment explanation
Indices: 39209577--39209621 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
39209567 ATTATGTGTA
*
39209577 TTAATTCATAATATAA-TTAATT
1 TTAATTCA-AATACAATTTAATT
*
39209599 TTAATTTAAATACAATTTAATT
1 TTAATTCAAATACAATTTAATT
39209621 T
1 T
39209622 GGGTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (22 bp):
TTAATTCAAATACAATTTAATT
Found at i:39217196 original size:46 final size:46
Alignment explanation
Indices: 39217144--39217237 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
39217134 ACATTGTAGG
39217144 TGTGACAAAATCTAGTTCTTATAATTCATGTATGAGCTGAATGAGT
1 TGTGACAAAATCTAGTTCTTATAATTCATGTATGAGCTGAATGAGT
39217190 TGTGACAAAATCTAGTTCTTATAATTCATGTATGAGCTGAATGAGT
1 TGTGACAAAATCTAGTTCTTATAATTCATGTATGAGCTGAATGAGT
39217236 TG
1 TG
39217238 GTGTCACATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.37
Consensus pattern (46 bp):
TGTGACAAAATCTAGTTCTTATAATTCATGTATGAGCTGAATGAGT
Found at i:39217837 original size:18 final size:18
Alignment explanation
Indices: 39217797--39217855 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
39217787 CATGAAAAAC
*
39217797 ATAAATAATTAAAAATA-
1 ATAAATATTTAAAAATAT
*
39217814 AAAAATATTTAAAAATAT
1 ATAAATATTTAAAAATAT
* *
39217832 ATAAAT-TAATAAAAAAAT
1 ATAAATAT-TTAAAAATAT
39217850 ATAAAT
1 ATAAAT
39217856 TCTTTTTCAG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
17 16 0.46
18 19 0.54
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAAATATTTAAAAATAT
Found at i:39218363 original size:19 final size:19
Alignment explanation
Indices: 39218341--39218467 Score: 155
Period size: 19 Copynumber: 6.5 Consensus size: 19
39218331 AGGGATATAC
39218341 AATCTTAGATATGATATGT
1 AATCTTAGATATGATATGT
* *
39218360 AATCTTAGATATAATATAT
1 AATCTTAGATATGATATGT
*
39218379 AATCTTAGATATGATATGC
1 AATCTTAGATATGATATGT
* *
39218398 AATCTTAGATATAATATAT
1 AATCTTAGATATGATATGT
*
39218417 AATCTTAGATATGATATGC
1 AATCTTAGATATGATATGT
*
39218436 AATCTTAGAAGATATGATTTTGT
1 AATCTT---AGATATGA-TATGT
39218459 AATCTTAGA
1 AATCTTAGA
39218468 GATTTAATTT
Statistics
Matches: 91, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
19 71 0.78
20 3 0.03
22 8 0.09
23 9 0.10
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (19 bp):
AATCTTAGATATGATATGT
Found at i:39218377 original size:38 final size:38
Alignment explanation
Indices: 39218335--39218444 Score: 202
Period size: 38 Copynumber: 2.9 Consensus size: 38
39218325 ATATTTAGGG
* *
39218335 ATATACAATCTTAGATATGATATGTAATCTTAGATATA
1 ATATATAATCTTAGATATGATATGCAATCTTAGATATA
39218373 ATATATAATCTTAGATATGATATGCAATCTTAGATATA
1 ATATATAATCTTAGATATGATATGCAATCTTAGATATA
39218411 ATATATAATCTTAGATATGATATGCAATCTTAGA
1 ATATATAATCTTAGATATGATATGCAATCTTAGA
39218445 AGATATGATT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 70 1.00
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (38 bp):
ATATATAATCTTAGATATGATATGCAATCTTAGATATA
Found at i:39218470 original size:22 final size:21
Alignment explanation
Indices: 39218347--39218501 Score: 101
Period size: 19 Copynumber: 7.7 Consensus size: 21
39218337 ATACAATCTT
*
39218347 AGATATGATATGTAATCTT--
1 AGATATGATTTGTAATCTTAG
* * *
39218366 AGATATAATATATAATCTT--
1 AGATATGATTTGTAATCTTAG
* *
39218385 AGATATGATATGCAATCTT--
1 AGATATGATTTGTAATCTTAG
* * *
39218404 AGATATAATATATAATCTT--
1 AGATATGATTTGTAATCTTAG
* *
39218423 AGATATGATATGCAATCTTAG
1 AGATATGATTTGTAATCTTAG
39218444 AAGATATGATTTTGTAATCTTAG
1 -AGATATGA-TTTGTAATCTTAG
* *
39218467 AGATTTAATTTGTAATCTTAG
1 AGATATGATTTGTAATCTTAG
* *
39218488 AGATTTAATTTGTA
1 AGATATGATTTGTA
39218502 GATACCCTTT
Statistics
Matches: 117, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
19 65 0.56
21 27 0.23
22 14 0.12
23 11 0.09
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.42
Consensus pattern (21 bp):
AGATATGATTTGTAATCTTAG
Found at i:39218480 original size:21 final size:21
Alignment explanation
Indices: 39218436--39218501 Score: 96
Period size: 21 Copynumber: 3.0 Consensus size: 21
39218426 TATGATATGC
* *
39218436 AATCTTAGAAGATATGATTTTGT
1 AATCTTAG-AGAT-TTAATTTGT
39218459 AATCTTAGAGATTTAATTTGT
1 AATCTTAGAGATTTAATTTGT
39218480 AATCTTAGAGATTTAATTTGT
1 AATCTTAGAGATTTAATTTGT
39218501 A
1 A
39218502 GATACCCTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
21 29 0.71
22 4 0.10
23 8 0.20
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (21 bp):
AATCTTAGAGATTTAATTTGT
Found at i:39221595 original size:3 final size:3
Alignment explanation
Indices: 39221587--39221613 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
39221577 TGAATGTGGT
39221587 GTA GTA GTA GTA GTA GTA GTA GTA GTA
1 GTA GTA GTA GTA GTA GTA GTA GTA GTA
39221614 TTAGAGTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GTA
Found at i:39234235 original size:7 final size:7
Alignment explanation
Indices: 39234223--39234250 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
39234213 CTTACACCGC
39234223 ATACCTT
1 ATACCTT
39234230 ATACCTT
1 ATACCTT
39234237 ATACCTT
1 ATACCTT
39234244 ATACCTT
1 ATACCTT
39234251 GCCACCATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (7 bp):
ATACCTT
Found at i:39243643 original size:45 final size:46
Alignment explanation
Indices: 39243570--39243694 Score: 125
Period size: 45 Copynumber: 2.8 Consensus size: 46
39243560 GACGGAAACG
* ** *
39243570 AGTAAGACCATAGCCT-AAAAACGTTATGGTAA-CATGATGAAAA-TA
1 AGTAAGACCATAG-CTGAAAGACACTATGGTAATCATGA-AAAAAGTA
*
39243615 AGTAAGACCATAGCTGAAAGACACTATGG-AATCATGAAAAAAGTG
1 AGTAAGACCATAGCTGAAAGACACTATGGTAATCATGAAAAAAGTA
* * *
39243660 AGTAAGACCATGGTTGAAAGACACAATGGT-ATCAT
1 AGTAAGACCATAGCTGAAAGACACTATGGTAATCAT
39243695 TGTAAATAGG
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
44 8 0.12
45 60 0.88
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.21
Consensus pattern (46 bp):
AGTAAGACCATAGCTGAAAGACACTATGGTAATCATGAAAAAAGTA
Found at i:39243711 original size:45 final size:45
Alignment explanation
Indices: 39243617--39243723 Score: 126
Period size: 45 Copynumber: 2.4 Consensus size: 45
39243607 TGAAAATAAG
* *
39243617 TAAGACCATAGCTGAAAGACACTATGGAATCATGAAAAAAGTGAG
1 TAAGACCATAGCTGAAAGACACAATGGAATCATGAAAAAAGTGAC
* * * * *
39243662 TAAGACCATGGTTGAAAGACACAATGGTATCATTGTAAATAG-GAC
1 TAAGACCATAGCTGAAAGACACAATGGAATCA-TGAAAAAAGTGAC
*
39243707 TAAGATCATAGCTGAAA
1 TAAGACCATAGCTGAAA
39243724 TACGCTACGA
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
45 44 0.86
46 7 0.14
ACGTcount: A:0.44, C:0.13, G:0.21, T:0.21
Consensus pattern (45 bp):
TAAGACCATAGCTGAAAGACACAATGGAATCATGAAAAAAGTGAC
Found at i:39249565 original size:33 final size:33
Alignment explanation
Indices: 39249528--39249604 Score: 145
Period size: 33 Copynumber: 2.3 Consensus size: 33
39249518 TGATCTTATA
39249528 ACACCAACCATTAAGCATCAAAGTGCCAAAAGC
1 ACACCAACCATTAAGCATCAAAGTGCCAAAAGC
*
39249561 ACACCAACCATTGAGCATCAAAGTGCCAAAAGC
1 ACACCAACCATTAAGCATCAAAGTGCCAAAAGC
39249594 ACACCAACCAT
1 ACACCAACCAT
39249605 CAAGGAATCA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.44, C:0.32, G:0.12, T:0.12
Consensus pattern (33 bp):
ACACCAACCATTAAGCATCAAAGTGCCAAAAGC
Found at i:39250895 original size:29 final size:29
Alignment explanation
Indices: 39250853--39251031 Score: 112
Period size: 29 Copynumber: 6.1 Consensus size: 29
39250843 GTGTGCTAAA
*
39250853 CGATGGTC-ATAACCGTCCCTTTTCATATT
1 CGATGGTCGA-AACCATCCCTTTTCATATT
39250882 CGATGGTCGAAACCATCCCTTTTCATTAGTT
1 CGATGGTCGAAACCATCCCTTTTCA-TA-TT
** *
39250913 -GATGGTCGTCACCATCCCTTTTCATAAT
1 CGATGGTCGAAACCATCCCTTTTCATATT
** * * *
39250941 CGACAG-CCAAAGCTATCCCTTTTCATAAT
1 CGATGGTCGAAA-CCATCCCTTTTCATATT
* * * * *
39250970 CTATAGCCGAAGCTATCCCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* * * *** *
39250999 CAATAGCCGAAGTTATCCCTTTTCATAAT
1 CGATGGTCGAAACCATCCCTTTTCATATT
39251028 CGAT
1 CGAT
39251032 AAACAAAGCT
Statistics
Matches: 125, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
28 3 0.02
29 92 0.74
30 28 0.22
31 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.13, T:0.35
Consensus pattern (29 bp):
CGATGGTCGAAACCATCCCTTTTCATATT
Found at i:39250919 original size:30 final size:30
Alignment explanation
Indices: 39250853--39250937 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
39250843 GTGTGCTAAA
*
39250853 CGATGGTC-ATAACCGTCCCTTTTCA-TATT
1 CGATGGTCGA-AACCATCCCTTTTCATTATT
39250882 CGATGGTCGAAACCATCCCTTTTCATTAGTT
1 CGATGGTCGAAACCATCCCTTTTCATTA-TT
**
39250913 -GATGGTCGTCACCATCCCTTTTCAT
1 CGATGGTCGAAACCATCCCTTTTCAT
39250938 AATCGACAGC
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
29 22 0.44
30 26 0.52
31 2 0.04
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.36
Consensus pattern (30 bp):
CGATGGTCGAAACCATCCCTTTTCATTATT
Found at i:39251044 original size:29 final size:29
Alignment explanation
Indices: 39250926--39251053 Score: 175
Period size: 29 Copynumber: 4.4 Consensus size: 29
39250916 GGTCGTCACC
*
39250926 ATCCCTTTTCATAATCGACAGCCAAAGCT
1 ATCCCTTTTCATAATCGATAGCCAAAGCT
* *
39250955 ATCCCTTTTCATAATCTATAGCCGAAGCT
1 ATCCCTTTTCATAATCGATAGCCAAAGCT
* * * *
39250984 ATCCCTTTTCATATTCAATAGCCGAAGTT
1 ATCCCTTTTCATAATCGATAGCCAAAGCT
**
39251013 ATCCCTTTTCATAATCGATAAACAAAGCT
1 ATCCCTTTTCATAATCGATAGCCAAAGCT
39251042 ATCCCTTTTCAT
1 ATCCCTTTTCAT
39251054 TGGTTGATGA
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 87 1.00
ACGTcount: A:0.30, C:0.27, G:0.09, T:0.34
Consensus pattern (29 bp):
ATCCCTTTTCATAATCGATAGCCAAAGCT
Found at i:39251561 original size:18 final size:18
Alignment explanation
Indices: 39251538--39251575 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
39251528 AAAAATCACT
39251538 TAACAA-AATACTTTTAAA
1 TAACAACAATA-TTTTAAA
39251556 TAACAACTAATATTTTAAA
1 TAACAAC-AATATTTTAAA
39251575 T
1 T
39251576 TCATAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 8 0.44
20 4 0.22
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (18 bp):
TAACAACAATATTTTAAA
Found at i:39258935 original size:23 final size:23
Alignment explanation
Indices: 39258903--39258946 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
39258893 ACTACCATTT
39258903 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
39258926 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
39258947 ATAGTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:39258939 original size:13 final size:11
Alignment explanation
Indices: 39258907--39258949 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
39258897 CCATTTTCTA
*
39258907 AATAAAATAAT
1 AATAAAATATT
39258918 AAT-AAATATCT
1 AATAAAATAT-T
39258929 AAGTAAAATATT
1 AA-TAAAATATT
39258941 AATAAAATA
1 AATAAAATA
39258950 GTTTTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:39259603 original size:17 final size:17
Alignment explanation
Indices: 39259562--39259594 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
39259552 TTCATTGTTG
39259562 AGTTTTTGGGTTTTTCA
1 AGTTTTTGGGTTTTTCA
39259579 AGTTTTTGGGTTTTTC
1 AGTTTTTGGGTTTTTC
39259595 GTGTTTTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.09, C:0.06, G:0.24, T:0.61
Consensus pattern (17 bp):
AGTTTTTGGGTTTTTCA
Found at i:39270165 original size:52 final size:52
Alignment explanation
Indices: 39270087--39270190 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
39270077 TGTTTCACAG
39270087 TTCTTTCACCTCCCAAGCCAAAATTCTAACTGGTTCTCACCATATGTCAGAT
1 TTCTTTCACCTCCCAAGCCAAAATTCTAACTGGTTCTCACCATATGTCAGAT
39270139 TTCTTTCACCTCCCAAGCCAAAATTCTAACTGGTTCTCACCATATGTCAGAT
1 TTCTTTCACCTCCCAAGCCAAAATTCTAACTGGTTCTCACCATATGTCAGAT
39270191 CAAGCTGTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.27, C:0.31, G:0.10, T:0.33
Consensus pattern (52 bp):
TTCTTTCACCTCCCAAGCCAAAATTCTAACTGGTTCTCACCATATGTCAGAT
Found at i:39272575 original size:2 final size:2
Alignment explanation
Indices: 39272570--39272671 Score: 197
Period size: 2 Copynumber: 51.5 Consensus size: 2
39272560 ACACACACAC
39272570 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
39272612 AG A- AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
39272653 AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG A
39272672 AGGAACCTGA
Statistics
Matches: 99, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 98 0.99
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39273965 original size:26 final size:26
Alignment explanation
Indices: 39273929--39273980 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
39273919 ATAATACATC
39273929 AACTCAGTAGCAAAAGTCATTCTTAA
1 AACTCAGTAGCAAAAGTCATTCTTAA
39273955 AACTCAGTAGCAAAAGTCATTCTTAA
1 AACTCAGTAGCAAAAGTCATTCTTAA
39273981 TAAGTGTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (26 bp):
AACTCAGTAGCAAAAGTCATTCTTAA
Found at i:39276285 original size:14 final size:13
Alignment explanation
Indices: 39276264--39276304 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 13
39276254 AATGTGTCTT
39276264 TTTAATGTTTATA
1 TTTAATGTTTATA
39276277 TTATAATGTTATATA
1 TT-TAATGTT-TATA
39276292 TTTAAT-TTTATA
1 TTTAATGTTTATA
39276304 T
1 T
39276305 AAATTACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 5 0.19
13 4 0.15
14 11 0.42
15 6 0.23
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (13 bp):
TTTAATGTTTATA
Found at i:39288688 original size:129 final size:129
Alignment explanation
Indices: 39288480--39288740 Score: 362
Period size: 129 Copynumber: 2.0 Consensus size: 129
39288470 AATTAATTCC
* * * *
39288480 AGAGGTAATCCTTGTCTAACTCCAACACTAATAAAAAAATACACGCTGAGGGGCATTTTGGGCAA
1 AGAGGTAATCCTTGTCCAACTCCAACACCAATAAAAAAATACACACTGAAGGGCATTTTGGGCAA
* *
39288545 AATTTTTAGGTTGTAATCAGAGTAAAAAGCCTTCTTTTGGTTGAGAGAAAGAAAAAATTGACTGT
66 AATTTTTAGGTTGTAATCAGAATAAAAAGCCTTCTTTTGGTTGAAAGAAAGAAAAAATT-ACTGT
* * * *
39288610 AGAGGTAGTTCTTGTCCAACTCCAACACCACT-AAAAAATACACACTGAAGGGCATTTTGGGCAT
1 AGAGGTAATCCTTGTCCAACTCCAACACCAATAAAAAAATACACACTGAAGGGCATTTTGGGCAA
* * ** * *
39288674 AATTTTTGGGTTGTAATTAGAATAAAAAGGTTTCTTTTGGTTGAAAGAAAGAGAAAATTACTTT
66 AATTTTTAGGTTGTAATCAGAATAAAAAGCCTTCTTTTGGTTGAAAGAAAGAAAAAATTACTGT
39288738 AGA
1 AGA
39288741 TTATTCAATT
Statistics
Matches: 115, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
128 7 0.06
129 81 0.70
130 27 0.23
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (129 bp):
AGAGGTAATCCTTGTCCAACTCCAACACCAATAAAAAAATACACACTGAAGGGCATTTTGGGCAA
AATTTTTAGGTTGTAATCAGAATAAAAAGCCTTCTTTTGGTTGAAAGAAAGAAAAAATTACTGT
Found at i:39291039 original size:14 final size:14
Alignment explanation
Indices: 39291020--39291048 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
39291010 AAAAAATCCC
39291020 TTTTTAGATCATTG
1 TTTTTAGATCATTG
39291034 TTTTTAGATCATTG
1 TTTTTAGATCATTG
39291048 T
1 T
39291049 GGACTACCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.59
Consensus pattern (14 bp):
TTTTTAGATCATTG
Found at i:39299107 original size:9 final size:9
Alignment explanation
Indices: 39299089--39299138 Score: 64
Period size: 9 Copynumber: 5.3 Consensus size: 9
39299079 CCCAAGTGTT
39299089 TTTATTTTA
1 TTTATTTTA
*
39299098 TTTCTTTTA
1 TTTATTTTA
39299107 TTTATTTTA
1 TTTATTTTA
39299116 TTTATTTTA
1 TTTATTTTA
*
39299125 CTTTCATATTA
1 -TTT-ATTTTA
39299136 TTT
1 TTT
39299139 TTATTATTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
9 25 0.69
10 6 0.17
11 5 0.14
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTATTTTA
Found at i:39299159 original size:21 final size:22
Alignment explanation
Indices: 39299133--39299176 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
39299123 TACTTTCATA
*
39299133 TTATTTTTATTA-TTACAAAAT
1 TTATTTTTATTATTTAAAAAAT
39299154 TTATTTTTATTATTTAAAAAAT
1 TTATTTTTATTATTTAAAAAAT
39299176 T
1 T
39299177 GAAAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TTATTTTTATTATTTAAAAAAT
Found at i:39301277 original size:21 final size:20
Alignment explanation
Indices: 39301251--39301291 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
39301241 CAATCACTGA
*
39301251 TTTATTTTAGTTTTTAGTTTT
1 TTTATTTTAATTTTTA-TTTT
39301272 TTTATTTTAATTTTTATTTT
1 TTTATTTTAATTTTTATTTT
39301292 CAGTTGTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTATTTTAATTTTTATTTT
Found at i:39301327 original size:21 final size:22
Alignment explanation
Indices: 39301274--39301334 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
39301264 TTAGTTTTTT
39301274 TATTTTAATTTTTATTTTCAGTTG
1 TATTTT-A-TTTTATTTTCAGTTG
39301298 TACTTTTATTTTATTGTT-AGTTG
1 TA-TTTTATTTTATT-TTCAGTTG
39301321 T-TTTTATTTTATTT
1 TATTTTATTTTATTT
39301335 GTGAGACTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
20 1 0.03
21 12 0.34
23 13 0.37
24 5 0.14
25 4 0.11
ACGTcount: A:0.18, C:0.03, G:0.08, T:0.70
Consensus pattern (22 bp):
TATTTTATTTTATTTTCAGTTG
Found at i:39316397 original size:33 final size:33
Alignment explanation
Indices: 39316354--39316430 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
39316344 TCCAAATAAT
* * * *
39316354 AACAACAAAATAGTAGCAAAATAGTGAGAAAAC
1 AACAAGAAAATAGTAGCAAAACAGTAAAAAAAC
* *
39316387 AACAAGAAAATAGTAGTAAAACAGTAAAAAAAT
1 AACAAGAAAATAGTAGCAAAACAGTAAAAAAAC
*
39316420 AGCAAGAAAAT
1 AACAAGAAAAT
39316431 TGAAGTTTTC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.64, C:0.09, G:0.14, T:0.13
Consensus pattern (33 bp):
AACAAGAAAATAGTAGCAAAACAGTAAAAAAAC
Found at i:39316418 original size:22 final size:22
Alignment explanation
Indices: 39316371--39316421 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
39316361 AAATAGTAGC
*
39316371 AAAATAGTGAGAAAACAACAAG
1 AAAATAGTGAGAAAACAACAAA
**
39316393 AAAATAGT-AGTAAAACAGTAAA
1 AAAATAGTGAG-AAAACAACAAA
39316415 AAAATAG
1 AAAATAG
39316422 CAAGAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.65, C:0.06, G:0.16, T:0.14
Consensus pattern (22 bp):
AAAATAGTGAGAAAACAACAAA
Found at i:39317718 original size:18 final size:18
Alignment explanation
Indices: 39317695--39317731 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
39317685 TATTTATGAG
*
39317695 AAATTAACTCTCAAGAAA
1 AAATTAAATCTCAAGAAA
*
39317713 AAATTAAATTTCAAGAAA
1 AAATTAAATCTCAAGAAA
39317731 A
1 A
39317732 TTAAATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.59, C:0.11, G:0.05, T:0.24
Consensus pattern (18 bp):
AAATTAAATCTCAAGAAA
Found at i:39318744 original size:10 final size:11
Alignment explanation
Indices: 39318709--39318750 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
39318699 AATAAAAATA
39318709 TAAAAATTATT
1 TAAAAATTATT
**
39318720 TAAATTTTATT
1 TAAAAATTATT
39318731 TAAAAATT-TT
1 TAAAAATTATT
39318741 TAAAAATTAT
1 TAAAAATTAT
39318751 AAAATATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TAAAAATTATT
Found at i:39318947 original size:19 final size:19
Alignment explanation
Indices: 39318925--39318998 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 19
39318915 ATTTTTTATG
39318925 ATTTTTATAAAATTTTACA
1 ATTTTTATAAAATTTTACA
* * *
39318944 ATTTTTATATATTTTTACG
1 ATTTTTATAAAATTTTACA
** *
39318963 ATTTTTATAATTTTTTTCTA
1 ATTTTTATAAAATTTTAC-A
39318983 ATTTTTAATAAAATTT
1 ATTTTT-ATAAAATTT
39318999 ATTATTTATT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 31 0.70
20 6 0.14
21 7 0.16
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (19 bp):
ATTTTTATAAAATTTTACA
Found at i:39319041 original size:9 final size:9
Alignment explanation
Indices: 39318909--39319042 Score: 74
Period size: 9 Copynumber: 14.4 Consensus size: 9
39318899 CTTTGATGCA
*
39318909 TTTTATATT
1 TTTTATAAT
*
39318918 TTTTATGAT
1 TTTTATAAT
*
39318927 TTTTATAAAA
1 TTTTAT-AAT
*
39318937 TTTTACAAT
1 TTTTATAAT
39318946 TTTTATATAT
1 TTTTATA-AT
**
39318956 TTTTACGAT
1 TTTTATAAT
39318965 TTTTATAATTT
1 TTTTATAA--T
*
39318976 TTTTCTAAT
1 TTTTATAAT
*
39318985 TTTTAATAAA
1 TTTT-ATAAT
* *
39318995 ATTTATTAT
1 TTTTATAAT
*
39319004 TTATTATAAC
1 TT-TTATAAT
***
39319014 TTTTATTGG
1 TTTTATAAT
39319023 TTTTAT--T
1 TTTTATAAT
39319030 TTTTATAAT
1 TTTTATAAT
39319039 TTTT
1 TTTT
39319043 TGCCACATGT
Statistics
Matches: 93, Mismatches: 24, Indels: 16
0.70 0.18 0.12
Matches are distributed among these distances:
7 6 0.06
9 53 0.57
10 26 0.28
11 8 0.09
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (9 bp):
TTTTATAAT
Found at i:39321532 original size:40 final size:39
Alignment explanation
Indices: 39321468--39321586 Score: 120
Period size: 40 Copynumber: 3.1 Consensus size: 39
39321458 AGTTTAGCAC
* *
39321468 CCAGTGCCTCATTAGATAATTCGAAGTAATAATTTGACA
1 CCAGTGCCTCATCAGATAAATCGAAGTAATAATTTGACA
* * *
39321507 TCCAGTGTCTCATCAGCTAAATCGAAGT-A-AATTGGTAC-
1 -CCAGTGCCTCATCAGATAAATCGAAGTAATAATTTG-ACA
*
39321545 CCAGTGCCTCATC-GAATATATCTGAAGTAATAATTTGACA
1 CCAGTGCCTCATCAG-ATAAATC-GAAGTAATAATTTGACA
39321585 CC
1 CC
39321587 CAGTATCTCA
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
36 1 0.02
37 17 0.27
38 10 0.16
39 6 0.09
40 30 0.47
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (39 bp):
CCAGTGCCTCATCAGATAAATCGAAGTAATAATTTGACA
Found at i:39321590 original size:41 final size:41
Alignment explanation
Indices: 39321465--39321600 Score: 117
Period size: 40 Copynumber: 3.4 Consensus size: 41
39321455 ACCAGTTTAG
*
39321465 CACCCAGTGCCTCAT-TAGATAAT-TCGAAGTAATAATTTGA
1 CACCCAGTGCCTCATCGAGATAATCT-GAAGTAATAATTTGA
* * * *
39321505 CATCCAGTGTCTCATC-AGCTAAATC-GAAGT-A-AA-TTGG
1 CACCCAGTGCCTCATCGAGAT-AATCTGAAGTAATAATTTGA
*
39321542 TACCCAGTGCCTCATCGA-ATATATCTGAAGTAATAATTTGA
1 CACCCAGTGCCTCATCGAGATA-ATCTGAAGTAATAATTTGA
**
39321583 CACCCAGTATCTCATCGA
1 CACCCAGTGCCTCATCGA
39321601 CTCGAAGTCG
Statistics
Matches: 75, Mismatches: 12, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
36 1 0.01
37 20 0.27
38 8 0.11
39 2 0.03
40 23 0.31
41 21 0.28
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (41 bp):
CACCCAGTGCCTCATCGAGATAATCTGAAGTAATAATTTGA
Found at i:39321783 original size:15 final size:15
Alignment explanation
Indices: 39321736--39321785 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 15
39321726 CAATTCAAAT
*
39321736 AATCAATATATATTC
1 AATCAATATAAATTC
39321751 AAT-ATATATACCAATTC
1 AATCA-ATATA--AATTC
39321768 AATCAATATAAATTC
1 AATCAATATAAATTC
39321783 AAT
1 AAT
39321786 AAATTCATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
14 1 0.03
15 16 0.53
17 12 0.40
18 1 0.03
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (15 bp):
AATCAATATAAATTC
Found at i:39321808 original size:24 final size:24
Alignment explanation
Indices: 39321763--39321809 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
39321753 TATATATACC
39321763 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
39321787 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
39321810 TCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:39323858 original size:7 final size:7
Alignment explanation
Indices: 39323846--39323898 Score: 54
Period size: 7 Copynumber: 7.1 Consensus size: 7
39323836 CATACATACT
39323846 TTTTATA
1 TTTTATA
39323853 TTTTATA
1 TTTTATA
39323860 TTTTACT-
1 TTTTA-TA
39323867 TTTCTAATA
1 TTT-T-ATA
*
39323876 TTTATACA
1 TTT-TATA
39323884 TTTTATA
1 TTTTATA
39323891 TTTTATA
1 TTTTATA
39323898 T
1 T
39323899 ATATGCATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
7 26 0.67
8 8 0.21
9 5 0.13
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (7 bp):
TTTTATA
Found at i:39324073 original size:16 final size:16
Alignment explanation
Indices: 39324040--39324073 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
39324030 TATTGTACAC
**
39324040 ATATATATGTATTTGA
1 ATATATATGTATACGA
39324056 ATATATATGTATACGA
1 ATATATATGTATACGA
39324072 AT
1 AT
39324074 TTTCATGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (16 bp):
ATATATATGTATACGA
Found at i:39325350 original size:21 final size:23
Alignment explanation
Indices: 39325324--39325375 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 23
39325314 AAAAGTTACA
39325324 AAAAAATTCAAAA-ATA-ATTTT
1 AAAAAATTCAAAATATATATTTT
*
39325345 AAAAAATTCAAAATTTATATTTT
1 AAAAAATTCAAAATATATATTTT
*
39325368 ATAAAATT
1 AAAAAATT
39325376 TTTAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 13 0.48
22 2 0.07
23 12 0.44
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (23 bp):
AAAAAATTCAAAATATATATTTT
Found at i:39325852 original size:21 final size:21
Alignment explanation
Indices: 39325828--39325867 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
39325818 ATTATATACT
39325828 ATTTTGATAAT-TTTTTAAATA
1 ATTTT-ATAATATTTTTAAATA
*
39325849 ATTTTATTATATTTTTAAA
1 ATTTTATAATATTTTTAAA
39325868 AATCCTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (21 bp):
ATTTTATAATATTTTTAAATA
Found at i:39326614 original size:27 final size:25
Alignment explanation
Indices: 39326584--39326641 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
39326574 AATATTAATA
*
39326584 TAAAATATAAAATTTTTATTATTTTTT
1 TAAAATAT-AAATTTTTA-TATATTTT
* **
39326611 TAAATTATTTATTTTTATATATTTT
1 TAAAATATAAATTTTTATATATTTT
39326636 TAAAAT
1 TAAAAT
39326642 TTATATATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 12 0.46
26 7 0.27
27 7 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
TAAAATATAAATTTTTATATATTTT
Found at i:39326645 original size:27 final size:25
Alignment explanation
Indices: 39326595--39326656 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
39326585 AAAATATAAA
* *
39326595 ATTTTTATTATTTTTTTAAATTATTT
1 ATTTTTATTA-TTTTTAAAATTATAT
39326621 ATTTTTATATATTTTTAAAATTTATAT
1 ATTTTTAT-TATTTTTAAAA-TTATAT
*
39326648 ATTATTATT
1 ATTTTTATT
39326657 TATTGCCAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 17 0.55
27 14 0.45
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (25 bp):
ATTTTTATTATTTTTAAAATTATAT
Found at i:39331485 original size:22 final size:22
Alignment explanation
Indices: 39331455--39331532 Score: 61
Period size: 22 Copynumber: 3.5 Consensus size: 22
39331445 TTAAGGAAAG
*
39331455 GAACCGTATTGTAGAATACTGC
1 GAACTGTATTGTAGAATACTGC
* *
39331477 GAACTGTATGTTTA-AA-AATGTC
1 GAACTGTAT-TGTAGAATACTG-C
*
39331499 GCAAACTGTATTGTAGAATACTAC
1 G--AACTGTATTGTAGAATACTGC
*
39331523 GAATTGTATT
1 GAACTGTATT
39331533 CCTCGTAAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
21 3 0.07
22 20 0.47
23 6 0.14
24 12 0.28
25 2 0.05
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (22 bp):
GAACTGTATTGTAGAATACTGC
Found at i:39331620 original size:39 final size:39
Alignment explanation
Indices: 39331544--39331620 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
39331534 CTCGTAAGTA
*
39331544 AAAGGTTGCGATCATAAATCAGCGAACCATGAGAAAGCT
1 AAAGGTTGCGATCATAAATCAGCGAACCATAAGAAAGCT
* * *
39331583 AAAGGTTGTGAT-AGTAAATCAGCGAACCGTAATAAAGC
1 AAAGGTTGCGATCA-TAAATCAGCGAACCATAAGAAAGC
39331621 CAAATGTCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 1 0.03
39 32 0.97
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.19
Consensus pattern (39 bp):
AAAGGTTGCGATCATAAATCAGCGAACCATAAGAAAGCT
Found at i:39331639 original size:39 final size:39
Alignment explanation
Indices: 39331553--39331650 Score: 97
Period size: 39 Copynumber: 2.5 Consensus size: 39
39331543 AAAAGGTTGC
* * * * **
39331553 GATCATAAATCAGCGAACCATGAGAAAGCTAAAGGTTGT
1 GATCGTAAATCAGCGAACCGTAAGAAAGCCAAAGGTCAT
* * *
39331592 GATAGTAAATCAGCGAACCGTAATAAAGCCAAATGTCAT
1 GATCGTAAATCAGCGAACCGTAAGAAAGCCAAAGGTCAT
* *
39331631 GATCGTAAATTAGTGAACCG
1 GATCGTAAATCAGCGAACCG
39331651 CGAGATTCAT
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.21
Consensus pattern (39 bp):
GATCGTAAATCAGCGAACCGTAAGAAAGCCAAAGGTCAT
Found at i:39331805 original size:93 final size:93
Alignment explanation
Indices: 39331583--39331882 Score: 379
Period size: 93 Copynumber: 3.2 Consensus size: 93
39331573 TGAGAAAGCT
* * * * * * *
39331583 AAAGGTTGTGATAGTAAATCAGCGAACCGTAATAAAGCCAAATGTCATGATCGTAAATTAG-TGA
1 AAAGGTCGTGATCGTAAATCAACGGACCGTAATAAAGCCAAAGGTCATGATCGTAAATCAGCAG-
* * *
39331647 ACCGCGAGATTCATTAAAT-TCGTAAGTA
65 ACCGCGAGATTCGTAAAATCCCGTAAGTA
* * * *
39331675 AAAGGTCGTGATTGTAAATCAATGGATCGTAAGAAAGCCAAAGGTCATGATCGTAAATCAGCAGA
1 AAAGGTCGTGATCGTAAATCAACGGACCGTAATAAAGCCAAAGGTCATGATCGTAAATCAGCAGA
*
39331740 CCGCAAGATTCGTAAAATCCCGTAAGTA
66 CCGCGAGATTCGTAAAATCCCGTAAGTA
* **
39331768 AAAGGTCGTGATCGTAAATCAACGGACCGTAATAAAGCTAAAGGTTGTGATCGTAAATCAGCAGA
1 AAAGGTCGTGATCGTAAATCAACGGACCGTAATAAAGCCAAAGGTCATGATCGTAAATCAGCAGA
* *
39331833 CCACGAGATTCGTAAAATCCCATAAGTA
66 CCGCGAGATTCGTAAAATCCCGTAAGTA
* *
39331861 AAAGGTCATGATCATAAATCAA
1 AAAGGTCGTGATCGTAAATCAA
39331883 TAGACCGCGA
Statistics
Matches: 180, Mismatches: 26, Indels: 3
0.86 0.12 0.01
Matches are distributed among these distances:
92 68 0.38
93 112 0.62
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (93 bp):
AAAGGTCGTGATCGTAAATCAACGGACCGTAATAAAGCCAAAGGTCATGATCGTAAATCAGCAGA
CCGCGAGATTCGTAAAATCCCGTAAGTA
Found at i:39331866 original size:54 final size:54
Alignment explanation
Indices: 39331807--39332051 Score: 265
Period size: 54 Copynumber: 4.5 Consensus size: 54
39331797 TAATAAAGCT
* * *
39331807 AAAGGTTGTGATCGTAAATCAGCAGACCACGAGATTCGTAAAATCCCATAAGTA
1 AAAGGTTGTGATCATAAATCAGCAGACCGCGAGATTCATAAAATCCCATAAGTA
** ** * *
39331861 AAAGGTCATGATCATAAATCAATAGACCGCGAGATTCATAAAATCTCGTAAGTA
1 AAAGGTTGTGATCATAAATCAGCAGACCGCGAGATTCATAAAATCCCATAAGTA
* * * *
39331915 AAAGGTTGTGATCATAAATCAGAAAACTGCGAGATTCATTAAATCCCATAAGTA
1 AAAGGTTGTGATCATAAATCAGCAGACCGCGAGATTCATAAAATCCCATAAGTA
* * * * * * ** *
39331969 AAAGGCTGTAATCTTAAATTAGCGGACTGCGAGATTTGTAAAATCCCGTAAGTA
1 AAAGGTTGTGATCATAAATCAGCAGACCGCGAGATTCATAAAATCCCATAAGTA
* * *
39332023 AAAGATCGTGATCATAAATCAGCGGACCG
1 AAAGGTTGTGATCATAAATCAGCAGACCG
39332052 TAAGAAAGCC
Statistics
Matches: 155, Mismatches: 36, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
54 155 1.00
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.24
Consensus pattern (54 bp):
AAAGGTTGTGATCATAAATCAGCAGACCGCGAGATTCATAAAATCCCATAAGTA
Done.