Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 94 of 182
Found at i:28436873 original size:129 final size:128
Alignment explanation
Indices: 28436535--28436931 Score: 580
Period size: 129 Copynumber: 3.1 Consensus size: 128
28436525 AGAACAAATC
* *
28436535 GAAGAAACCAATCCTATCTCCCTGAAGTTGTAGTGGAGTGAATTAAAACCACAGATCTTATCTCT
1 GAAGAAACCAATCCTATCTCCCTGAAGTT-AAGTGGAGCGAATTAAAACCACAGATCTTATCTCT
* * *
28436600 CTGAAGTTGCAGTAGAGCAGATCGCATCCAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGAC-
65 CTGAAGTTGCAGTAGAGCATATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACA
* * * * *
28436663 GAAGAAACCAATCATCTCTCTCTAAAGTTGAAGTGGAGCGGATTAAAACCACAGATCTTATCTCT
1 GAAGAAACCAATCCTATCTCCCTGAAGTT-AAGTGGAGCGAATTAAAACCACAGATCTTATCTCT
* * *
28436728 CTGAAGTTGCAATAGAGCATATCGCATCCAGTCTTATCTCTCTGAAGATGCAGTGGAGCAGACA
65 CTGAAGTTGCAGTAGAGCATATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACA
*
28436792 GAAGAAACCAATCCTATCTCCCTGAAGTTACAGTGGAGCGAATTAAAACCACAGATCTTATCCCT
1 GAAGAAACCAATCCTATCTCCCTGAAGTTA-AGTGGAGCGAATTAAAACCACAGATCTTATCTCT
* ** * * *
28436857 TTGAAGTTTTAGTAGAGCATATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGAGAAGCAGACA
65 CTGAAGTTGCAGTAGAGCATATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACA
28436921 GAAGAAACCAA
1 GAAGAAACCAA
28436932 AAGCAGACAG
Statistics
Matches: 239, Mismatches: 28, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
128 116 0.49
129 123 0.51
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (128 bp):
GAAGAAACCAATCCTATCTCCCTGAAGTTAAGTGGAGCGAATTAAAACCACAGATCTTATCTCTC
TGAAGTTGCAGTAGAGCATATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACA
Found at i:28436937 original size:20 final size:20
Alignment explanation
Indices: 28436912--28436951 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
28436902 AGTTGCAGAG
28436912 AAGCAGACAGAAGAAACCAA
1 AAGCAGACAGAAGAAACCAA
28436932 AAGCAGACAGAAGAAACCAA
1 AAGCAGACAGAAGAAACCAA
28436952 TCCTATCTCC
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:0.60, C:0.20, G:0.20, T:0.00
Consensus pattern (20 bp):
AAGCAGACAGAAGAAACCAA
Found at i:28437057 original size:149 final size:149
Alignment explanation
Indices: 28436784--28437077 Score: 464
Period size: 149 Copynumber: 2.0 Consensus size: 149
28436774 GATGCAGTGG
*
28436784 AGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTACAGTGGAGCGAATTAAAACCACAGATC
1 AGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTACAGTGGAGCGAATTAAAACCACAAATC
* * * *
28436849 TTATCCCTTTGAAGTTTTAGTAGAGCATATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGAGAA
66 TTATCCCTCTGAAGTTGTAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGAGAA
*
28436914 GCAGACAGAAGAAACCAAA
131 GCAAACAGAAGAAACCAAA
*
28436933 AGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGC-AGATTAAAACCACAAAT
1 AGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTACAGTGGAGCGA-ATTAAAACCACAAAT
* * * * *
28436997 CTTATCTCTCTGAAGTTGTAGTAGAGCAGATTGCATCCAGTCTTATCTCCCTGAATTTGCAGTGG
65 CTTATCCCTCTGAAGTTGTAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGAGA
28437062 AGCAAACAGAAGAAAC
130 AGCAAACAGAAGAAAC
28437078 TAATCCTATC
Statistics
Matches: 132, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
148 1 0.01
149 131 0.99
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.23
Consensus pattern (149 bp):
AGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTACAGTGGAGCGAATTAAAACCACAAATC
TTATCCCTCTGAAGTTGTAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGAGAA
GCAAACAGAAGAAACCAAA
Found at i:28437098 original size:85 final size:85
Alignment explanation
Indices: 28436955--28437413 Score: 275
Period size: 85 Copynumber: 5.3 Consensus size: 85
28436945 AAACCAATCC
** * * * *
28436955 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAAATCTTATCTCTCTGAAGTTGTAGTA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAACAAAACAACAAATCCTATCTCCCTGAAGTTGCAGTA
28437020 GAGCAGATTGCATCCAGTCT
66 GAGCAGATTGCATCCAGTCT
* *
28437040 TATCTCCCTGAATTTGCAGTGGAGCA-AACAGAAGA-AACTAATCCTATCTCCCTGAAGTTGCAG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAACA-AA-ACAACAAATCCTATCTCCCTGAAGTTGCAG
* * ** *
28437103 TGGAGTAGATTAAAACCACAGATCT
64 TAGAGCAGATT-GCATC-CAG-TCT
* * * *** * * * * *
28437128 TATCTCTCTGAAGTTGTAGTAGAGCAG---ATTGCATCCAGTCTTATCTCCCTGAAGTTGCAGTG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAACAAAACAACAAATCCTATCTCCCTGAAGTTGCAGTA
** * * * *
28437190 GAGCAGACAAAAGAAACCAATCC
66 GAGCAG---ATTGCATCCAGTCT
* * * ** * * * * *
28437213 TATCTCCTTAAAGTTGCAGTGGAGCGGATTAAAACCACATATCTTATCTCTCTGAAGTTGCAATA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAACAAAACAACAAATCCTATCTCCCTGAAGTTGCAGTA
*
28437278 GAGCAGATCGCATCCAGTCT
66 GAGCAGATTGCATCCAGTCT
*** * * *
28437298 TATCTTTTTGAAGTTGCAATGGAGCAG-ACAGAAGA-AACCAATCCTATCTCCCTAAAGTTGCAG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAACA-AA-ACAACAAATCCTATCTCCCTGAAGTTGCAG
* ** *
28437361 TAGAGCGGATTAAAACCACAGATCT
64 TAGAGCAGATT-GCATC-CAG-TCT
* *
28437386 TATCTCCTTGAAGTTGCAGTAGAGCAGA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA
28437414 TCGCATCGAG
Statistics
Matches: 278, Mismatches: 77, Indels: 34
0.71 0.20 0.09
Matches are distributed among these distances:
84 3 0.01
85 175 0.63
86 9 0.03
87 9 0.03
88 82 0.29
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (85 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGAACAAAACAACAAATCCTATCTCCCTGAAGTTGCAGTA
GAGCAGATTGCATCCAGTCT
Found at i:28437168 original size:129 final size:129
Alignment explanation
Indices: 28436933--28437454 Score: 812
Period size: 129 Copynumber: 4.0 Consensus size: 129
28436923 AGAAACCAAA
* *
28436933 AGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAAATC
1 AGCAGACAGAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAACCACAGATC
* * *
28436998 TTATCTCTCTGAAGTTGTAGTAGAGCAGATTGCATCCAGTCTTATCTCCCTGAATTTGCAGTGG
66 TTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGG
* * * *
28437062 AGCAAACAGAAGAAACTAATCCTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAACCACAGATC
1 AGCAGACAGAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAACCACAGATC
* *
28437127 TTATCTCTCTGAAGTTGTAGTAGAGCAGATTGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGG
66 TTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGG
* * * *
28437191 AGCAGACAAAAGAAACCAATCCTATCTCCTTAAAGTTGCAGTGGAGCGGATTAAAACCACATATC
1 AGCAGACAGAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAACCACAGATC
* *** *
28437256 TTATCTCTCTGAAGTTGCAATAGAGCAGATCGCATCCAGTCTTATCTTTTTGAAGTTGCAATGG
66 TTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGG
* *
28437320 AGCAGACAGAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTAGAGCGGATTAAAACCACAGATC
1 AGCAGACAGAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAACCACAGATC
* *
28437385 TTATCTC-CTTGAAGTTGCAGTAGAGCAGATCGCATCGAGTCTTATCTTCCTGAAGTTGCAGTGG
66 TTATCTCTC-TGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGG
28437449 AGCAGA
1 AGCAGA
28437455 TCCAAATGAT
Statistics
Matches: 363, Mismatches: 29, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
128 1 0.00
129 362 1.00
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (129 bp):
AGCAGACAGAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAACCACAGATC
TTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGG
Found at i:28437443 original size:85 final size:84
Alignment explanation
Indices: 28437084--28437515 Score: 302
Period size: 85 Copynumber: 5.1 Consensus size: 84
28437074 AAACTAATCC
* *
28437084 TATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGTAGTA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCT-TGAAGTTGCAGTA
*
28437149 GAGCAGATTGCATCCAGTCT
65 GAGCAGATAGCATCCAGTCT
* ** * *
28437169 TATCTCCCTGAAGTTGCAGTGGAGCAGA-CAAAAGAAACCA-ATCCTATCTCCTTAAAGTTGCAG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAA-CCA-CAGATCTTATCT-CTTGAAGTTGCAG
* * ** * *
28437232 TGGAGCGGATTAAAACCACATATCT
63 TAGAGCAGA-TAGCATC-CA-GTCT
* * * *** * *
28437257 TATCTCTCTGAAGTTGCAATAGAGCAGA-TCGCATC-CAG-TCTTATCTTTTTGAAGTTGCAATG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATC-TCTTGAAGTTGC-A-G
* * * * *
28437319 GAGCAGACAGA-AGAAACCAATCC
63 TAG-AG-CAGATAGCATCCAGTCT
* * *
28437342 TATCTCCCTAAAGTTGCAGTAGAGCGGATTAAAACCACAGATCTTATCTCCTTGAAGTTGCAGTA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCT-CTTGAAGTTGCAGTA
* *
28437407 GAGCAGATCGCATCGAGTCT
65 GAGCAGATAGCATCCAGTCT
* ** ** ** * *
28437427 TATCTTCCTGAAGTTGCAGTGGAGCAGATCCAAATGATGGATCTCATCTCTCTGAAGTTACAGTA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCT-TGAAGTTGCAGTA
* *
28437492 GAGCAGATCGCAT-CAGACT
65 GAGCAGATAGCATCCAGTCT
28437511 TATCT
1 TATCT
28437516 TTAAGTTGTA
Statistics
Matches: 267, Mismatches: 62, Indels: 37
0.73 0.17 0.10
Matches are distributed among these distances:
84 19 0.07
85 167 0.63
86 17 0.06
87 13 0.05
88 48 0.18
89 3 0.01
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.28
Consensus pattern (84 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTTGAAGTTGCAGTAG
AGCAGATAGCATCCAGTCT
Found at i:28437456 original size:41 final size:40
Alignment explanation
Indices: 28437383--28437515 Score: 137
Period size: 41 Copynumber: 3.2 Consensus size: 40
28437373 AAACCACAGA
28437383 TCTTATCTCCTTGAAGTTGCAGTAGAGCAGATCGCATCGAG
1 TCTTATCTCC-TGAAGTTGCAGTAGAGCAGATCGCATCGAG
*
28437424 TCTTATCTTCCTGAAGTTGCAGTGGAGCAGATC-CAAAT-GATGG
1 TCTTATC-TCCTGAAGTTGCAGTAGAGCAGATCGC--ATCGA--G
* *
28437467 ATCTCATCTCTCTGAAGTTACAGTAGAGCAGATCGCATC-AG
1 -TCTTATCTC-CTGAAGTTGCAGTAGAGCAGATCGCATCGAG
*
28437508 ACTTATCT
1 TCTTATCT
28437516 TTAAGTTGTA
Statistics
Matches: 77, Mismatches: 6, Indels: 19
0.75 0.06 0.19
Matches are distributed among these distances:
40 7 0.09
41 31 0.40
42 5 0.06
43 6 0.08
44 27 0.35
45 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (40 bp):
TCTTATCTCCTGAAGTTGCAGTAGAGCAGATCGCATCGAG
Found at i:28438368 original size:6 final size:7
Alignment explanation
Indices: 28438352--28438376 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28438342 GCTGCTGTTC
28438352 TTTTTAT
1 TTTTTAT
28438359 TTTTTAT
1 TTTTTAT
28438366 TTTTTAT
1 TTTTTAT
28438373 TTTT
1 TTTT
28438377 GATTGATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:28439017 original size:3 final size:3
Alignment explanation
Indices: 28439009--28439108 Score: 103
Period size: 3 Copynumber: 33.7 Consensus size: 3
28438999 TTAGTTTAAG
* * * *
28439009 ATT ATT ATT AAT -TT AGT ATC ATT ATT ATT ATT ATT ATT ATT ATT AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* ** * *
28439056 ACT ATT ATT ATT ATT ATT GGT ATT ATT ATT CTT ATT ATT TTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
28439104 TTT AT
1 ATT AT
28439109 CAACTTATTT
Statistics
Matches: 77, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
2 1 0.01
3 76 0.99
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:28439501 original size:29 final size:28
Alignment explanation
Indices: 28439463--28439539 Score: 100
Period size: 29 Copynumber: 2.7 Consensus size: 28
28439453 CTCTTTTAAA
*
28439463 TATTTTAATATCTTTAATTTATTTCAACT
1 TATTTTAATAT-TTTAATTTATTTAAACT
* *
28439492 TATTTCAATATTGTTAATTTATTTAAATT
1 TATTTTAATATT-TTAATTTATTTAAACT
*
28439521 TATTTTAACATTTTAATTT
1 TATTTTAATATTTTAATTT
28439540 TTATATATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 8 0.19
29 34 0.81
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.60
Consensus pattern (28 bp):
TATTTTAATATTTTAATTTATTTAAACT
Found at i:28441168 original size:20 final size:20
Alignment explanation
Indices: 28441131--28441168 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28441121 CCAAACTCTT
*
28441131 AAACCTTGAACTTGAACCCC
1 AAACCTTGAACTTAAACCCC
28441151 AAACC-TGAACCTTAAACC
1 AAACCTTGAA-CTTAAACC
28441169 TTAAATCTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.39, C:0.34, G:0.08, T:0.18
Consensus pattern (20 bp):
AAACCTTGAACTTAAACCCC
Found at i:28441753 original size:28 final size:28
Alignment explanation
Indices: 28441688--28441765 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
28441678 ATGAAAGCTA
**
28441688 AGAAGAGAAAGAAAAGCAAGAGAAGTTG
1 AGAAGAGAAAGAAAAGCAAGAGAAGCAG
*
28441716 AGGAA-AGAAAGAAAAGCGAGAGAAGCAG
1 A-GAAGAGAAAGAAAAGCAAGAGAAGCAG
*
28441744 AGAAGTGAAAGAAGAA-CAAGAG
1 AGAAGAGAAAGAA-AAGCAAGAG
28441766 GTTGATGAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
27 3 0.07
28 34 0.81
29 5 0.12
ACGTcount: A:0.58, C:0.05, G:0.33, T:0.04
Consensus pattern (28 bp):
AGAAGAGAAAGAAAAGCAAGAGAAGCAG
Found at i:28441778 original size:6 final size:6
Alignment explanation
Indices: 28441769--28441800 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
28441759 ACAAGAGGTT
28441769 GATGAA GATGAA GATGAA GATGAA GATGAA GA
1 GATGAA GATGAA GATGAA GATGAA GATGAA GA
28441801 GAGAAAACAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.34, T:0.16
Consensus pattern (6 bp):
GATGAA
Found at i:28442328 original size:28 final size:28
Alignment explanation
Indices: 28442297--28442350 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
28442287 AAGAATCTCA
*
28442297 AACCATGAACCCAAAAC-CTATAACCTTG
1 AACCATAAACCCAAAACTC-ATAACCTTG
* *
28442325 AACCCTAAATCCAAAACTCATAACCT
1 AACCATAAACCCAAAACTCATAACCT
28442351 ATAACCCCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 21 0.95
29 1 0.05
ACGTcount: A:0.44, C:0.33, G:0.04, T:0.19
Consensus pattern (28 bp):
AACCATAAACCCAAAACTCATAACCTTG
Found at i:28442936 original size:28 final size:28
Alignment explanation
Indices: 28442901--28442996 Score: 140
Period size: 28 Copynumber: 3.4 Consensus size: 28
28442891 AAAGCAGAGA
28442901 AGAGAAAGAAAAGCAAAAGAAGAAAATG
1 AGAGAAAGAAAAGCAAAAGAAGAAAATG
*
28442929 AGAGAAAGAAAAGCAAAAGAAGAAGA-G
1 AGAGAAAGAAAAGCAAAAGAAGAAAATG
* * *
28442956 AAGAGAAATAAAACCAAAAGAAGAAAATA
1 -AGAGAAAGAAAAGCAAAAGAAGAAAATG
28442985 AGAGAAAGAAAA
1 AGAGAAAGAAAA
28442997 ATAAGAGGTT
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
27 1 0.02
28 59 0.98
ACGTcount: A:0.70, C:0.04, G:0.23, T:0.03
Consensus pattern (28 bp):
AGAGAAAGAAAAGCAAAAGAAGAAAATG
Found at i:28442992 original size:17 final size:17
Alignment explanation
Indices: 28442916--28443003 Score: 58
Period size: 19 Copynumber: 5.0 Consensus size: 17
28442906 AAGAAAAGCA
*
28442916 AAAGAAGAAAATGAGAG
1 AAAGAAGAAAATAAGAG
28442933 AAAGAA-AAGCAA-AAGAAG
1 AAAGAAGAA--AATAAG-AG
* *
28442951 AAGAGAAGAGAAATAAAACCA
1 AA-AGAAGA-AAATAAGA--G
28442972 AAAGAAGAAAATAAGAG
1 AAAGAAGAAAATAAGAG
28442989 AAAG-A-AAAATAAGAG
1 AAAGAAGAAAATAAGAG
28443004 GTTGATCAAG
Statistics
Matches: 57, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
15 10 0.18
16 3 0.05
17 12 0.21
18 6 0.11
19 14 0.25
20 9 0.16
21 3 0.05
ACGTcount: A:0.69, C:0.03, G:0.23, T:0.05
Consensus pattern (17 bp):
AAAGAAGAAAATAAGAG
Found at i:28444147 original size:28 final size:28
Alignment explanation
Indices: 28444125--28444185 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
28444115 GAAAGAAATG
* * * *
28444125 CAAGAGAAGTAGAGTAGAAAAAGAAAAA
1 CAAGAAAAGCAGAGAAGAGAAAGAAAAA
28444153 CAAGAAAAGCAGAGAAGAGAAAGAAAAA
1 CAAGAAAAGCAGAGAAGAGAAAGAAAAA
28444181 CAAGA
1 CAAGA
28444186 GGTTGATGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.66, C:0.07, G:0.25, T:0.03
Consensus pattern (28 bp):
CAAGAAAAGCAGAGAAGAGAAAGAAAAA
Found at i:28445405 original size:28 final size:28
Alignment explanation
Indices: 28445365--28445448 Score: 123
Period size: 28 Copynumber: 3.0 Consensus size: 28
28445355 GGAAACGTGA
*
28445365 AAGCAGAGAAGAGAAAGAAAAGCAAGCG
1 AAGCAGAGAAGAGAAAGAAAAGCAAGAG
* *
28445393 AAGTAGAGTAGAGAAAGAAAAGCAAGAG
1 AAGCAGAGAAGAGAAAGAAAAGCAAGAG
* *
28445421 AAGCAGAGAAGAGAAATAAAAACAAGAG
1 AAGCAGAGAAGAGAAAGAAAAGCAAGAG
28445449 GTTGACAAAG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.60, C:0.07, G:0.30, T:0.04
Consensus pattern (28 bp):
AAGCAGAGAAGAGAAAGAAAAGCAAGAG
Found at i:28446370 original size:28 final size:27
Alignment explanation
Indices: 28446334--28446417 Score: 123
Period size: 28 Copynumber: 3.0 Consensus size: 27
28446324 ACATGAAAGG
28446334 AGAGAAGAGAAAGAAAAGCAAGAGAAGT
1 AGAGAAGAGAAAGAAAA-CAAGAGAAGT
* *
28446362 AGAGGAGAGAAAGAAACACAAAAGAAGT
1 AGAGAAGAGAAAGAAA-ACAAGAGAAGT
28446390 AGAGAAGAGAAAGAAAAACAAGAGAAGT
1 AGAGAAGAGAAAG-AAAACAAGAGAAGT
28446418 GTAACATCCC
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
28 46 0.92
29 4 0.08
ACGTcount: A:0.62, C:0.05, G:0.30, T:0.04
Consensus pattern (27 bp):
AGAGAAGAGAAAGAAAACAAGAGAAGT
Found at i:28450043 original size:28 final size:28
Alignment explanation
Indices: 28450004--28450106 Score: 107
Period size: 28 Copynumber: 3.7 Consensus size: 28
28449994 ATGAAAGGAG
* *
28450004 AGAAAAGAAAGAAACACAAGAGAAGCAG
1 AGAAGAGAAAGAAACACAAGAGAAGCAA
* * * *
28450032 ATAAGTGAAAGAAAAACAAAAGAAGCAA
1 AGAAGAGAAAGAAACACAAGAGAAGCAA
* * *
28450060 AGGAGAGAAAGAAACGCAAGAGAAACAA
1 AGAAGAGAAAGAAACACAAGAGAAGCAA
* *
28450088 AGCAGAGAAAGAAAAACAA
1 AGAAGAGAAAGAAACACAA
28450107 AAGGTTGATG
Statistics
Matches: 59, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 59 1.00
ACGTcount: A:0.65, C:0.10, G:0.23, T:0.02
Consensus pattern (28 bp):
AGAAGAGAAAGAAACACAAGAGAAGCAA
Found at i:28450083 original size:15 final size:13
Alignment explanation
Indices: 28450058--28450101 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
28450048 CAAAAGAAGC
*
28450058 AAAGGAGAGAAAG
1 AAAGCAGAGAAAG
*
28450071 AAACGCAAGAGAAAC
1 AAA-GC-AGAGAAAG
28450086 AAAGCAGAGAAAG
1 AAAGCAGAGAAAG
28450099 AAA
1 AAA
28450102 AACAAAAGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 13 0.50
14 3 0.12
15 10 0.38
ACGTcount: A:0.64, C:0.09, G:0.27, T:0.00
Consensus pattern (13 bp):
AAAGCAGAGAAAG
Found at i:28459735 original size:40 final size:39
Alignment explanation
Indices: 28459679--28459860 Score: 222
Period size: 40 Copynumber: 4.6 Consensus size: 39
28459669 GAAGTATAAA
*
28459679 CAGGGGCACGTATGTGCAATCAGATGTACCGAAATACAAG
1 CAGGGGCACGTATGTGCAATCAG-GGTACCGAAATACAAG
*
28459719 TAGGGGCACGTATGTGCAATCATGGGTACC-AAAGTACAAG
1 CAGGGGCACGTATGTGCAATCA-GGGTACCGAAA-TACAAG
* * *
28459759 TAGGGGCACGTATGTGCAATCAGGGGTATCGAAGTACAAG
1 CAGGGGCACGTATGTGCAATCA-GGGTACCGAAATACAAG
* * * *
28459799 CAGGGGCACATATATGCAATCAGGGATACCGAAGTACAAA
1 CAGGGGCACGTATGTGCAATCAGGG-TACCGAAATACAAG
*
28459839 CAGAGGCACGTATGTGCAATCA
1 CAGGGGCACGTATGTGCAATCA
28459861 TGTATAATTA
Statistics
Matches: 125, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
39 6 0.05
40 116 0.93
41 3 0.02
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.18
Consensus pattern (39 bp):
CAGGGGCACGTATGTGCAATCAGGGTACCGAAATACAAG
Found at i:28459804 original size:80 final size:80
Alignment explanation
Indices: 28459670--28459860 Score: 258
Period size: 80 Copynumber: 2.4 Consensus size: 80
28459660 GAAATTACTG
* * * * *
28459670 AAGTATAAACAGGGGCACGTATGTGCAATCAGATGTACCGAAATACAAGTAGGGGCACGTATGTG
1 AAGTACAAACAGGGGCACGTATGTGCAATCAGAGGTACCGAAATACAAGCAGGGGCACATATATG
28459735 CAATCATGGG-TACCA
66 CAATCA-GGGATACCA
** * * *
28459750 AAGTACAAGTAGGGGCACGTATGTGCAATCAGGGGTATCGAAGTACAAGCAGGGGCACATATATG
1 AAGTACAAACAGGGGCACGTATGTGCAATCAGAGGTACCGAAATACAAGCAGGGGCACATATATG
*
28459815 CAATCAGGGATACCG
66 CAATCAGGGATACCA
*
28459830 AAGTACAAACAGAGGCACGTATGTGCAATCA
1 AAGTACAAACAGGGGCACGTATGTGCAATCA
28459861 TGTATAATTA
Statistics
Matches: 96, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
79 3 0.03
80 93 0.97
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.18
Consensus pattern (80 bp):
AAGTACAAACAGGGGCACGTATGTGCAATCAGAGGTACCGAAATACAAGCAGGGGCACATATATG
CAATCAGGGATACCA
Found at i:28460355 original size:14 final size:14
Alignment explanation
Indices: 28460321--28460348 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28460311 AACAATTTCA
28460321 ACAAAATTCACCTT
1 ACAAAATTCACCTT
28460335 ACAAAATTCACCTT
1 ACAAAATTCACCTT
28460349 TAAAAATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.29, G:0.00, T:0.29
Consensus pattern (14 bp):
ACAAAATTCACCTT
Found at i:28463786 original size:25 final size:25
Alignment explanation
Indices: 28463758--28463814 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
28463748 CTAGAATCAT
28463758 ATCAAACTCACCAAAAGGTAAAAAC
1 ATCAAACTCACCAAAAGGTAAAAAC
28463783 ATCAAACTCACCAAAAGGTAAAAAC
1 ATCAAACTCACCAAAAGGTAAAAAC
28463808 ATCAAAC
1 ATCAAAC
28463815 ATCAAACTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.56, C:0.25, G:0.07, T:0.12
Consensus pattern (25 bp):
ATCAAACTCACCAAAAGGTAAAAAC
Found at i:28469369 original size:20 final size:20
Alignment explanation
Indices: 28469344--28469489 Score: 98
Period size: 20 Copynumber: 7.3 Consensus size: 20
28469334 AAAGTATAAA
28469344 CAGGGGCACGTATGTGCAAT
1 CAGGGGCACGTATGTGCAAT
* * * * *
28469364 CAGGGGTACCTAAGTACAAG
1 CAGGGGCACGTATGTGCAAT
*
28469384 CAGGGGCACGTTTGTGCAAT
1 CAGGGGCACGTATGTGCAAT
* * * * *
28469404 CATGGGTATCG-AAGTACAAG
1 CAGGGGCA-CGTATGTGCAAT
* *
28469424 CAGGGGCACGTATGAGGAAT
1 CAGGGGCACGTATGTGCAAT
* * * *
28469444 CAGGGGTACCG-AAGTACAAA
1 CAGGGGCA-CGTATGTGCAAT
*
28469464 CAAGGGCACGTATGTGCAAT
1 CAGGGGCACGTATGTGCAAT
28469484 CAGGGG
1 CAGGGG
28469490 TACCAAGTAC
Statistics
Matches: 86, Mismatches: 36, Indels: 8
0.66 0.28 0.06
Matches are distributed among these distances:
19 4 0.05
20 78 0.91
21 4 0.05
ACGTcount: A:0.30, C:0.18, G:0.34, T:0.17
Consensus pattern (20 bp):
CAGGGGCACGTATGTGCAAT
Found at i:28469390 original size:40 final size:40
Alignment explanation
Indices: 28469335--28469524 Score: 240
Period size: 40 Copynumber: 4.8 Consensus size: 40
28469325 GAAATTACTA
* *
28469335 AAGTATAAACAGGGGCACGTATGTGCAATCAGGGGTACCT
1 AAGTACAAACAGGGGCACGTATGTGCAATCAGGGGTACCG
* * * *
28469375 AAGTACAAGCAGGGGCACGTTTGTGCAATCATGGGTATCG
1 AAGTACAAACAGGGGCACGTATGTGCAATCAGGGGTACCG
* * *
28469415 AAGTACAAGCAGGGGCACGTATGAGGAATCAGGGGTACCG
1 AAGTACAAACAGGGGCACGTATGTGCAATCAGGGGTACCG
*
28469455 AAGTACAAACAAGGGCACGTATGTGCAATCAGGGGTACC-
1 AAGTACAAACAGGGGCACGTATGTGCAATCAGGGGTACCG
* * *
28469494 AAGTACAAA-TGGGGCCCTTTATGTGCAATCA
1 AAGTACAAACAGGGGCAC-GTATGTGCAATCA
28469525 TGTATAATTA
Statistics
Matches: 130, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
38 5 0.04
39 21 0.16
40 104 0.80
ACGTcount: A:0.32, C:0.18, G:0.31, T:0.19
Consensus pattern (40 bp):
AAGTACAAACAGGGGCACGTATGTGCAATCAGGGGTACCG
Found at i:28476576 original size:42 final size:42
Alignment explanation
Indices: 28476528--28476681 Score: 231
Period size: 42 Copynumber: 3.7 Consensus size: 42
28476518 TACACCGGCT
* *
28476528 TTAAGCCTGCTAAACTTATAGT-TCGAATTTATTTCACTGGCA
1 TTAAGCCTGCTAAACGTAAAGTCT-GAATTTATTTCACTGGCA
*
28476570 TTAAGCCTGCTAGACGTAAAGTCTGAATTTATTTCACTGGCA
1 TTAAGCCTGCTAAACGTAAAGTCTGAATTTATTTCACTGGCA
*
28476612 TTAAGCCTGCTAAACGTAAAGTCTGAATTTATTTCACTAGCA
1 TTAAGCCTGCTAAACGTAAAGTCTGAATTTATTTCACTGGCA
*
28476654 TTAAGCATGC-AAGACGTAAAGTCTGAAT
1 TTAAGCCTGCTAA-ACGTAAAGTCTGAAT
28476682 GGTTTCACTG
Statistics
Matches: 104, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
41 2 0.02
42 101 0.97
43 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (42 bp):
TTAAGCCTGCTAAACGTAAAGTCTGAATTTATTTCACTGGCA
Found at i:28482785 original size:12 final size:12
Alignment explanation
Indices: 28482768--28482797 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
28482758 GTTCTTAAAG
28482768 GTATGAGGCCAA
1 GTATGAGGCCAA
*
28482780 GTATGAGGCCGA
1 GTATGAGGCCAA
28482792 GTATGA
1 GTATGA
28482798 CTGAGCCGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.13, G:0.37, T:0.20
Consensus pattern (12 bp):
GTATGAGGCCAA
Found at i:28490365 original size:24 final size:24
Alignment explanation
Indices: 28490338--28490389 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
28490328 TATTTCTTGC
28490338 TTTTCATTTTAGTTTATTTTCAGT
1 TTTTCATTTTAGTTTATTTTCAGT
** *
28490362 TTTTTTTTTTAGTTTATTTTCTGT
1 TTTTCATTTTAGTTTATTTTCAGT
28490386 TTTT
1 TTTT
28490390 TATCTTTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.12, C:0.06, G:0.08, T:0.75
Consensus pattern (24 bp):
TTTTCATTTTAGTTTATTTTCAGT
Found at i:28490390 original size:24 final size:24
Alignment explanation
Indices: 28490344--28490390 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
28490334 TTGCTTTTCA
28490344 TTTTAGTTTATTTTCAGTTTTTTT
1 TTTTAGTTTATTTTCAGTTTTTTT
*
28490368 TTTTAGTTTATTTTCTGTTTTTT
1 TTTTAGTTTATTTTCAGTTTTTT
28490391 ATCTTTGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.11, C:0.04, G:0.09, T:0.77
Consensus pattern (24 bp):
TTTTAGTTTATTTTCAGTTTTTTT
Found at i:28490400 original size:24 final size:25
Alignment explanation
Indices: 28490345--28490400 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 25
28490335 TGCTTTTCAT
* *
28490345 TTTAGTTTATTTTCAGTTTTTT-TT
1 TTTAGTTTATTTTCTGTTTTTTATC
28490369 TTTAGTTTATTTTCTGTTTTTTATC
1 TTTAGTTTATTTTCTGTTTTTTATC
28490394 TTT-GTTT
1 TTTAGTTT
28490401 TTTAATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 25 0.86
25 4 0.14
ACGTcount: A:0.11, C:0.05, G:0.09, T:0.75
Consensus pattern (25 bp):
TTTAGTTTATTTTCTGTTTTTTATC
Found at i:28495882 original size:21 final size:22
Alignment explanation
Indices: 28495857--28495903 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
28495847 ATAAAATTAA
* *
28495857 TATTATATACTC-ATTCTTATT
1 TATTATATACTCTAATCTAATT
*
28495878 TATTATATTCTCTAATCTAATT
1 TATTATATACTCTAATCTAATT
28495900 TATT
1 TATT
28495904 TAATTAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (22 bp):
TATTATATACTCTAATCTAATT
Found at i:28512474 original size:36 final size:36
Alignment explanation
Indices: 28512434--28512503 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
28512424 TTTCGTTAAG
*
28512434 AAATTGATTATAATAATTTGTGTATAATATATAAAT
1 AAATTGATTATAATAATTTGTATATAATATATAAAT
28512470 AAATTGATTATAATAATTTGTATATAATATATAA
1 AAATTGATTATAATAATTTGTATATAATATATAA
28512504 TTAATATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (36 bp):
AAATTGATTATAATAATTTGTATATAATATATAAAT
Found at i:28512915 original size:27 final size:27
Alignment explanation
Indices: 28512882--28512947 Score: 107
Period size: 27 Copynumber: 2.4 Consensus size: 27
28512872 TAAAAAATAT
*
28512882 CCAAAATGT-TATAAATTTTTTTATTTA
1 CCAAAATATATAT-AATTTTTTTATTTA
28512909 CCAAAATATATATAATTTTTTTATTTA
1 CCAAAATATATATAATTTTTTTATTTA
28512936 CCAAAATATATA
1 CCAAAATATATA
28512948 AAAAAACAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
27 34 0.92
28 3 0.08
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (27 bp):
CCAAAATATATATAATTTTTTTATTTA
Found at i:28512980 original size:11 final size:11
Alignment explanation
Indices: 28512947--28512973 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
28512937 CAAAATATAT
28512947 AAAAAAACAAA
1 AAAAAAACAAA
28512958 AAAAAAACAAA
1 AAAAAAACAAA
28512969 AAAAA
1 AAAAA
28512974 TAAAAAACAG
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:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:28513060 original size:27 final size:27
Alignment explanation
Indices: 28513021--28513073 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
28513011 TCCCTGGGTG
*
28513021 AAGGGAACACTGTTGGCGGCATCAAAC
1 AAGGGAACACTGTTGGCGGCACCAAAC
*
28513048 AAGGGAACCCTGTTGGCGGCACCAAA
1 AAGGGAACACTGTTGGCGGCACCAAA
28513074 TATTTTGGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.32, C:0.25, G:0.30, T:0.13
Consensus pattern (27 bp):
AAGGGAACACTGTTGGCGGCACCAAAC
Found at i:28513119 original size:19 final size:19
Alignment explanation
Indices: 28513072--28513122 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
28513062 GGCGGCACCA
** *
28513072 AATATTTTGGTATTTTTTT
1 AATATTTTATTATTTTTGT
28513091 AATATTTTATTATTTTTGT
1 AATATTTTATTATTTTTGT
*
28513110 AATGTTTTATTAT
1 AATATTTTATTAT
28513123 GGGTTTTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (19 bp):
AATATTTTATTATTTTTGT
Found at i:28513210 original size:27 final size:28
Alignment explanation
Indices: 28513160--28513228 Score: 115
Period size: 27 Copynumber: 2.5 Consensus size: 28
28513150 AAATAAAAAA
28513160 TTACCAAAATAT-TATAACTTTTTTTTAT
1 TTACCAAAATATATATAAC-TTTTTTTAT
28513188 TTACCAAAATATATATAA-TTTTTTTAT
1 TTACCAAAATATATATAACTTTTTTTAT
28513215 TTACCAAAATATAT
1 TTACCAAAATATAT
28513229 CAAAAAAAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
27 23 0.57
28 12 0.30
29 5 0.12
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (28 bp):
TTACCAAAATATATATAACTTTTTTTAT
Found at i:28513258 original size:16 final size:17
Alignment explanation
Indices: 28513229--28513261 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28513219 CAAAATATAT
28513229 CAAAAAAAAGTAAAAAA
1 CAAAAAAAAGTAAAAAA
*
28513246 CAAAAAGAA-TAAAAAA
1 CAAAAAAAAGTAAAAAA
28513262 AGGAAAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.82, C:0.06, G:0.06, T:0.06
Consensus pattern (17 bp):
CAAAAAAAAGTAAAAAA
Found at i:28513678 original size:26 final size:26
Alignment explanation
Indices: 28513623--28513699 Score: 109
Period size: 26 Copynumber: 2.9 Consensus size: 26
28513613 TTATTCAAGG
**
28513623 TGGTGCCGCCAACAGGGAACCCTTGTT
1 TGGTGCCGCCAACA-GGTTCCCTTGTT
28513650 TGGTGCCGCCAACAGGTTCCCTTGTT
1 TGGTGCCGCCAACAGGTTCCCTTGTT
*
28513676 TGGTGCCGCCAATAGTGTTCCCTT
1 TGGTGCCGCCAACAG-GTTCCCTT
28513700 CACCTAGGGA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 24 0.52
27 22 0.48
ACGTcount: A:0.14, C:0.30, G:0.27, T:0.29
Consensus pattern (26 bp):
TGGTGCCGCCAACAGGTTCCCTTGTT
Found at i:28513749 original size:15 final size:15
Alignment explanation
Indices: 28513729--28513762 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
28513719 TCAGTTCAGG
*
28513729 TTTTTTT-TTTCTAT
1 TTTTTTTATTTTTAT
28513743 TTTTTTTATTTTTAT
1 TTTTTTTATTTTTAT
28513758 TTTTT
1 TTTTT
28513763 GATATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.09, C:0.03, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTTTTATTTTTAT
Found at i:28513798 original size:28 final size:29
Alignment explanation
Indices: 28513764--28513830 Score: 111
Period size: 28 Copynumber: 2.4 Consensus size: 29
28513754 TTATTTTTTG
28513764 ATATATTTTGGTAAAT-AAAAAAATTTAT
1 ATATATTTTGGTAAATAAAAAAAATTTAT
28513792 ATATATTTTGGTAAATAAAAAAAATTTAT
1 ATATATTTTGGTAAATAAAAAAAATTTAT
*
28513821 A-ACATTTTGG
1 ATATATTTTGG
28513831 ATATTTTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
28 24 0.65
29 13 0.35
ACGTcount: A:0.48, C:0.01, G:0.09, T:0.42
Consensus pattern (29 bp):
ATATATTTTGGTAAATAAAAAAAATTTAT
Found at i:28513953 original size:20 final size:19
Alignment explanation
Indices: 28513902--28513953 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
28513892 TTTGATGGGA
*
28513902 TAAAT-TTTAAAAATAATT
1 TAAATATTTAAAAGTAATT
*
28513920 TTAATATATT-AAAGTAAATT
1 TAAATAT-TTAAAAGT-AATT
28513940 TAAATATTTAAAAG
1 TAAATATTTAAAAG
28513954 AGTTATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 4 0.15
19 7 0.26
20 16 0.59
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (19 bp):
TAAATATTTAAAAGTAATT
Found at i:28516756 original size:27 final size:27
Alignment explanation
Indices: 28516718--28516771 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
28516708 GTTGGATGGC
28516718 ATAAACTTTATGATCAGTTCTTTTTAT
1 ATAAACTTTATGATCAGTTCTTTTTAT
28516745 ATAAACTTTATGATCAGTTCTTTTTAT
1 ATAAACTTTATGATCAGTTCTTTTTAT
28516772 CTTTGTTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (27 bp):
ATAAACTTTATGATCAGTTCTTTTTAT
Found at i:28519313 original size:11 final size:11
Alignment explanation
Indices: 28519274--28519323 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
28519264 CTTCTCCTAA
28519274 TTTCCTTTGTT
1 TTTCCTTTGTT
* * *
28519285 TTTCATTGGGT
1 TTTCCTTTGTT
28519296 TTT-CTTTGTT
1 TTTCCTTTGTT
28519306 TTTCCTTT-TAT
1 TTTCCTTTGT-T
28519317 TTTCCTT
1 TTTCCTT
28519324 AGGATTGAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
10 8 0.26
11 23 0.74
ACGTcount: A:0.04, C:0.16, G:0.10, T:0.70
Consensus pattern (11 bp):
TTTCCTTTGTT
Found at i:28525317 original size:27 final size:27
Alignment explanation
Indices: 28525259--28525447 Score: 172
Period size: 27 Copynumber: 7.1 Consensus size: 27
28525249 GGGTATAACA
*
28525259 GTCATTTTACCCTAT-GAGGTATTTTG
1 GTCATTTTACCCTATAGAGGTATTTCG
*
28525285 GACATTTTACCCTATAGAGGTATTTCG
1 GTCATTTTACCCTATAGAGGTATTTCG
* * * **
28525312 GTCATTCTACCTTATAGGGGTATTTTA
1 GTCATTTTACCCTATAGAGGTATTTCG
*
28525339 GTAATTTTACCCTATA-AGGGTATTTCG
1 GTCATTTTACCCTATAGA-GGTATTTCG
* * *
28525366 ATCATTCTACCCCT-TAG-GGTATTT-A
1 GTCATTTTA-CCCTATAGAGGTATTTCG
* * *
28525391 GTCATTTTACCTTATGGGGGTATTTCG
1 GTCATTTTACCCTATAGAGGTATTTCG
* * *
28525418 GTCATTTTACCCTATTGGGGTATCTCG
1 GTCATTTTACCCTATAGAGGTATTTCG
28525445 GTC
1 GTC
28525448 GGGGGTATCT
Statistics
Matches: 130, Mismatches: 26, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
24 3 0.02
25 9 0.07
26 28 0.22
27 86 0.66
28 4 0.03
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.42
Consensus pattern (27 bp):
GTCATTTTACCCTATAGAGGTATTTCG
Found at i:28525439 original size:79 final size:80
Alignment explanation
Indices: 28525246--28525440 Score: 218
Period size: 79 Copynumber: 2.5 Consensus size: 80
28525236 TTTCATCTCC
** * * *
28525246 TAGGGGTATAACAGTCATTTTACCCTA-TGAGGTATTTTGGACATTTTACCCTATAGAGGTATTT
1 TAGGGGTATTTCAGTCATTTTACCCTATTGGGGTA-TTTCGACATTCTACCCTATAGAGGTATTT
*
28525310 CGGTCATTCTACCTTA
65 CAGTCATTCTACCTTA
* * **
28525326 TAGGGGTATTTTAGTAATTTTACCCTATAAGGGTATTTCGATCATTCTACCCCT-TAG-GGTATT
1 TAGGGGTATTTCAGTCATTTTACCCTATTGGGGTATTTCGA-CATTCTA-CCCTATAGAGGTATT
*
28525389 T-AGTCATTTTACCTTA
64 TCAGTCATTCTACCTTA
* *
28525405 TGGGGGTATTTCGGTCATTTTACCCTATTGGGGTAT
1 TAGGGGTATTTCAGTCATTTTACCCTATTGGGGTAT
28525441 CTCGGTCGGG
Statistics
Matches: 95, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
79 43 0.45
80 35 0.37
81 13 0.14
82 4 0.04
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (80 bp):
TAGGGGTATTTCAGTCATTTTACCCTATTGGGGTATTTCGACATTCTACCCTATAGAGGTATTTC
AGTCATTCTACCTTA
Found at i:28525467 original size:42 final size:41
Alignment explanation
Indices: 28525406--28525488 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 41
28525396 TTTACCTTAT
*
28525406 GGGGGTATTTCGGTCATTTTACCCTATTGGGGTATCTCGGTC
1 GGGGGTATCTCGGTCATTTTACCCTA-TGGGGTATCTCGGTC
* *
28525448 GGGGGTATCTCGGTTATTTTACCCTATGGGGTATTTCGGTC
1 GGGGGTATCTCGGTCATTTTACCCTATGGGGTATCTCGGTC
28525489 ATTTTACCCT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
41 14 0.37
42 24 0.63
ACGTcount: A:0.12, C:0.18, G:0.31, T:0.39
Consensus pattern (41 bp):
GGGGGTATCTCGGTCATTTTACCCTATGGGGTATCTCGGTC
Found at i:28525520 original size:26 final size:27
Alignment explanation
Indices: 28525448--28525519 Score: 110
Period size: 26 Copynumber: 2.7 Consensus size: 27
28525438 TATCTCGGTC
* *
28525448 GGGGGTATCTCGGTTATTTTACCCTAT
1 GGGGGTATTTCGGTCATTTTACCCTAT
*
28525475 -GGGGTATTTCGGTCATTTTACCCTGT
1 GGGGGTATTTCGGTCATTTTACCCTAT
28525501 GGGGGTATTTCGGTCATTT
1 GGGGGTATTTCGGTCATTT
28525520 ATTGACCTCT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
26 23 0.56
27 18 0.44
ACGTcount: A:0.12, C:0.17, G:0.29, T:0.42
Consensus pattern (27 bp):
GGGGGTATTTCGGTCATTTTACCCTAT
Found at i:28531785 original size:15 final size:15
Alignment explanation
Indices: 28531744--28531792 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
28531734 AGAATAAGAT
28531744 TAAACATAAAT-ATAA
1 TAAACA-AAATAATAA
28531759 TAAACAAAATAATAA
1 TAAACAAAATAATAA
*
28531774 TAAACAAAATAAAAA
1 TAAACAAAATAATAA
28531789 TAAA
1 TAAA
28531793 AAGAAGGGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 4 0.12
15 28 0.88
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.20
Consensus pattern (15 bp):
TAAACAAAATAATAA
Found at i:28532712 original size:12 final size:11
Alignment explanation
Indices: 28532687--28532725 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
28532677 GTGTGCACCC
*
28532687 TTTTTTTT-TA
1 TTTTTTTTCAA
28532697 TTTTTTTTCAA
1 TTTTTTTTCAA
*
28532708 TTTTTTTTCCA
1 TTTTTTTTCAA
28532719 TTTTTTT
1 TTTTTTT
28532726 AGAAAATAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.10, C:0.08, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:28535906 original size:36 final size:36
Alignment explanation
Indices: 28535757--28535906 Score: 194
Period size: 36 Copynumber: 4.2 Consensus size: 36
28535747 CAACCAAAAT
* *
28535757 ACACCAGAAGCTCATAACAGCTAATCCATCCGAAAC
1 ACACCAGATGCTCATAAGAGCTAATCCATCCGAAAC
* *
28535793 ACACC-GAATGCTCATAAGAGCTAACCCATTCGAAAC
1 ACACCAG-ATGCTCATAAGAGCTAATCCATCCGAAAC
* * * * **
28535829 AAACTAGATGCTCATAAGAGCTATTCTATCTTAAAC
1 ACACCAGATGCTCATAAGAGCTAATCCATCCGAAAC
28535865 ACACCAGATGCTCATAAGAGCTAATCCATCCGAAAC
1 ACACCAGATGCTCATAAGAGCTAATCCATCCGAAAC
28535901 ACACCA
1 ACACCA
28535907 AAATATGGAG
Statistics
Matches: 94, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
35 1 0.01
36 92 0.98
37 1 0.01
ACGTcount: A:0.40, C:0.29, G:0.12, T:0.19
Consensus pattern (36 bp):
ACACCAGATGCTCATAAGAGCTAATCCATCCGAAAC
Found at i:28540688 original size:17 final size:17
Alignment explanation
Indices: 28540656--28540688 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28540646 CAACCAAAGA
28540656 TAACAAATTTTATAAAT
1 TAACAAATTTTATAAAT
28540673 TAACACAATTTT-TAAA
1 TAACA-AATTTTATAAA
28540689 GTTTTACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (17 bp):
TAACAAATTTTATAAAT
Found at i:28544078 original size:17 final size:17
Alignment explanation
Indices: 28544056--28544100 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
28544046 TTGCTAGGTG
28544056 TATGGATAAATATATTT
1 TATGGATAAATATATTT
** *
28544073 TATGGATCGACATATTT
1 TATGGATAAATATATTT
*
28544090 TAAGGATAAAT
1 TATGGATAAAT
28544101 CTTTAGTATG
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (17 bp):
TATGGATAAATATATTT
Found at i:28549360 original size:21 final size:21
Alignment explanation
Indices: 28549326--28549366 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28549316 TTGCTAAATG
*
28549326 GTAAATTTGGTATTTGTGAAT
1 GTAAACTTGGTATTTGTGAAT
* *
28549347 GTAAACTTGTTATTTTTGAA
1 GTAAACTTGGTATTTGTGAA
28549367 CGCAAATTTG
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:0.29, C:0.02, G:0.20, T:0.49
Consensus pattern (21 bp):
GTAAACTTGGTATTTGTGAAT
Found at i:28554114 original size:40 final size:40
Alignment explanation
Indices: 28554070--28554157 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 40
28554060 AAGTGTAACC
* * *
28554070 AGGGCACGAAAGTGAAATCAGGGGTACTGAAGTACAAACA
1 AGGGCACAAAAGTGAAATCAAGGGTACCGAAGTACAAACA
* *
28554110 AGGGCACAAAAGTGCAATCAAGTGTACCGAAGTACAAACA
1 AGGGCACAAAAGTGAAATCAAGGGTACCGAAGTACAAACA
*
28554150 GGGGCACA
1 AGGGCACA
28554158 TATGTCCAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.42, C:0.18, G:0.28, T:0.11
Consensus pattern (40 bp):
AGGGCACAAAAGTGAAATCAAGGGTACCGAAGTACAAACA
Found at i:28554131 original size:20 final size:20
Alignment explanation
Indices: 28554070--28554131 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 20
28554060 AAGTGTAACC
* *
28554070 AGGGCACGAAAGTGAAATCA
1 AGGGCACAAAAGTGCAATCA
* * ** * *
28554090 GGGGTACTGAAGTACAAACA
1 AGGGCACAAAAGTGCAATCA
28554110 AGGGCACAAAAGTGCAATCA
1 AGGGCACAAAAGTGCAATCA
28554130 AG
1 AG
28554132 TGTACCGAAG
Statistics
Matches: 29, Mismatches: 13, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.16, G:0.29, T:0.11
Consensus pattern (20 bp):
AGGGCACAAAAGTGCAATCA
Found at i:28566670 original size:19 final size:19
Alignment explanation
Indices: 28566623--28566672 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
28566613 AATCATATCT
** *
28566623 TCTAAGATTATATATCATA
1 TCTAAGATTGCATACCATA
28566642 TCTAAGATTGCATACCATA
1 TCTAAGATTGCATACCATA
28566661 TCTAAGATTGCA
1 TCTAAGATTGCA
28566673 GATCCTCGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATACCATA
Found at i:28567692 original size:45 final size:43
Alignment explanation
Indices: 28567020--28567752 Score: 232
Period size: 44 Copynumber: 16.8 Consensus size: 43
28567010 GATTTGTTTA
* * * * * *
28567020 TTTAGTATGCCCCACTGCAATTTCAGGGGGATAAGGCTTGCTTTC
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAA-GATTGC-ATC
* * * *
28567065 TTGAGTCTGCTCCACTACAAATTCAGGGAGATAAGACT-CGAT-
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTGC-ATC
* * * * ** *
28567107 GTGA-TCTACTCTACTGCAACTTCAAAGAGATAAGATCTAAG-GT-
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGAT-T--GCATC
* ** * * * *
28567150 TTTAATCCACTCCACTGCAACTTTAGGAAGATAGGATTATCGA-C
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GC-ATC
** * * * *
28567194 TTTAACCTGCTCCACTGCAACTTCAGCGAGACAGGATTCGCCAAC
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGATT-G-CATC
* *
28567239 TTCAGTCTAC-CTCACTGCAACTTCA-GGAGGATAAGACTTG-AT-
1 TTTAGTCTGCTC-CACTGCAACTTCAGGGA-GATAAGA-TTGCATC
* * *
28567281 TACTTAGTGTGCTCCACTGCAACTTTAGGGAGATAAGACTAG-ATGC
1 T--TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGCAT-C
* * * * * * *
28567327 --GA-TCGGCT-CTCTACAACTTCAGAGAGATAAAATCTAAG-GT-
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGAT-T--GCATC
* ** * * *
28567367 TTTAATCCACTCCACTGCAACTTCAGGAAGATAGGATTATCGA-C
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GC-ATC
**
28567411 TTTAACCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATC
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTG-CATC
* * * * *
28567456 TTCAGTCTGC-CTCACTACAACTTTA-GAAGGATAAGACTTGCTTGC
1 TTTAGTCTGCTC-CACTGCAACTTCAGGGA-GATAAGA-TTGCAT-C
* * * *
28567501 -TTAGTCTGCTTCATTGCAACTTCAAGGAGATAAGACTAG-ATGC
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGCAT-C
* ** *
28567544 TATA-TACT-CT---CTGCAACTTCAGAAAGATAAGATCTGAGAT-
1 TTTAGT-CTGCTCCACTGCAACTTCAGGGAGATAAGAT-TG-CATC
* * * **
28567584 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGTCGGC
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTG-CATC
* * *
28567628 TTTAATCTGCTCCCCTGCAACCTCAGGGAGATAAGATTTGCCATC
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTG-CATC
*
28567673 TTTAGTCTGGCT-CACTGCAACTTCA-GGAGGATAAGACTTGCTTAC
1 TTTAGTCT-GCTCCACTGCAACTTCAGGGA-GATAAGA-TTGCAT-C
*
28567718 -TTAGTCTGCTCCACTGCAACTTCAGGGAAATAAGA
1 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
28567753 CTAGATGCGA
Statistics
Matches: 511, Mismatches: 123, Indels: 109
0.69 0.17 0.15
Matches are distributed among these distances:
39 2 0.00
40 42 0.08
41 32 0.06
42 13 0.03
43 23 0.05
44 263 0.51
45 131 0.26
46 5 0.01
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (43 bp):
TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTGCATC
Found at i:28567831 original size:217 final size:217
Alignment explanation
Indices: 28567027--28567827 Score: 1098
Period size: 217 Copynumber: 3.7 Consensus size: 217
28567017 TTATTTAGTA
* * * * * * *
28567027 TGCCCCACTGCAATTTCAGGGGGATAAGGCTTGCTTTCTTGAGTCTGCTCCACTACAAATTCAGG
1 TGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTT-AGTCTGCTCCACTGCAACTTCAGG
* * * *
28567092 GAGATAAGACTCGATGTGATCTACTCTACTGCAACTTCAAAGAGATAAGATCTAAGGTTTTAATC
65 GAGATAAGACTAGATGCGATCTACTCT-CTACAACTTCAGAGAGATAAGATCTAAGGTTTTAATC
* *
28567157 CACTCCACTGCAACTTTAGGAAGATAGGATTATCGACTTTAACCTGCTCCACTGCAACTTCAGCG
129 CACTCCACTGCAACTTCAGGAAGATAGGATTATCGACTTTAACCTGCTCCACTGCAACTTCAGGG
* * * *
28567222 AGACAGGATTCGCCAACTTCAGTC
194 AGATAAGATTTGCCATCTTCAGTC
* * * *
28567246 TACCTCACTGCAACTTCAGGAGGATAAGACTTGATTACTTAGTGTGCTCCACTGCAACTTTAGGG
1 TGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGG
** *
28567311 AGATAAGACTAGATGCGATCGGCTCTCTACAACTTCAGAGAGATAAAATCTAAGGTTTTAATCCA
66 AGATAAGACTAGATGCGATCTACTCTCTACAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCA
28567376 CTCCACTGCAACTTCAGGAAGATAGGATTATCGACTTTAACCTGCTCCACTGCAACTTCAGGGAG
131 CTCCACTGCAACTTCAGGAAGATAGGATTATCGACTTTAACCTGCTCCACTGCAACTTCAGGGAG
28567441 ATAAGATTTGCCATCTTCAGTC
196 ATAAGATTTGCCATCTTCAGTC
* * * * * * *
28567463 TGCCTCACTACAACTTTAGAAGGATAAGACTTGCTTGCTTAGTCTGCTTCATTGCAACTTCAAGG
1 TGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGG
* * * * * * *
28567528 AGATAAGACTAGATGCTATATACTCTCTGCAACTTCAGAAAGATAAGATCTGAGATTTTAATCCG
66 AGATAAGACTAGATGCGATCTACTCTCTACAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCA
* * * * * *
28567593 CTCCACTGCAACTTCAGGGAGATAGGATTGTCGGCTTTAATCTGCTCCCCTGCAACCTCAGGGAG
131 CTCCACTGCAACTTCAGGAAGATAGGATTATCGACTTTAACCTGCTCCACTGCAACTTCAGGGAG
*
28567658 ATAAGATTTGCCATCTTTAGTC
196 ATAAGATTTGCCATCTTCAGTC
*
28567680 TGGCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGG
1 TGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGG
* * * * * **
28567745 AAATAAGACTAGATGCGATCTGCTCTCTACAACTTCAGAGATATACGATCCAAGGTTTTAATCTG
66 AGATAAGACTAGATGCGATCTACTCTCTACAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCA
*
28567810 CTCCATTGCAACTTCAGG
131 CTCCACTGCAACTTCAGG
28567828 GAGACAAGGC
Statistics
Matches: 509, Mismatches: 73, Indels: 2
0.87 0.12 0.00
Matches are distributed among these distances:
217 433 0.85
218 43 0.08
219 33 0.06
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (217 bp):
TGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGG
AGATAAGACTAGATGCGATCTACTCTCTACAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCA
CTCCACTGCAACTTCAGGAAGATAGGATTATCGACTTTAACCTGCTCCACTGCAACTTCAGGGAG
ATAAGATTTGCCATCTTCAGTC
Found at i:28567967 original size:132 final size:132
Alignment explanation
Indices: 28567823--28568103 Score: 447
Period size: 132 Copynumber: 2.1 Consensus size: 132
28567813 CATTGCAACT
*
28567823 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATATA-ATTTGCC
1 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGAAAAGATA-AGATTTGCC
** * * * *
28567887 GTTTTCGATCTGCTCCACTACTGCCTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGC
65 GTCCTCGATCTACTCCACTACTGCCTAGGAAAATAAGATCTACAATCCTCAACCTACTCCGCTGC
28567952 TGC
130 TGC
*
28567955 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGAAAAGATAAGATTTTCCG
1 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGAAAAGATAAGATTTGCCG
* * *
28568020 TCCTCGATCTACTCCACTACTGCTTAGGAAAATAAGATCTACGATCCTCAACCTACTCCGCTGTT
66 TCCTCGATCTACTCCACTACTGCCTAGGAAAATAAGATCTACAATCCTCAACCTACTCCGCTGCT
28568085 GC
131 GC
28568087 TCAGGGAGACAAGGCTT
1 TCAGGGAGACAAGGCTT
28568104 AGTGTTTTAC
Statistics
Matches: 137, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
131 1 0.01
132 136 0.99
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (132 bp):
TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGAAAAGATAAGATTTGCCG
TCCTCGATCTACTCCACTACTGCCTAGGAAAATAAGATCTACAATCCTCAACCTACTCCGCTGCT
GC
Found at i:28575088 original size:29 final size:29
Alignment explanation
Indices: 28575046--28575104 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
28575036 GATTAAAATA
28575046 TACATATGATTTACAAATAAATTTTTGGG
1 TACATATGATTTACAAATAAATTTTTGGG
28575075 TACATATGATTTACAAATAAATTTTTGGG
1 TACATATGATTTACAAATAAATTTTTGGG
28575104 T
1 T
28575105 TATGGAACGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (29 bp):
TACATATGATTTACAAATAAATTTTTGGG
Found at i:28575460 original size:4 final size:4
Alignment explanation
Indices: 28575451--28575509 Score: 50
Period size: 4 Copynumber: 14.8 Consensus size: 4
28575441 ATTTGTTTTA
* * * *
28575451 AAAT AAAT AAAT AAAT AAAC AAAC AAAT ATATAT AAAT AAA- AACT AATT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-A-AT AAAT AAAT AAAT AAAT
28575500 AAA- AAAT AAA
1 AAAT AAAT AAA
28575510 AGAAATAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
3 5 0.11
4 36 0.78
5 2 0.04
6 3 0.07
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:28576127 original size:23 final size:22
Alignment explanation
Indices: 28576084--28576141 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
28576074 AAAGGGTATC
* *
28576084 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
28576105 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
28576128 TACATATCATATCT
1 TACAAATCATATCT
28576142 AAGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:28576144 original size:19 final size:19
Alignment explanation
Indices: 28576097--28576194 Score: 106
Period size: 19 Copynumber: 4.8 Consensus size: 19
28576087 AAATTAAATC
*
28576097 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
28576117 TCTTCTAAGATTACATATCATA
1 ---TCTAAGATTACATATCATA
*
28576139 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
28576160 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
28576179 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
28576195 CTCGAAGATT
Statistics
Matches: 69, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
19 33 0.48
21 18 0.26
22 7 0.10
23 11 0.16
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:28576157 original size:21 final size:21
Alignment explanation
Indices: 28576131--28576193 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
28576121 CTAAGATTAC
28576131 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
28576152 ATATCATATCTAAGATTGC--
1 ATATCATATCTAAGATTGCAT
28576171 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
28576192 AT
1 AT
28576194 CCTCGAAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
19 19 0.47
21 21 0.52
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:28580007 original size:12 final size:12
Alignment explanation
Indices: 28579990--28580014 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28579980 GAACTCCTTT
28579990 AAAAAATTATAA
1 AAAAAATTATAA
28580002 AAAAAATTATAA
1 AAAAAATTATAA
28580014 A
1 A
28580015 TAATATAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAAATTATAA
Found at i:28582216 original size:30 final size:30
Alignment explanation
Indices: 28582180--28582238 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
28582170 TGGGTAACCT
28582180 TGATATAATACCAACTTGTGTGAGCAACTG
1 TGATATAATACCAACTTGTGTGAGCAACTG
* * *
28582210 TGATATAATATCAGCTTGTGTGAGGAACT
1 TGATATAATACCAACTTGTGTGAGCAACT
28582239 TATTCCCGCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (30 bp):
TGATATAATACCAACTTGTGTGAGCAACTG
Found at i:28591315 original size:138 final size:138
Alignment explanation
Indices: 28591064--28591655 Score: 891
Period size: 138 Copynumber: 4.3 Consensus size: 138
28591054 TAGATAAAGC
* * * * * *
28591064 TAATAAATGAATTTAATTTATACAAAATATTAATTGTACATATTTTATCGAAA-TTATTAATAGA
1 TAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTA-CCAAATTTATTAATA-T
* * *
28591128 AAAAAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTGTTGGAA
64 AAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAA
28591193 AGAATATAAT
129 AGAATATAAT
28591203 TAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTATT-CCAAATTTATTAATATA
1 TAATATATGAATTTGATTCATACAAAATATTAATTGTATATATT-TTACCAAATTTATTAATATA
* * * *
28591267 AATAGTTATATTAATTCATTTCGGTCAAAATATAAAAGACATGTAAATTAATATTCTTTTAGAAA
65 AACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAAA
28591332 GAATATAAT
130 GAATATAAT
* *
28591341 TAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCGAATTTATTAATATAA
1 TAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATATAA
* * * * *
28591406 ACATTTCTATTAATTAATTTCGATCAAAATATAAAGGACATGAAAATTAATATTCTTTTGGAAAG
66 ACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAAAG
28591471 AATATAAT
131 AATATAAT
* * *
28591479 TAATATATGAATTTGATTCATATAAAATATTAATTGTATATATTTTACCGAATTTATGAATATAA
1 TAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATATAA
* * *
28591544 ACAGTTATATTAATTAATTGCGGTCAAAATATTAAATACATGGAAATTAATATTCTTTTGGAAAG
66 ACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAAAG
28591609 AATATAAT
131 AATATAAT
* *
28591617 TAATATATAAATTTTATTCATACAAAATATTAATTGTAT
1 TAATATATGAATTTGATTCATACAAAATATTAATTGTAT
28591656 TTATATAGAG
Statistics
Matches: 414, Mismatches: 36, Indels: 7
0.91 0.08 0.02
Matches are distributed among these distances:
137 2 0.00
138 361 0.87
139 49 0.12
140 2 0.00
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (138 bp):
TAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATATAA
ACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAAAG
AATATAAT
Found at i:28591369 original size:71 final size:71
Alignment explanation
Indices: 28591154--28591508 Score: 185
Period size: 71 Copynumber: 5.1 Consensus size: 71
28591144 TAATTTCGGT
* * *
28591154 CAAAATATAAAAGACATGGAAATTAATATTCTGTTGGAAAGAATATAATTAATATATGAATTTGA
1 CAAAATATAAAAGACATGTAAATTAATATTCTTTTAGAAAGAATATAATTAATATATGAATTTGA
28591219 TTCATA
66 TTCATA
** * * * * * * *
28591225 CAAAATATTAATTG-TATATATTATTCCAA-ATT-TATTA-ATATAA-ATAGTT-ATAT-T-AA-
1 CAAAATA-TAAAAGACATGTA-AATT--AATATTCTTTTAGAAAGAATATAATTAATATATGAAT
* *
28591281 TTCATTTCGGT-
62 TTGA-TTC-ATA
28591292 CAAAATATAAAAGACATGTAAATTAATATTCTTTTAGAAAGAATATAATTAATATATGAATTTGA
1 CAAAATATAAAAGACATGTAAATTAATATTCTTTTAGAAAGAATATAATTAATATATGAATTTGA
28591357 TTCATA
66 TTCATA
* * * * * ** * * *
28591363 CAAAATAT--TA-A-TTGT--A-T-ATATT-TTATCGAATTTATTAATATAAACATTTCTATTAA
1 CAAAATATAAAAGACATGTAAATTAATATTCTTTTAGAA---A-GAATATAATTA-ATATATGAA
*
28591419 -TTAATTTCGAT-
61 TTTGA-TTC-ATA
* * *
28591430 CAAAATATAAAGGACATGAAAATTAATATTCTTTTGGAAAGAATATAATTAATATATGAATTTGA
1 CAAAATATAAAAGACATGTAAATTAATATTCTTTTAGAAAGAATATAATTAATATATGAATTTGA
28591495 TTCATA
66 TTCATA
*
28591501 TAAAATAT
1 CAAAATAT
28591509 TAATTGTATA
Statistics
Matches: 201, Mismatches: 49, Indels: 68
0.63 0.15 0.21
Matches are distributed among these distances:
62 6 0.03
63 5 0.02
64 3 0.01
65 5 0.02
66 25 0.12
67 40 0.20
68 10 0.05
69 9 0.04
70 10 0.05
71 45 0.22
72 24 0.12
73 5 0.02
74 3 0.01
75 5 0.02
76 6 0.03
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (71 bp):
CAAAATATAAAAGACATGTAAATTAATATTCTTTTAGAAAGAATATAATTAATATATGAATTTGA
TTCATA
Found at i:28597651 original size:22 final size:22
Alignment explanation
Indices: 28597626--28597668 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
28597616 TGTATGTAAT
*
28597626 TATTTTCTT-TTTAAATATATAA
1 TATTTTATTATTTAAA-ATATAA
28597648 TATTTTATTATTTAAAATATA
1 TATTTTATTATTTAAAATATA
28597669 GTTTAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TATTTTATTATTTAAAATATAA
Found at i:28597997 original size:13 final size:13
Alignment explanation
Indices: 28597940--28598000 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
28597930 ACCAAAATTT
*
28597940 TCAAAAGTACTTC
1 TCAAAAGCACTTC
* *
28597953 TCAAAATCACTTT
1 TCAAAAGCACTTC
* * * *
28597966 TCCACAGCATTTT
1 TCAAAAGCACTTC
*
28597979 TTAAAAGCACTTC
1 TCAAAAGCACTTC
28597992 TCAAAAGCA
1 TCAAAAGCA
28598001 ATGCTAAACT
Statistics
Matches: 35, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.38, C:0.25, G:0.07, T:0.31
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:28624224 original size:23 final size:23
Alignment explanation
Indices: 28624194--28624238 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
28624184 CATTATTATT
28624194 ATTTTTTACTT-TTCTTTGTTTAA
1 ATTTTTTACTTCTTC-TTGTTTAA
28624217 ATTTTTTACTTCTTCTTGTTTA
1 ATTTTTTACTTCTTCTTGTTTA
28624239 TTTAAGTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.16, C:0.11, G:0.04, T:0.69
Consensus pattern (23 bp):
ATTTTTTACTTCTTCTTGTTTAA
Found at i:28624283 original size:17 final size:18
Alignment explanation
Indices: 28624261--28624294 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28624251 TGTAGTTTTT
*
28624261 TTTTCA-AATATTTTTAG
1 TTTTCATAAAATTTTTAG
28624278 TTTTCATAAAATTTTTA
1 TTTTCATAAAATTTTTA
28624295 AACTATTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTTCATAAAATTTTTAG
Found at i:28626747 original size:14 final size:14
Alignment explanation
Indices: 28626725--28626756 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
28626715 TTATATACGT
*
28626725 TTTATGATTTAGGG
1 TTTAGGATTTAGGG
28626739 TTTAGGATTTAGGG
1 TTTAGGATTTAGGG
28626753 TTTA
1 TTTA
28626757 TATATGTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (14 bp):
TTTAGGATTTAGGG
Found at i:28628975 original size:66 final size:65
Alignment explanation
Indices: 28628851--28628977 Score: 155
Period size: 66 Copynumber: 1.9 Consensus size: 65
28628841 TTTGGTATTT
* * *
28628851 GGTTAATGCTGCTGCAAGTTCTTTTTTGCTGGAAGTTCTGCTTAATGTTGCTGGTTAATGTTAGG
1 GGTTAATGCTGCTGCAAGTTCTTTTTTGCTGCAAGTTCTGCTTAATATTGCTGCTTAATGTTAGG
* * * * * * *
28628916 GGTTAATGTTGTTGCAAGTTATTTTTTTGTTGCACGTTGTGGTTAATATTGCTGCTTAATGT
1 GGTTAATGCTGCTGCAAGTT-CTTTTTTGCTGCAAGTTCTGCTTAATATTGCTGCTTAATGT
28628978 ATTTATTTCT
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
65 18 0.35
66 33 0.65
ACGTcount: A:0.17, C:0.10, G:0.26, T:0.46
Consensus pattern (65 bp):
GGTTAATGCTGCTGCAAGTTCTTTTTTGCTGCAAGTTCTGCTTAATATTGCTGCTTAATGTTAGG
Found at i:28629833 original size:9 final size:9
Alignment explanation
Indices: 28629806--28629853 Score: 64
Period size: 9 Copynumber: 5.6 Consensus size: 9
28629796 GTTCAAATTT
28629806 CATAACTTA
1 CATAACTTA
* *
28629815 CGTAATTTA
1 CATAACTTA
28629824 CATAACTTA
1 CATAACTTA
28629833 CATAA-TT-
1 CATAACTTA
28629840 CATAACTTA
1 CATAACTTA
28629849 CATAA
1 CATAA
28629854 TTTAAATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
7 5 0.15
8 4 0.12
9 24 0.73
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (9 bp):
CATAACTTA
Found at i:28629845 original size:16 final size:16
Alignment explanation
Indices: 28629804--28629882 Score: 83
Period size: 16 Copynumber: 5.0 Consensus size: 16
28629794 AAGTTCAAAT
*
28629804 TTCATAACTTACGTAA
1 TTCATAACTTACATAA
28629820 TTTACATAACTTACATAA
1 -TT-CATAACTTACATAA
28629838 TTCATAACTTACATAA
1 TTCATAACTTACATAA
* *
28629854 TT--TAAATT-TATAA
1 TTCATAACTTACATAA
*
28629867 TACATAACTTACATAA
1 TTCATAACTTACATAA
28629883 ATTATTAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
13 5 0.10
14 5 0.10
15 5 0.10
16 20 0.38
17 4 0.08
18 13 0.25
ACGTcount: A:0.44, C:0.15, G:0.01, T:0.39
Consensus pattern (16 bp):
TTCATAACTTACATAA
Found at i:28629911 original size:19 final size:18
Alignment explanation
Indices: 28629887--28629940 Score: 69
Period size: 17 Copynumber: 3.1 Consensus size: 18
28629877 ACATAAATTA
28629887 TTAATATTTATATATAGTT
1 TTAATATTTATATATA-TT
28629906 TTAATA--TATATATA-T
1 TTAATATTTATATATATT
*
28629921 TTAAAATTTATATATATT
1 TTAATATTTATATATATT
28629939 TT
1 TT
28629941 TAAAAATTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 6 0.19
17 16 0.52
18 3 0.10
19 6 0.19
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
TTAATATTTATATATATT
Found at i:28630070 original size:34 final size:34
Alignment explanation
Indices: 28630032--28630180 Score: 115
Period size: 34 Copynumber: 4.2 Consensus size: 34
28630022 GTAATAGATA
28630032 ATAATACATAACCTACATAAATTAAATAAGTTAC
1 ATAATACATAACCTACATAAATTAAATAAGTTAC
* * * ** *
28630066 ATAATACACGAA--AACAGAAACTTACGTAACTTAC
1 ATAATACA-TAACCTACATAAA-TTAAATAAGTTAC
* * * *
28630100 ATAATACATAACTTATATAACTTAAATTTGTAATAGATA-
1 ATAATACATAACCTACATAAATTAAA----T-A-AGTTAC
28630139 ATAATACATAACCTACATAAATTAAATAAGTTAC
1 ATAATACATAACCTACATAAATTAAATAAGTTAC
28630173 ATAATACA
1 ATAATACA
28630181 CGAAAACAGA
Statistics
Matches: 85, Mismatches: 19, Indels: 22
0.67 0.15 0.17
Matches are distributed among these distances:
33 12 0.14
34 38 0.45
35 7 0.08
38 1 0.01
39 24 0.28
40 3 0.04
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.30
Consensus pattern (34 bp):
ATAATACATAACCTACATAAATTAAATAAGTTAC
Found at i:28630107 original size:107 final size:107
Alignment explanation
Indices: 28629991--28630227 Score: 465
Period size: 107 Copynumber: 2.2 Consensus size: 107
28629981 ATAAACTTAC
28629991 ACATAATACATAACTTATATAACTTAAATTTGTAATAGATAATAATACATAACCTACATAAATTA
1 ACATAATACATAACTTATATAACTTAAATTTGTAATAGATAATAATACATAACCTACATAAATTA
28630056 AATAAGTTACATAATACACGAAAACAGAAACTTACGTAACTT
66 AATAAGTTACATAATACACGAAAACAGAAACTTACGTAACTT
28630098 ACATAATACATAACTTATATAACTTAAATTTGTAATAGATAATAATACATAACCTACATAAATTA
1 ACATAATACATAACTTATATAACTTAAATTTGTAATAGATAATAATACATAACCTACATAAATTA
28630163 AATAAGTTACATAATACACGAAAACAGAAACTTACGTAACTT
66 AATAAGTTACATAATACACGAAAACAGAAACTTACGTAACTT
*
28630205 ACATAATACATAACTTACATAAC
1 ACATAATACATAACTTATATAAC
28630228 CTACTTAATA
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
107 129 1.00
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.30
Consensus pattern (107 bp):
ACATAATACATAACTTATATAACTTAAATTTGTAATAGATAATAATACATAACCTACATAAATTA
AATAAGTTACATAATACACGAAAACAGAAACTTACGTAACTT
Found at i:28630205 original size:9 final size:9
Alignment explanation
Indices: 28630191--28630423 Score: 180
Period size: 9 Copynumber: 27.9 Consensus size: 9
28630181 CGAAAACAGA
*
28630191 AACTTACGT
1 AACTTACAT
28630200 AACTTACAT
1 AACTTACAT
28630209 AA--TACAT
1 AACTTACAT
28630216 AACTTACAT
1 AACTTACAT
* *
28630225 AACCTACTT
1 AACTTACAT
28630234 AA--TACAT
1 AACTTACAT
28630241 AACTTACAT
1 AACTTACAT
** *
28630250 AACACACAC
1 AACTTACAT
28630259 AACTTACAT
1 AACTTACAT
28630268 AACTTACAT
1 AACTTACAT
*
28630277 AACTTATAT
1 AACTTACAT
*
28630286 AA--GAC--
1 AACTTACAT
28630291 AACTTACAT
1 AACTTACAT
*
28630300 AA-TGTACTT
1 AACT-TACAT
28630309 AA--TACAT
1 AACTTACAT
28630316 AACTTACAT
1 AACTTACAT
*
28630325 AACCTACAT
1 AACTTACAT
*
28630334 AA--GACAT
1 AACTTACAT
28630341 AACTTACAT
1 AACTTACAT
* *
28630350 AAGTTTCAT
1 AACTTACAT
*
28630359 AA--TACAC
1 AACTTACAT
28630366 AACTTACAT
1 AACTTACAT
28630375 AACTTACAT
1 AACTTACAT
28630384 AA--TACAT
1 AACTTACAT
28630391 AACTTACAT
1 AACTTACAT
* *
28630400 AATTTACTT
1 AACTTACAT
28630409 AA--TACAT
1 AACTTACAT
28630416 AACTTACA
1 AACTTACA
28630424 CAAATATATG
Statistics
Matches: 178, Mismatches: 27, Indels: 38
0.73 0.11 0.16
Matches are distributed among these distances:
5 2 0.01
7 46 0.26
8 1 0.01
9 129 0.72
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.31
Consensus pattern (9 bp):
AACTTACAT
Found at i:28630219 original size:25 final size:25
Alignment explanation
Indices: 28630191--28630423 Score: 274
Period size: 25 Copynumber: 9.3 Consensus size: 25
28630181 CGAAAACAGA
*
28630191 AACTTACGTAACTTACATAATACAT
1 AACTTACATAACTTACATAATACAT
* *
28630216 AACTTACATAACCTACTTAATACAT
1 AACTTACATAACTTACATAATACAT
** *
28630241 AACTTACATAACACACACAACTTACAT
1 AACTTACATAACTTACATAA--TACAT
* *
28630268 AACTTACATAACTTATATAAGAC--
1 AACTTACATAACTTACATAATACAT
*
28630291 AACTTACATAA-TGTACTTAATACAT
1 AACTTACATAACT-TACATAATACAT
* *
28630316 AACTTACATAACCTACATAAGACAT
1 AACTTACATAACTTACATAATACAT
* * *
28630341 AACTTACATAAGTTTCATAATACAC
1 AACTTACATAACTTACATAATACAT
28630366 AACTTACATAACTTACATAATACAT
1 AACTTACATAACTTACATAATACAT
* *
28630391 AACTTACATAATTTACTTAATACAT
1 AACTTACATAACTTACATAATACAT
28630416 AACTTACA
1 AACTTACA
28630424 CAAATATATG
Statistics
Matches: 174, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
22 1 0.01
23 18 0.10
25 134 0.77
27 21 0.12
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.31
Consensus pattern (25 bp):
AACTTACATAACTTACATAATACAT
Found at i:28630220 original size:16 final size:16
Alignment explanation
Indices: 28630199--28630402 Score: 119
Period size: 16 Copynumber: 12.8 Consensus size: 16
28630189 GAAACTTACG
28630199 TAACTTACATAATACA
1 TAACTTACATAATACA
28630215 TAACTTACAT-A-AC-
1 TAACTTACATAATACA
*
28630228 ---C-TACTTAATACA
1 TAACTTACATAATACA
*
28630240 TAACTTACATAACACACA
1 TAACTTACAT-A-ATACA
*
28630258 CAACTTACATAACTTACA
1 TAACTTACATAA--TACA
* *
28630276 TAACTTATATAAGAC-
1 TAACTTACATAATACA
*
28630291 -AACTTACATAATGTACT
1 TAACTTACATAA--TACA
28630308 TAA--TACATAACTTACA
1 TAACTTACATAA--TACA
* *
28630324 TAACCTACATAAGACA
1 TAACTTACATAATACA
*
28630340 TAACTTACATAAGTTTCA
1 TAACTTACATAA--TACA
*
28630358 TAA--TACACAACTTACA
1 TAACTTACATAA--TACA
28630374 TAACTTACATAATACA
1 TAACTTACATAATACA
28630390 TAACTTACATAAT
1 TAACTTACATAAT
28630403 TTACTTAATA
Statistics
Matches: 146, Mismatches: 21, Indels: 42
0.70 0.10 0.20
Matches are distributed among these distances:
9 4 0.03
10 2 0.01
11 2 0.01
14 12 0.08
15 2 0.01
16 76 0.52
17 2 0.01
18 46 0.32
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.30
Consensus pattern (16 bp):
TAACTTACATAATACA
Found at i:28633738 original size:87 final size:87
Alignment explanation
Indices: 28633587--28633763 Score: 246
Period size: 87 Copynumber: 2.0 Consensus size: 87
28633577 GAACACATTT
* * * * *
28633587 GAGGTTCAAAGGAAATATGAAGAACTTCAGCTACAACTTAAAGTAAAGGTGGCAGCGAGGGAAGC
1 GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAAAGGCGGCAGCGAGAGAAGC
*
28633652 AAAGGCTGCAGCGAGAAAAGCA
66 AAACGCTGCAGCGAGAAAAGCA
* * *
28633674 GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGATGCGGCATCGAGAGAAGC
1 GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAAAGGCGGCAGCGAGAGAAGC
* **
28633739 AGACGCTGCAGCGAGGGAAGCA
66 AAACGCTGCAGCGAGAAAAGCA
28633761 GAG
1 GAG
28633764 CAGAGCAGAA
Statistics
Matches: 78, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
87 78 1.00
ACGTcount: A:0.40, C:0.17, G:0.30, T:0.13
Consensus pattern (87 bp):
GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAAAGGCGGCAGCGAGAGAAGC
AAACGCTGCAGCGAGAAAAGCA
Found at i:28633740 original size:21 final size:21
Alignment explanation
Indices: 28633714--28633762 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
28633704 CTACAACTTA
* *
28633714 AAGCAGATGCGGCATCGAGAG
1 AAGCAGACGCGGCAGCGAGAG
* *
28633735 AAGCAGACGCTGCAGCGAGGG
1 AAGCAGACGCGGCAGCGAGAG
28633756 AAGCAGA
1 AAGCAGA
28633763 GCAGAGCAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.39, T:0.06
Consensus pattern (21 bp):
AAGCAGACGCGGCAGCGAGAG
Found at i:28634202 original size:43 final size:43
Alignment explanation
Indices: 28634112--28634423 Score: 306
Period size: 43 Copynumber: 7.3 Consensus size: 43
28634102 ACTAAACAAA
* *
28634112 TAGCGGCGTTTGTGGAAAAAGCGCTGCTAAAAGAACATGACCTT
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCT-AAAGAACATGATCTT
* *
28634156 TAGCAGCGTTTGTGGAAGAAGCGCCGCTAAAGAACATGATCTT
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGATCTT
* * * * * *
28634199 TAGCGGCATTTGTGGAAAAATCACCACTAAGGAGCATGATCTT
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGATCTT
*
28634242 TAGCGGCGTTTGTGGAACAAGCGCCGCTAAAGAACATGATCTT
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGATCTT
* * * * * *
28634285 CAACGGCGTTTGTTGAAAAAGCGGCTCTAAAGAACATGACCTT
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGATCTT
* * * *
28634328 TAACGGCGTTTGTAGG-AAAAGCGCTGCTAAAGACCCTGA-CTTT
1 TAGCGGCGTTTGT-GGAAAAAGCGCCGCTAAAGAACATGATC-TT
* ****** * *
28634371 TAGCGGTGTTT-TTTCTGTAGCGTCGCTAAAGAACATGACCTT
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGATCTT
28634413 TAGCGGCGTTT
1 TAGCGGCGTTT
28634424 ATAAAAATAA
Statistics
Matches: 219, Mismatches: 45, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
42 30 0.14
43 163 0.74
44 26 0.12
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGAACATGATCTT
Found at i:28634560 original size:22 final size:22
Alignment explanation
Indices: 28634517--28634560 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
28634507 TAGTGGCGCT
* **
28634517 AAAAAGCGCCGCTAAAGGCCTG
1 AAAAAACGCCGCTAAAAACCTG
28634539 AAAAAACGCCGCTAAAAACCTG
1 AAAAAACGCCGCTAAAAACCTG
28634561 TTTTGGTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.27, G:0.20, T:0.09
Consensus pattern (22 bp):
AAAAAACGCCGCTAAAAACCTG
Found at i:28635042 original size:18 final size:15
Alignment explanation
Indices: 28634998--28635030 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
28634988 CTTGGATGAG
28634998 AATAAATTTTTAATTA
1 AATAAA-TTTTAATTA
28635014 AATAAA-TTTAATTA
1 AATAAATTTTAATTA
28635028 AAT
1 AAT
28635031 CAAAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 11 0.65
16 6 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAAATTTTAATTA
Found at i:28636234 original size:41 final size:40
Alignment explanation
Indices: 28636175--28636543 Score: 407
Period size: 41 Copynumber: 9.0 Consensus size: 40
28636165 AGTTTTCGGG
* * *
28636175 GGCTTTACCGGTGTTTTTGAGGAAGC-CCAGCTAATGCTCA
1 GGCTTTAGCGGCGTTTTTGAGAAAGCGCC-GCTAATGCTCA
* *
28636215 GGCTTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCTCA
1 GGC-TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* *
28636256 GGCCTTTAGCGGTGTTTTTGACAAAGCGCCGCTAATGCTCA
1 GG-CTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* * * *
28636297 GGGCTTTAGCGGCGTTTTTGAGGAAGTGCCACTAATGGTCA
1 -GGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* * *
28636338 GAGCTTTAGCAGCATTTTTGAGGAAGCGCCGCTAATGCTCA
1 G-GCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
** * *
28636379 GGGCTTTAGCGGTATTTTTGATAAAGTGCCGCTAATGCTCA
1 -GGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* *
28636420 GGGCTTTAGCGGCGTTTTTGATAAAGCGCCGCTGATGCTCA
1 -GGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* * * *
28636461 GGGCTTTAGCAGCGTTTTTGGGAAAGTGCCGCTAATGCTTA
1 -GGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* * *
28636502 GGGTTTTAGCGGTGTTTTTAAGAAAGCGCCGCTAATGCTCA
1 -GGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
28636543 G
1 G
28636544 AAGCGCCGCT
Statistics
Matches: 282, Mismatches: 41, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
40 5 0.02
41 271 0.96
42 6 0.02
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (40 bp):
GGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
Found at i:28636315 original size:82 final size:82
Alignment explanation
Indices: 28636174--28636543 Score: 474
Period size: 82 Copynumber: 4.5 Consensus size: 82
28636164 GAGTTTTCGG
* * *
28636174 GGGCTTTACCGGTGTTTTTGAGGAAGC-CCAGCTAATGCTCA-GGCTTTTAGCGGCATTTTTGAA
1 GGGCTTTAGCGGTGTTTTTGAGAAAGCGCC-GCTAATGCTCAGGGC-TTTAGCGGCATTTTTGAG
*
28636237 AAAGCGCCGCTAATGCTCA
64 AAAGTGCCGCTAATGCTCA
* * * *
28636256 GGCCTTTAGCGGTGTTTTTGACAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGGA
1 GGGCTTTAGCGGTGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCATTTTTGAGAA
* *
28636321 AGTGCCACTAATGGTCA
66 AGTGCCGCTAATGCTCA
* * ** * * *
28636338 GAGCTTTAGCAGCATTTTTGAGGAAGCGCCGCTAATGCTCAGGGCTTTAGCGGTATTTTTGATAA
1 GGGCTTTAGCGGTGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCATTTTTGAGAA
28636403 AGTGCCGCTAATGCTCA
66 AGTGCCGCTAATGCTCA
* * * * * *
28636420 GGGCTTTAGCGGCGTTTTTGATAAAGCGCCGCTGATGCTCAGGGCTTTAGCAGCGTTTTTGGGAA
1 GGGCTTTAGCGGTGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCATTTTTGAGAA
*
28636485 AGTGCCGCTAATGCTTA
66 AGTGCCGCTAATGCTCA
* *
28636502 GGGTTTTAGCGGTGTTTTTAAGAAAGCGCCGCTAATGCTCAG
1 GGGCTTTAGCGGTGTTTTTGAGAAAGCGCCGCTAATGCTCAG
28636544 AAGCGCCGCT
Statistics
Matches: 246, Mismatches: 40, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
82 241 0.98
83 5 0.02
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (82 bp):
GGGCTTTAGCGGTGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCATTTTTGAGAA
AGTGCCGCTAATGCTCA
Found at i:28636397 original size:123 final size:121
Alignment explanation
Indices: 28636174--28636543 Score: 481
Period size: 123 Copynumber: 3.0 Consensus size: 121
28636164 GAGTTTTCGG
* * * * **
28636174 GGGCTTTACCGGTGTTTTTGAGGAAGCCCAGCTAATGCTCAGGCTTTTAGCGGCATTTTTGAAAA
1 GGGCTTTAGCGGCGTTTTTGAGGAAGGCCA-CTAATGCTCAGGC-TTTAGCAGCATTTTTGAGGA
*
28636239 AGCGCCGCTAATGCTCAGGCCTTTAGCGGTGTTTTTGACAAAGCGCCGCTAATGCTCA
64 AGCGCCGCTAATGCTCAGGGCTTTAGCGGTGTTTTTGACAAAGCGCCGCTAATGCTCA
*
28636297 GGGCTTTAGCGGCGTTTTTGAGGAAGTGCCACTAATGGTCAGAGCTTTAGCAGCATTTTTGAGGA
1 GGGCTTTAGCGGCGTTTTTGAGGAAG-GCCACTAATGCTCAG-GCTTTAGCAGCATTTTTGAGGA
* * *
28636362 AGCGCCGCTAATGCTCAGGGCTTTAGCGGTATTTTTGATAAAGTGCCGCTAATGCTCA
64 AGCGCCGCTAATGCTCAGGGCTTTAGCGGTGTTTTTGACAAAGCGCCGCTAATGCTCA
** * * *
28636420 GGGCTTTAGCGGCGTTTTTGATAAAGCGCCGCTGATGCTCAGGGCTTTAGCAGCGTTTTTG-GGA
1 GGGCTTTAGCGGCGTTTTTGAGGAAG-GCCACTAATGCTCA-GGCTTTAGCAGCATTTTTGAGG-
* * * * *
28636484 AAGTGCCGCTAATGCTTAGGGTTTTAGCGGTGTTTTTAAGAAAGCGCCGCTAATGCTCA
63 AAGCGCCGCTAATGCTCAGGGCTTTAGCGGTGTTTTTGACAAAGCGCCGCTAATGCTCA
28636543 G
1 G
28636544 AAGCGCCGCT
Statistics
Matches: 218, Mismatches: 25, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
122 2 0.01
123 210 0.96
124 6 0.03
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (121 bp):
GGGCTTTAGCGGCGTTTTTGAGGAAGGCCACTAATGCTCAGGCTTTAGCAGCATTTTTGAGGAAG
CGCCGCTAATGCTCAGGGCTTTAGCGGTGTTTTTGACAAAGCGCCGCTAATGCTCA
Found at i:28636549 original size:19 final size:19
Alignment explanation
Indices: 28636525--28636562 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
28636515 GTTTTTAAGA
28636525 AAGCGCCGCTAATGCTCAG
1 AAGCGCCGCTAATGCTCAG
28636544 AAGCGCCGCTAATGCTCAG
1 AAGCGCCGCTAATGCTCAG
28636563 GGCTTTAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.16
Consensus pattern (19 bp):
AAGCGCCGCTAATGCTCAG
Found at i:28636981 original size:14 final size:14
Alignment explanation
Indices: 28636936--28636985 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
28636926 TTAAAGGCTT
*
28636936 GGGTTTAAGGTTTA
1 GGGTTTATGGTTTA
*
28636950 GAGG-TTATGTGTTAA
1 G-GGTTTATG-GTTTA
28636965 GGGTTTATGGTTTA
1 GGGTTTATGGTTTA
28636979 GGGTTTA
1 GGGTTTA
28636986 GATTAACTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.20, C:0.00, G:0.36, T:0.44
Consensus pattern (14 bp):
GGGTTTATGGTTTA
Found at i:28637293 original size:14 final size:14
Alignment explanation
Indices: 28637276--28637309 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28637266 GATTTAAGGT
*
28637276 TTAGGGGTTAGGAG
1 TTAGGGGTTAAGAG
*
28637290 TTAGGGGTTAATAG
1 TTAGGGGTTAAGAG
28637304 TTAGGG
1 TTAGGG
28637310 ATTTAGGGTT
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:0.24, C:0.00, G:0.44, T:0.32
Consensus pattern (14 bp):
TTAGGGGTTAAGAG
Found at i:28637791 original size:14 final size:14
Alignment explanation
Indices: 28637772--28637799 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28637762 TTATCAAAAT
28637772 TTTAAATAATATTA
1 TTTAAATAATATTA
28637786 TTTAAATAATATTA
1 TTTAAATAATATTA
28637800 ATAATGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAAATAATATTA
Found at i:28638092 original size:83 final size:81
Alignment explanation
Indices: 28637942--28638144 Score: 226
Period size: 83 Copynumber: 2.4 Consensus size: 81
28637932 GCGTTTGGTC
* * * *
28637942 AAAAATGCCGCAAAAAATATATTTAAAATTTAACCAAACGGCGCCGTTTCATTGACGAATTAAAT
1 AAAAACGCC-CAAAAAATATA-TTAAAATTTAACAAAACAGCACCGTTTCATTGACGAATTAAAT
*
28638007 ATTAATGGTGTTTTGTAT
64 ATTAATGGCGTTTTGTAT
* * * *
28638025 ACAAACGCCACAAAAAATATATTAAGAATTTAACAAAACAGCACCGTTTTATTGATGAATTATAT
1 AAAAACGCC-CAAAAAATATATTAA-AATTTAACAAAACAGCACCGTTTCATTGACGAATTAAAT
* *
28638090 ATTAGTGGCGTTTTTTAT
64 ATTAATGGCGTTTTGTAT
* * * *
28638108 AAAAATGCCGAAAAAATACATTAAAAATTTAAAAAAA
1 AAAAACGCCCAAAAAATATATT-AAAATTTAACAAAA
28638145 TGGCGCTGTT
Statistics
Matches: 101, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
82 26 0.26
83 75 0.74
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (81 bp):
AAAAACGCCCAAAAAATATATTAAAATTTAACAAAACAGCACCGTTTCATTGACGAATTAAATAT
TAATGGCGTTTTGTAT
Found at i:28640571 original size:21 final size:21
Alignment explanation
Indices: 28640547--28640590 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
28640537 TAGTTGGAGT
28640547 TTCTAGTTTTATAGTTTCTAA
1 TTCTAGTTTTATAGTTTCTAA
28640568 TTCTAGTTTTATAGTTTCTAA
1 TTCTAGTTTTATAGTTTCTAA
28640589 TT
1 TT
28640591 TTACCCGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.59
Consensus pattern (21 bp):
TTCTAGTTTTATAGTTTCTAA
Found at i:28642650 original size:42 final size:43
Alignment explanation
Indices: 28642515--28642713 Score: 251
Period size: 43 Copynumber: 4.7 Consensus size: 43
28642505 ACCAAAGTGT
* *
28642515 CGCTAAAGGTCTTGAGCTATAGCGGTGTTTGTAGGAAAA-CTGC
1 CGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGGAAAAGC-GC
* * *
28642558 CGCTAAAGGTCTTGATCTATCGCGGCGTTTGTGGTAAAAGCGC
1 CGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGGAAAAGCGC
* *
28642601 CGCTAAAGGTCTTGAGCTATAGCAGCGTTTGT-GTAAAAGCGC
1 CGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGGAAAAGCGC
* * *
28642643 CCCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGCGC
1 CGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGGAAAAGCGC
* * *
28642686 CGCTAAAGATCAT-ATCTATAGCGGCGTT
1 CGCTAAAGGTCTTGAGCTATAGCGGCGTT
28642714 GACAACAGCG
Statistics
Matches: 138, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
42 53 0.38
43 84 0.61
44 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.27
Consensus pattern (43 bp):
CGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGGGAAAAGCGC
Found at i:28642675 original size:85 final size:86
Alignment explanation
Indices: 28642515--28642693 Score: 272
Period size: 85 Copynumber: 2.1 Consensus size: 86
28642505 ACCAAAGTGT
* * * * *
28642515 CGCTAAAGGTCTTGAGCTATAGCGGTGTTTGTAGGAAAACTGCCGCTAAAGGTCTTGATCTATCG
1 CGCTAAAGGTCTTGAGCTATAGCAGCGTTTGTAGGAAAACTGCCCCTAAAGGTCCTGATCTATAG
*
28642580 CGGCGTTTGTGGTAAAAGCGC
66 CGGCGTTTGTGGGAAAAGCGC
*
28642601 CGCTAAAGGTCTTGAGCTATAGCAGCGTTTGT-GTAAAAGC-GCCCCTAAAGGTCCTGATCTATA
1 CGCTAAAGGTCTTGAGCTATAGCAGCGTTTGTAGGAAAA-CTGCCCCTAAAGGTCCTGATCTATA
28642664 GCGGCGTTTGTGGGAAAAGCGC
65 GCGGCGTTTGTGGGAAAAGCGC
28642686 CGCTAAAG
1 CGCTAAAG
28642694 ATCATATCTA
Statistics
Matches: 85, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
85 54 0.64
86 31 0.36
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.26
Consensus pattern (86 bp):
CGCTAAAGGTCTTGAGCTATAGCAGCGTTTGTAGGAAAACTGCCCCTAAAGGTCCTGATCTATAG
CGGCGTTTGTGGGAAAAGCGC
Found at i:28643381 original size:57 final size:57
Alignment explanation
Indices: 28643301--28643437 Score: 175
Period size: 57 Copynumber: 2.4 Consensus size: 57
28643291 TTATTTCTAC
** * * **
28643301 ATTTATGTTGTCTTAATGTAATTTATAGATGTTGTCAAAATGTCTCTTAATGTGCAT
1 ATTTATGTTGTCAAAATGGAATTTATAGATGTTGCCAAAATGTCTCTTAATGCACAT
* * *
28643358 ATTTATGTAGTCCAAATGGAATTTATAGATGTTGCCATAATGTCTCTTAATGCACAT
1 ATTTATGTTGTCAAAATGGAATTTATAGATGTTGCCAAAATGTCTCTTAATGCACAT
*
28643415 ATTTTTGTTGTCAAAATGTGAAT
1 ATTTATGTTGTCAAAATG-GAAT
28643438 AATAGTTGTT
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
57 64 0.94
58 4 0.06
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.44
Consensus pattern (57 bp):
ATTTATGTTGTCAAAATGGAATTTATAGATGTTGCCAAAATGTCTCTTAATGCACAT
Found at i:28645914 original size:50 final size:51
Alignment explanation
Indices: 28645839--28646027 Score: 197
Period size: 50 Copynumber: 3.7 Consensus size: 51
28645829 GGGAATGAGG
**
28645839 TCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATAAGA-GT-
1 TCCCATG-AAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAGAGGTC
* *
28645889 TCCCATGGAAGACCATGTCTAGGACATGGCATTGGCACCGAGATGAGAGGTC
1 TCCCAT-GAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAGAGGTC
* * * * **
28645941 CCCCAT-AAGACCATGTCTGGGACATGGCATGGGCACTGATATAAGA-AAC
1 TCCCATGAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAGAGGTC
* * *
28645990 ATCCCATGTAAGACCATATCTAGGATATGGCATTGGCA
1 -TCCCATG-AAGACCATGTCTGGGACATGGCATTGGCA
28646028 GTACAAGAAA
Statistics
Matches: 116, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
49 1 0.01
50 82 0.71
51 3 0.03
52 30 0.26
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (51 bp):
TCCCATGAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAGAGGTC
Found at i:28646048 original size:49 final size:51
Alignment explanation
Indices: 28645946--28646066 Score: 138
Period size: 49 Copynumber: 2.4 Consensus size: 51
28645936 AGGTCCCCCA
* * *
28645946 TAAGACCATGTCTGGGACATGGCATGGGCACTGATATAAGAAACATCCCATG
1 TAAGACCATATCTAGGACATGGCATGGGCAC-GATACAAGAAACATCCCATG
* * *
28645998 TAAGACCATATCTAGGATATGGCATTGGCA-G-TACAAGAAACATCTCATG
1 TAAGACCATATCTAGGACATGGCATGGGCACGATACAAGAAACATCCCATG
* * *
28646047 TAAGACTATGTCTGGGACAT
1 TAAGACCATATCTAGGACAT
28646067 AGCTTTGGCA
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
49 32 0.54
50 1 0.02
52 26 0.44
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (51 bp):
TAAGACCATATCTAGGACATGGCATGGGCACGATACAAGAAACATCCCATG
Found at i:28646075 original size:49 final size:51
Alignment explanation
Indices: 28645839--28646076 Score: 184
Period size: 50 Copynumber: 4.7 Consensus size: 51
28645829 GGGAATGAGG
** * * **
28645839 TCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATAAG--AGT
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CGATACAAGAAACA
* * * ** **
28645889 TCCCATGGAAGACCATGTCTAGGACATGGCATTGGCACCGAGATGAGAGGTC-
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CGATACAAGA-AACA
* * *
28645941 CCCCA--TAAGACCATGTCTGGGACATGGCATGGGCACTGATATAAGAAACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAC-GATACAAGAAACA
* * *
28645991 TCCCATGTAAGACCATATCTAGGATATGGCATTGGCA-G-TACAAGAAACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACGATACAAGAAACA
* * * *
28646040 TCTCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
28646077 TCTTATATTC
Statistics
Matches: 153, Mismatches: 28, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
49 42 0.27
50 81 0.53
52 30 0.20
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (51 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACGATACAAGAAACA
Found at i:28648497 original size:15 final size:15
Alignment explanation
Indices: 28648477--28648510 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
28648467 AAATGGCAAA
28648477 TCAATTGATAACACT
1 TCAATTGATAACACT
*
28648492 TCAATTGATAATACT
1 TCAATTGATAACACT
28648507 TCAA
1 TCAA
28648511 GCCAACCACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (15 bp):
TCAATTGATAACACT
Found at i:28651315 original size:21 final size:21
Alignment explanation
Indices: 28651291--28651370 Score: 133
Period size: 21 Copynumber: 3.8 Consensus size: 21
28651281 ACGTGTTCCC
*
28651291 CCTTCATACGGGCGTGTGTGG
1 CCTTCACACGGGCGTGTGTGG
28651312 CCTTCACACGGGCGTGTGTGG
1 CCTTCACACGGGCGTGTGTGG
28651333 CCTTCACACGGGCGTGTGTGG
1 CCTTCACACGGGCGTGTGTGG
**
28651354 CCTTCACATAGGCGTGT
1 CCTTCACACGGGCGTGT
28651371 AGACCCTCAC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.11, C:0.28, G:0.35, T:0.26
Consensus pattern (21 bp):
CCTTCACACGGGCGTGTGTGG
Found at i:28651552 original size:22 final size:22
Alignment explanation
Indices: 28651527--28651570 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
28651517 GGCTAGGACT
28651527 TATGAGTTATTTATAATCGTTA
1 TATGAGTTATTTATAATCGTTA
28651549 TATGAGTTATTTATAATCGTTA
1 TATGAGTTATTTATAATCGTTA
28651571 CACTAGGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.05, G:0.14, T:0.50
Consensus pattern (22 bp):
TATGAGTTATTTATAATCGTTA
Found at i:28655794 original size:16 final size:16
Alignment explanation
Indices: 28655773--28655844 Score: 108
Period size: 16 Copynumber: 4.5 Consensus size: 16
28655763 TGTTTAGTTT
28655773 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
28655789 GCTGTAATTGAATAGA
1 GCTGTAATGGAATAGA
*
28655805 GTTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
* *
28655821 GCTATAATAGAATAGA
1 GCTGTAATGGAATAGA
28655837 GCTGTAAT
1 GCTGTAAT
28655845 AGGTATTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.29
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:28656066 original size:17 final size:18
Alignment explanation
Indices: 28656032--28656079 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
28656022 TTATTATTAA
28656032 ATATAATTTAATAAAAAAT
1 ATATAATTTAAT-AAAAAT
* *
28656051 ATATAATTTACTAAAATT
1 ATATAATTTAATAAAAAT
*
28656069 CT-TAATTTAAT
1 ATATAATTTAAT
28656080 TATTCTTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 8 0.32
18 6 0.24
19 11 0.44
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:28657665 original size:20 final size:20
Alignment explanation
Indices: 28657627--28657670 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
28657617 GCAGAAATCG
*
28657627 AGAGAAAATCAAAGAAAAAT
1 AGAGAAAATCAAAGAAAAAA
*
28657647 AGAGAAAAT-AAGAGGAAAAA
1 AGAGAAAATCAA-AGAAAAAA
28657667 AGAG
1 AGAG
28657671 GGATTCGACG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.68, C:0.02, G:0.23, T:0.07
Consensus pattern (20 bp):
AGAGAAAATCAAAGAAAAAA
Found at i:28658682 original size:15 final size:15
Alignment explanation
Indices: 28658649--28658686 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
28658639 TAGGAAAATG
28658649 TTAATATATTATTAT
1 TTAATATATTATTAT
*
28658664 TTAATTTATTATTCA-
1 TTAATATATTATT-AT
28658679 TTAATATA
1 TTAATATA
28658687 CATTTTTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 19 0.95
16 1 0.05
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAATATATTATTAT
Found at i:28658995 original size:17 final size:17
Alignment explanation
Indices: 28658973--28659006 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
28658963 AAAAAGAAAA
28658973 AAATTTACT-TATTTATG
1 AAATTTA-TATATTTATG
28658990 AAATTTATATATTTATG
1 AAATTTATATATTTATG
28659007 TGTATGGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 15 0.94
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (17 bp):
AAATTTATATATTTATG
Found at i:28662486 original size:21 final size:21
Alignment explanation
Indices: 28662461--28662513 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
28662451 AGCGGTGGTA
*
28662461 GTGAGATTAGTTACTGTAGCG
1 GTGAGATTAGATACTGTAGCG
*
28662482 GTGAGATTGGATACTGTAGCG
1 GTGAGATTAGATACTGTAGCG
28662503 GTGAGATTAGA
1 GTGAGATTAGA
28662514 AACAATGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.26, C:0.08, G:0.36, T:0.30
Consensus pattern (21 bp):
GTGAGATTAGATACTGTAGCG
Found at i:28665251 original size:36 final size:36
Alignment explanation
Indices: 28665211--28665282 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
28665201 AAGAAAGTAC
*
28665211 TTTGATATGGAAAACAAATATAGAATTTTGCATATT
1 TTTGATATGGAAAACAAATACAGAATTTTGCATATT
28665247 TTTGATATGGAAAACAAATACAGAATTTTGCATATT
1 TTTGATATGGAAAACAAATACAGAATTTTGCATATT
28665283 ATATATAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.38
Consensus pattern (36 bp):
TTTGATATGGAAAACAAATACAGAATTTTGCATATT
Found at i:28669671 original size:21 final size:22
Alignment explanation
Indices: 28669634--28669686 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
28669624 TTTTAAAATA
* **
28669634 TTTTTAAAAT-ACTTTTTTTTG
1 TTTTTAAAATAAATTTTTGGTG
28669655 TTTTTAAAATAAATTTTTGGTG
1 TTTTTAAAATAAATTTTTGGTG
28669677 TTTATTAAAA
1 TTT-TTAAAA
28669687 AATGGGCCGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 10 0.37
22 11 0.41
23 6 0.22
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (22 bp):
TTTTTAAAATAAATTTTTGGTG
Found at i:28671364 original size:21 final size:21
Alignment explanation
Indices: 28671340--28671403 Score: 94
Period size: 21 Copynumber: 3.0 Consensus size: 21
28671330 TGTAGATCAA
28671340 ACTTATCATAATACA-TGTCAT
1 ACTTATCATAATACAGT-TCAT
*
28671361 ACTTATCATAACACAGTTCAT
1 ACTTATCATAATACAGTTCAT
*
28671382 ACTTATCATAATACAGATCAT
1 ACTTATCATAATACAGTTCAT
28671403 A
1 A
28671404 TTGAGCATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
21 38 0.97
22 1 0.03
ACGTcount: A:0.41, C:0.20, G:0.05, T:0.34
Consensus pattern (21 bp):
ACTTATCATAATACAGTTCAT
Found at i:28691854 original size:29 final size:28
Alignment explanation
Indices: 28691818--28691925 Score: 83
Period size: 29 Copynumber: 3.8 Consensus size: 28
28691808 AAAGGACAAC
28691818 CTTTGTGGCAAAACTCTAAAAGGGTAAG
1 CTTTGTGGCAAAACTCTAAAAGGGTAAG
* * * * ** *
28691846 CGTATGTGGCGAACCTATTAAAA-GACAGG
1 C-TTTGTGGCAAAACT-CTAAAAGGGTAAG
* *
28691875 CTTTGTGGCAAAAATCTAGAAGGGTAAG
1 CTTTGTGGCAAAACTCTAAAAGGGTAAG
* *
28691903 CCTTTGTGGCAAACCTCTTAAAG
1 -CTTTGTGGCAAAACTCTAAAAG
28691926 AATGACTTTA
Statistics
Matches: 56, Mismatches: 20, Indels: 7
0.67 0.24 0.08
Matches are distributed among these distances:
27 4 0.07
28 14 0.25
29 33 0.59
30 5 0.09
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (28 bp):
CTTTGTGGCAAAACTCTAAAAGGGTAAG
Found at i:28691918 original size:57 final size:57
Alignment explanation
Indices: 28691762--28691924 Score: 209
Period size: 57 Copynumber: 2.9 Consensus size: 57
28691752 AAGAAAAACT
* * ** *
28691762 TTTGTGGCAAAAATCTGGAAAGGTAAGCCTATGTGGCGAACCGGTTAAAGGACAACC
1 TTTGTGGCAAAAATCTAGAAGGGTAAGCCTATGTGGCGAACCTATTAAAAGACAACC
* * * **
28691819 TTTGTGGCAAAACTCTAAAAGGGTAAGCGTATGTGGCGAACCTATTAAAAGACAGGC
1 TTTGTGGCAAAAATCTAGAAGGGTAAGCCTATGTGGCGAACCTATTAAAAGACAACC
* * *
28691876 TTTGTGGCAAAAATCTAGAAGGGTAAGCCTTTGTGGCAAACCTCTTAAA
1 TTTGTGGCAAAAATCTAGAAGGGTAAGCCTATGTGGCGAACCTATTAAA
28691925 GAATGACTTT
Statistics
Matches: 90, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 90 1.00
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.24
Consensus pattern (57 bp):
TTTGTGGCAAAAATCTAGAAGGGTAAGCCTATGTGGCGAACCTATTAAAAGACAACC
Found at i:28692883 original size:26 final size:26
Alignment explanation
Indices: 28692846--28692909 Score: 101
Period size: 26 Copynumber: 2.4 Consensus size: 26
28692836 TAATGATCAA
28692846 TTGAGTGATTTTATACTTGGTAAAATT
1 TTGA-TGATTTTATACTTGGTAAAATT
28692873 TTGATGATTTTATACTTGGTAAAATT
1 TTGATGATTTTATACTTGGTAAAATT
* *
28692899 TTAACGATTTT
1 TTGATGATTTT
28692910 GCCCCCTGGC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 31 0.89
27 4 0.11
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.50
Consensus pattern (26 bp):
TTGATGATTTTATACTTGGTAAAATT
Done.