Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 92 of 202
Found at i:27671059 original size:25 final size:24
Alignment explanation
Indices: 27670985--27671078 Score: 93
Period size: 25 Copynumber: 3.8 Consensus size: 24
27670975 GCTATGAATC
* *
27670985 GGTATGCTCTCACGAGCTGTAAATC
1 GGTAAGCTCTCACGAGCTG-AAATT
*
27671010 GGTAAGCTCAT-ACGAGATGAGAATT
1 GGTAAGCTC-TCACGAGCTGA-AATT
*
27671035 GGTAAGCTCTCATGAGCTGCAAATT
1 GGTAAGCTCTCACGAGCTG-AAATT
27671060 GGTAAGCTCAT-ACGAGCTG
1 GGTAAGCTC-TCACGAGCTG
27671079 TGGTGTGTCT
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
24 2 0.03
25 53 0.91
26 3 0.05
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.26
Consensus pattern (24 bp):
GGTAAGCTCTCACGAGCTGAAATT
Found at i:27678046 original size:25 final size:25
Alignment explanation
Indices: 27678017--27678090 Score: 89
Period size: 25 Copynumber: 3.0 Consensus size: 25
27678007 AACAAGCTGT
* *
27678017 AAATCAGTAAGCTCATACGAGCTA-
1 AAATCGGTAAGCTCATATGAGCTAC
27678041 AGAATCGGTAAGCTC-TCATGAGCTAC
1 A-AATCGGTAAGCTCAT-ATGAGCTAC
*
27678067 AAATTGGTAAGCTCATATGAGCTA
1 AAATCGGTAAGCTCATATGAGCTA
27678091 TGGTGTGTCC
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
24 2 0.05
25 39 0.91
26 2 0.05
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.24
Consensus pattern (25 bp):
AAATCGGTAAGCTCATATGAGCTAC
Found at i:27678153 original size:22 final size:22
Alignment explanation
Indices: 27678128--27678211 Score: 114
Period size: 22 Copynumber: 3.8 Consensus size: 22
27678118 ACAACCAAAT
*
27678128 CTCTCATGTTTCACGTACTAAG
1 CTCTCATGTTTAACGTACTAAG
27678150 CTCTCATGTTTAACGTACTAAG
1 CTCTCATGTTTAACGTACTAAG
* *
27678172 CTCTCATGTTTAACGAACTAAA
1 CTCTCATGTTTAACGTACTAAG
* **
27678194 CCCTCATGGCTAACGTAC
1 CTCTCATGTTTAACGTAC
27678212 GATATTTATA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.32
Consensus pattern (22 bp):
CTCTCATGTTTAACGTACTAAG
Found at i:27682269 original size:121 final size:121
Alignment explanation
Indices: 27682109--27682350 Score: 387
Period size: 121 Copynumber: 2.0 Consensus size: 121
27682099 TAGGGTGAGA
* * * * *
27682109 CTATTATTGTTTTCTCGATGGATACTTGTGGTATAATCAGATTATAGTAGCGCTAGAAGATCAAC
1 CTATTACTATTTTCTCAATGGATACTTGTGGTATAATCAGATTATAATAGCGCTAGAAGATCAAA
* *
27682174 ACAAAACAACATTCACATGCCCATACGATACATTTGCACTTAGACGCATGTCATTT
66 ACAAAACAACATTCACATGCCCATACGATACACTTGCACTTAGACGCATGCCATTT
27682230 CTATTACTATTTTCTCAATGGATACTTG-GGATATAATCAGATTATAATAGCGCTAGAAGATCAA
1 CTATTACTATTTTCTCAATGGATACTTGTGG-TATAATCAGATTATAATAGCGCTAGAAGATCAA
* *
27682294 AACAAAACAACATTCACATGCCTATACGATACACTTGCATTTAGACGCATGCCATTT
65 AACAAAACAACATTCACATGCCCATACGATACACTTGCACTTAGACGCATGCCATTT
27682351 GGTTTATGTA
Statistics
Matches: 111, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
120 2 0.02
121 109 0.98
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (121 bp):
CTATTACTATTTTCTCAATGGATACTTGTGGTATAATCAGATTATAATAGCGCTAGAAGATCAAA
ACAAAACAACATTCACATGCCCATACGATACACTTGCACTTAGACGCATGCCATTT
Found at i:27685542 original size:16 final size:16
Alignment explanation
Indices: 27685521--27685555 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
27685511 TGCACCAGTC
* *
27685521 CTGCTCTCATACGCTG
1 CTGCTCCCACACGCTG
27685537 CTGCTCCCACACGCTG
1 CTGCTCCCACACGCTG
27685553 CTG
1 CTG
27685556 TCATTTCTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.11, C:0.43, G:0.20, T:0.26
Consensus pattern (16 bp):
CTGCTCCCACACGCTG
Found at i:27691954 original size:17 final size:16
Alignment explanation
Indices: 27691915--27691971 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
27691905 CATACATTTC
* *
27691915 AAAAAGAAAAAAAACA
1 AAAAATAAAAAAAATA
27691931 AATAAATAAATAAAAATA
1 AA-AAATAAA-AAAAATA
*
27691949 AAAAATAAAACCAAATA
1 AAAAATAAAA-AAAATA
27691966 AAAAAT
1 AAAAAT
27691972 TAAAGGTCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
16 3 0.09
17 24 0.69
18 8 0.23
ACGTcount: A:0.81, C:0.05, G:0.02, T:0.12
Consensus pattern (16 bp):
AAAAATAAAAAAAATA
Found at i:27695600 original size:88 final size:88
Alignment explanation
Indices: 27695502--27695862 Score: 453
Period size: 88 Copynumber: 4.1 Consensus size: 88
27695492 GTAGTGGAGT
*
27695502 AGATCGAAGACACTAGCATTGCCTCCCTGGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTG
1 AGATCGAAGACACTAGCATTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAGATAGCAGATCTTG
* *
27695567 CCTTCCTGTACTGACTA-TGAAAC
66 CCTTCCTGTACTGAC-AGCGAAGC
* * *
27695590 AGATCAAAGACACTAG-ACTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGATCTT
1 AGATCGAAGACACTAGCA-TTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAGATAGCAGATCTT
27695654 GCCTTCC--TACATCGACAGCGAAGC
65 GCCTTCCTGTAC-T-GACAGCGAAGC
* * * *
27695678 AGATCGAAGACACTAGCCTTGCCTCCCTAGGTTACAGCAGAGCAGGTTGAAGATAGCAGATCTTG
1 AGATCGAAGACACTAGCATTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAGATAGCAGATCTTG
* * *
27695743 CCTTCCTGCACTGGCAGCGAATC
66 CCTTCCTGTACTGACAGCGAAGC
* * * *
27695766 AGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAA-AGCACCAGATCTT
1 AGATCGAAGACACTAGCATTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAGA-TAGCAGATCTT
* * **
27695830 GCCTTCCTGTATTGGCAATGAAGC
65 GCCTTCCTGTACTGACAGCGAAGC
27695854 AGATCGAAG
1 AGATCGAAG
27695863 CCAATAATCC
Statistics
Matches: 238, Mismatches: 27, Indels: 16
0.85 0.10 0.06
Matches are distributed among these distances:
86 3 0.01
87 4 0.02
88 228 0.96
89 1 0.00
90 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.22
Consensus pattern (88 bp):
AGATCGAAGACACTAGCATTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAGATAGCAGATCTTG
CCTTCCTGTACTGACAGCGAAGC
Found at i:27695796 original size:176 final size:176
Alignment explanation
Indices: 27695502--27695837 Score: 512
Period size: 176 Copynumber: 1.9 Consensus size: 176
27695492 GTAGTGGAGT
* * **
27695502 AGATCGAAGACACTAGCATTGCCTCCCTGGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTG
1 AGATCGAAGACACTAGCATTGCCTCCCTAGGTTACAGCAGAGCAGGTTGAAGATAGCAGATCTTG
* * *
27695567 CCTTCCTGTACTGACTATGAAACAGATCAAAGACACTAGACTTGCCTCCCTGGGTTGCAGCGGAG
66 CCTTCCTGCACTGACTACGAAACAGATCAAAGACACCAGACTTGCCTCCCTGGGTTGCAGCGGAG
* *
27695632 CAGGTTAAAAATAGCAGATCTTGCCTTCCTACATCGACAGCGAAGC
131 CAGGTTAAAAACACCAGATCTTGCCTTCCTACATCGACAGCGAAGC
*
27695678 AGATCGAAGACACTAGCCTTGCCTCCCTAGGTTACAGCAGAGCAGGTTGAAGATAGCAGATCTTG
1 AGATCGAAGACACTAGCATTGCCTCCCTAGGTTACAGCAGAGCAGGTTGAAGATAGCAGATCTTG
* * * *
27695743 CCTTCCTGCACTGGC-AGCGAATCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGA
66 CCTTCCTGCACTGACTA-CGAAACAGATCAAAGACACCAGACTTGCCTCCCTGGGTTGCAGCGGA
* *
27695807 GCAGGTTGAAAGCACCAGATCTTGCCTTCCT
130 GCAGGTTAAAAACACCAGATCTTGCCTTCCT
27695838 GTATTGGCAA
Statistics
Matches: 143, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
175 1 0.01
176 142 0.99
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.22
Consensus pattern (176 bp):
AGATCGAAGACACTAGCATTGCCTCCCTAGGTTACAGCAGAGCAGGTTGAAGATAGCAGATCTTG
CCTTCCTGCACTGACTACGAAACAGATCAAAGACACCAGACTTGCCTCCCTGGGTTGCAGCGGAG
CAGGTTAAAAACACCAGATCTTGCCTTCCTACATCGACAGCGAAGC
Found at i:27695831 original size:44 final size:44
Alignment explanation
Indices: 27695520--27695838 Score: 171
Period size: 44 Copynumber: 7.2 Consensus size: 44
27695510 GACACTAGCA
* * *
27695520 TTGCCTCCCTGGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATC
1 TTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAGACACCAGATC
* *** * * * * ** *
27695564 TTGCCTTCCTGTACTGACTA-TGAAACAGATCAAAGACACTAGA-C
1 TTGCCTCCCTGGGTTG-C-AGCGGAGCAGGTTGAAGACACCAGATC
* * * *
27695608 TTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGATC
1 TTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAGACACCAGATC
* *** * * * * * *
27695652 TTGCCTTCCTACATCGACAGCGAAGCAGATCGAAGACACTAG-CC
1 TTGCCTCCCTGGGTTG-CAGCGGAGCAGGTTGAAGACACCAGATC
* * * * *
27695696 TTGCCTCCCTAGGTTACAGCAGAGCAGGTTGAAGATAGCAGATC
1 TTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAGACACCAGATC
* ** * * * * * *
27695740 TTGCCTTCCTGCACTGGCAGCGAATCAGATCGAAGACACCAG-CC
1 TTGCCTCCCTG-GGTTGCAGCGGAGCAGGTTGAAGACACCAGATC
27695784 TTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAA-AGCACCAGATC
1 TTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAGA-CACCAGATC
*
27695828 TTGCCTTCCTG
1 TTGCCTCCCTG
27695839 TATTGGCAAT
Statistics
Matches: 190, Mismatches: 76, Indels: 18
0.67 0.27 0.06
Matches are distributed among these distances:
42 2 0.01
43 54 0.28
44 81 0.43
45 52 0.27
46 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.26, T:0.23
Consensus pattern (44 bp):
TTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAGACACCAGATC
Found at i:27696011 original size:44 final size:45
Alignment explanation
Indices: 27695951--27696042 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 45
27695941 TGGATCGCAT
* * *
27695951 CAAGTCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAA-AG
1 CAAGCCTTATCCCCCTGAAGTTGCAGCGGAGCAGACTGAGAATAG
* * *
27695995 CAAGCCTTATCCCCCTGAAGTTGCAGTGGGGTAGACTGAGAATAG
1 CAAGCCTTATCCCCCTGAAGTTGCAGCGGAGCAGACTGAGAATAG
27696040 CAA
1 CAA
27696043 ATCTTACTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 36 0.88
45 5 0.12
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (45 bp):
CAAGCCTTATCCCCCTGAAGTTGCAGCGGAGCAGACTGAGAATAG
Found at i:27696235 original size:41 final size:41
Alignment explanation
Indices: 27696189--27696332 Score: 137
Period size: 41 Copynumber: 3.4 Consensus size: 41
27696179 AAATAAAAGA
*
27696189 TCTTATCTCTCT-AGAGTTACAGTAGAGTAGATCACATCATG
1 TCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCACATCAAG
* * * ** * * *
27696230 TCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAG
1 TCTTATCTCTCTGAAGTTACAGTAGAGTAGA-TCACAT-CAAG
* *
27696273 ATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
1 -TCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCAAG
*
27696315 TCTTATCTCCCTGAAGTT
1 TCTTATCTCTCTGAAGTT
27696333 GCAGCGGAGC
Statistics
Matches: 79, Mismatches: 20, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
41 41 0.52
42 7 0.09
43 5 0.06
44 26 0.33
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (41 bp):
TCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCAAG
Found at i:27696292 original size:85 final size:85
Alignment explanation
Indices: 27696148--27696369 Score: 329
Period size: 85 Copynumber: 2.6 Consensus size: 85
27696138 TTACAAATCC
* *
27696148 TATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAATAAAAGATCTTATCTCTCTAGAGTTACAGTA
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTAGAGTTACAGTA
*
27696213 GAGTAGATCACATCATGTCT
66 GAGTAGATCACATCAGGTCT
27696233 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCT-GAAGTTACAGT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTAG-AGTTACAGT
*
27696297 AGAGTAGATCGCATCAGGTCT
65 AGAGTAGATCACATCAGGTCT
* * * * *
27696318 TATCTCCCTGAAGTTGCAGCGGAGCTGATCGAAGAATTACAGATCTTATCTC
1 TATCTCCCTGAAGTTGCAGTGGAGCGGAT-TAA-AATAAAAGATCTTATCTC
27696370 CCTAAGCAGT
Statistics
Matches: 125, Mismatches: 9, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
84 1 0.01
85 106 0.85
86 2 0.02
87 16 0.13
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (85 bp):
TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTAGAGTTACAGTA
GAGTAGATCACATCAGGTCT
Found at i:27696348 original size:41 final size:41
Alignment explanation
Indices: 27696218--27696347 Score: 118
Period size: 41 Copynumber: 3.1 Consensus size: 41
27696208 CAGTAGAGTA
* *
27696218 GATCACATCATGTCTTATCTCCCTGAAGTTGCAGTGGAGCG
1 GATCACATCAGGTCTTATCTCCCTGAAGTTGCAGTGGAGCT
* * * * * * *
27696259 GATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGTAGAG-T
1 GA-TCACAT--CAGGTCTTATCTCCCTGAAGTTGCAGTGGAGCT
* *
27696302 AGATCGCATCAGGTCTTATCTCCCTGAAGTTGCAGCGGAGCT
1 -GATCACATCAGGTCTTATCTCCCTGAAGTTGCAGTGGAGCT
27696344 GATC
1 GATC
27696348 GAAGAATTAC
Statistics
Matches: 66, Mismatches: 18, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
41 31 0.47
42 5 0.08
43 3 0.05
44 27 0.41
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (41 bp):
GATCACATCAGGTCTTATCTCCCTGAAGTTGCAGTGGAGCT
Found at i:27696412 original size:44 final size:45
Alignment explanation
Indices: 27696315--27696432 Score: 148
Period size: 44 Copynumber: 2.6 Consensus size: 45
27696305 TCGCATCAGG
* * * * *
27696315 TCTTATCTCCCTGAAGTTGCAGCGGAGCTGATCGAAGAATTACAGA
1 TCTTATCTCCCT-AAGTAGTAGCGGAGCAGATCAAAGAATGACAGA
* *
27696361 TCTTATCTCCCTAAGCAGTAGCGGAGCAGATCAAAG-ATGGCAGA
1 TCTTATCTCCCTAAGTAGTAGCGGAGCAGATCAAAGAATGACAGA
*
27696405 TCTTATCTCCCTAAGTAGTAGTGGAGCA
1 TCTTATCTCCCTAAGTAGTAGCGGAGCA
27696433 AATTGTAGCC
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 32 0.51
45 19 0.30
46 12 0.19
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (45 bp):
TCTTATCTCCCTAAGTAGTAGCGGAGCAGATCAAAGAATGACAGA
Found at i:27696573 original size:173 final size:172
Alignment explanation
Indices: 27696384--27696778 Score: 610
Period size: 173 Copynumber: 2.3 Consensus size: 172
27696374 AGCAGTAGCG
* *
27696384 GAGCAGATCAAAGATGGCAGATCTTATCTCCCTAAGTAGTAGTGGAGCAAATTGTAGCCAGTAAT
1 GAGCAGATCGAAGATGGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATTGTAGCCAGTAAT
* *
27696449 CCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGATATTATCTCTCTGGAGTTGTAG
66 CCTATCTCCCTGAAGTTGCAGTGGAGCGGATT-AAATAAAAGATATTAACTCTCTAGAGTTGTAG
* * *
27696514 TAGAGTAGATCGCATCATGTCTTATCTCACTGAAGTTGCAGTA
130 TAGAGTAGATCACATCAGGTCTTATCTCACTGAAGTTACAGTA
* *
27696557 GAGCAGATCGAAGATGGCAGATCTTATCTCCCTAAGCAGTAGTGGAACAGATTGTAGCCAGTAAT
1 GAGCAGATCGAAGATGGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATTGTAGCCAGTAAT
* * *
27696622 CCTATCTCCCTGAAGTTGTAGTGGAGCGTATTAAATAAAAGATCTTAACTCTCTAGAGTTGTAGT
66 CCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAATAAAAGATATTAACTCTCTAGAGTTGTAGT
*
27696687 AGAGTAGATCACATCAGGTCTTATCTCCCTGAAGTTACAGTA
131 AGAGTAGATCACATCAGGTCTTATCTCACTGAAGTTACAGTA
* *** *
27696729 GAGCAGACCGAAGAATTATAGATCTTATCTCCCTAAGCAGTAGCGGAGCA
1 GAGCAGATCGAAG-ATGGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCA
27696779 GATCGAAGAT
Statistics
Matches: 202, Mismatches: 19, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
172 80 0.40
173 122 0.60
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (172 bp):
GAGCAGATCGAAGATGGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATTGTAGCCAGTAAT
CCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAATAAAAGATATTAACTCTCTAGAGTTGTAGT
AGAGTAGATCACATCAGGTCTTATCTCACTGAAGTTACAGTA
Found at i:27696757 original size:218 final size:217
Alignment explanation
Indices: 27696557--27697171 Score: 966
Period size: 218 Copynumber: 2.8 Consensus size: 217
27696547 AGTTGCAGTA
*
27696557 GAGCAGATCGAAGATGGCAGATCTTATCTCCCTAAGCAGTAGTGGAACAGATTGTAGCCAGTAAT
1 GAGCAGATCGAAGATGGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGTAGCCAGTAAT
* * * *
27696622 CCTATCTCCCTGAAGTTGTAGTGGAGCGTATT-AAATAAAAGATCTTAACTCTCT-AGAGTTGTA
66 CCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGA-AGTTGCA
* * *
27696685 GTAGAGTAGATCACATCAGGTCTTATCTCCCTGAAGTTACAGTAGAGCAGACCGAAGAATTATAG
130 GTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAAGTTACAGCAGAGCAGACCGAAGAATTAGAG
*
27696750 ATCTTATCTCCCTAAGCAGTAGCG
195 ATCTTATCT-CCTAAGCAGTAGTG
*
27696774 GAGCAGATCGAAGATGGCAGATCTAATCTCCCTAAGCAGTAGTGGAGCAGATTGTAGCCAGTAAT
1 GAGCAGATCGAAGATGGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGTAGCCAGTAAT
* *
27696839 CCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAAGATCTTATCCCTCTGAAGTTGCAG
66 CCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTGCAG
* * *
27696904 TAGAGTAGATCGCATCAGGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGAATTAGAGA
131 TAGAGTAGATCGCATCAGGTCTTATCTCCCTGAAGTTACAGCAGAGCAGACCGAAGAATTAGAGA
27696969 TCTTATCTCCTTAAGCAGTAGTG
196 TCTTATCTCC-TAAGCAGTAGTG
* * * *
27696992 GAGCAGATTGAAGATGGCAGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATTGAAACCAGTAAT
1 GAGCAGATCGAAGATGGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGTAGCCAGTAAT
* *
27697057 CCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATAAAAGATCTTATCTCTCTGAAGTGGCAG
66 CCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTGCAG
* *
27697122 TAGAGTAGATCGCATCAGGTCTTATCTCCCT-AAGGTTGCAGCGGAGCAGA
131 TAGAGTAGATCGCATCAGGTCTTATCTCCCTGAA-GTTACAGCAGAGCAGA
27697172 TCAAGGAAGC
Statistics
Matches: 370, Mismatches: 24, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
217 96 0.26
218 273 0.74
219 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (217 bp):
GAGCAGATCGAAGATGGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGTAGCCAGTAAT
CCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTGCAG
TAGAGTAGATCGCATCAGGTCTTATCTCCCTGAAGTTACAGCAGAGCAGACCGAAGAATTAGAGA
TCTTATCTCCTAAGCAGTAGTG
Found at i:27696763 original size:390 final size:392
Alignment explanation
Indices: 27696233--27697001 Score: 1224
Period size: 390 Copynumber: 2.0 Consensus size: 392
27696223 CATCATGTCT
*
27696233 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGTA
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGATCTTAACTCTCTGAAGTTACAGTA
* * * * *
27696298 GAGTAGATCGCATCAGGTCTTATCTCCCTGAAGTTGCAGCGGAGCTGATCGAAGAATTACAGATC
66 GAGTAGATCACATCAGGTCTTATCTCCCTGAAGTTACAGCAGAGCAGACCGAAGAATTACAGATC
* *
27696363 TTATCTCCCTAAGCAGTAGCGGAGCAGATCAAAGATGGCAGATCTTATCTCCCTAAGTAGTAGTG
131 TTATCTCCCTAAGCAGTAGCGGAGCAGATCAAAGATGGCAGATCTAATCTCCCTAAGCAGTAGTG
*
27696428 GAGCAAATTGTAGCCAGTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGAT
196 GAGCAAATTGTAGCCAGTAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAAGAT
* * * * *
27696493 ATTATCTCTCTGGAGTTGTAGTAGAGTAGATCGCATCATGTCTTATCTCACTGAAGTTGCAGTAG
261 ATTATCCCTCTGAAGTTGCAGTAGAGTAGATCGCATCAGGTCTTATCTCACTGAAGTTGCAGCAG
*
27696558 AGCAGA-TCGAAG-A-TGGCAGATCTTATCTCCCTAAGCAGTAGTGGAACAGATTGTAGCCAGTA
326 AGCAGACT-GAAGAATTAG-AGATCTTATCTCCCTAAGCAGTAGTGGAACAGATTGTAGCCAGTA
27696620 ATCC
389 ATCC
* * **
27696624 TATCTCCCTGAAGTTGTAGTGGAGCGTATT-AAATAAAAGATCTTAACTCTCT-AGAGTTGTAGT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGATCTTAACTCTCTGA-AGTTACAGT
* *
27696687 AGAGTAGATCACATCAGGTCTTATCTCCCTGAAGTTACAGTAGAGCAGACCGAAGAATTATAGAT
65 AGAGTAGATCACATCAGGTCTTATCTCCCTGAAGTTACAGCAGAGCAGACCGAAGAATTACAGAT
*
27696752 CTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCAGATCTAATCTCCCTAAGCAGTAGT
130 CTTATCTCCCTAAGCAGTAGCGGAGCAGATCAAAGATGGCAGATCTAATCTCCCTAAGCAGTAGT
*
27696817 GGAGCAGATTGTAGCCAGTAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAAGA
195 GGAGCAAATTGTAGCCAGTAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAAGA
* * *
27696882 TCTTATCCCTCTGAAGTTGCAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAAGTTGCAGCG
260 TATTATCCCTCTGAAGTTGCAGTAGAGTAGATCGCATCAGGTCTTATCTCACTGAAGTTGCAGCA
* *
27696947 GAGCAGACTGAAGAATTAGAGATCTTATCTCCTTAAGCAGTAGTGGAGCAGATTG
325 GAGCAGACTGAAGAATTAGAGATCTTATCTCCCTAAGCAGTAGTGGAACAGATTG
27697002 AAGATGGCAG
Statistics
Matches: 346, Mismatches: 28, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
389 1 0.00
390 279 0.81
391 64 0.18
392 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.27
Consensus pattern (392 bp):
TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGATCTTAACTCTCTGAAGTTACAGTA
GAGTAGATCACATCAGGTCTTATCTCCCTGAAGTTACAGCAGAGCAGACCGAAGAATTACAGATC
TTATCTCCCTAAGCAGTAGCGGAGCAGATCAAAGATGGCAGATCTAATCTCCCTAAGCAGTAGTG
GAGCAAATTGTAGCCAGTAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAAGAT
ATTATCCCTCTGAAGTTGCAGTAGAGTAGATCGCATCAGGTCTTATCTCACTGAAGTTGCAGCAG
AGCAGACTGAAGAATTAGAGATCTTATCTCCCTAAGCAGTAGTGGAACAGATTGTAGCCAGTAAT
CC
Found at i:27696786 original size:45 final size:44
Alignment explanation
Indices: 27696729--27696825 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 44
27696719 AGTTACAGTA
* * * *
27696729 GAGCAGACCGAAGAATTATAGATCTTATCTCCCTAAGCAGTAGCG
1 GAGCAGATCGAAG-ATGACAGATCTAATCTCCCTAAGCAGTAGCG
* *
27696774 GAGCAGATCGAAGATGGCAGATCTAATCTCCCTAAGCAGTAGTG
1 GAGCAGATCGAAGATGACAGATCTAATCTCCCTAAGCAGTAGCG
27696818 GAGCAGAT
1 GAGCAGAT
27696826 TGTAGCCAGT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 34 0.74
45 12 0.26
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.21
Consensus pattern (44 bp):
GAGCAGATCGAAGATGACAGATCTAATCTCCCTAAGCAGTAGCG
Found at i:27697004 original size:45 final size:44
Alignment explanation
Indices: 27696923--27697047 Score: 144
Period size: 44 Copynumber: 2.8 Consensus size: 44
27696913 TCGCATCAGG
** * * *
27696923 TCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGAATTAG-AGA
1 TCTTATCTCCCT-AAGCAGTAGTGGAGCAGATTGAAG-A-TAGCAGA
* *
27696969 TCTTATCTCCTTAAGCAGTAGTGGAGCAGATTGAAGATGGCAGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATAGCAGA
*
27697013 TCTTATCTCCCTAAGCAGTAGTAGAGCAGATTGAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAA
27697048 ACCAGTAATC
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
43 2 0.03
44 37 0.54
45 19 0.28
46 11 0.16
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.26
Consensus pattern (44 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATAGCAGA
Found at i:27697028 original size:44 final size:45
Alignment explanation
Indices: 27696923--27697116 Score: 139
Period size: 44 Copynumber: 4.4 Consensus size: 45
27696913 TCGCATCAGG
* * * *
27696923 TCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGAATTAG-AGA
1 TCTTATCTCCCTGAAGTAGTAGTGGAGCAGATTGAAG-A-TAGCAGA
* * *
27696969 TCTTATCT-CCTTAAGCAGTAGTGGAGCAGATTGAAGATGGCAGA
1 TCTTATCTCCCTGAAGTAGTAGTGGAGCAGATTGAAGATAGCAGA
* * * *
27697013 TCTTATCTCCCT-AAGCAGTAGTAGAGCAGATTGAA-ACCAGTA-A
1 TCTTATCTCCCTGAAGTAGTAGTGGAGCAGATTGAAGA-TAGCAGA
* * * ** * **
27697056 TCCTATCTCCCTGAAGTTGCAGTGGAGTGGATT-AAAATAAAAGA
1 TCTTATCTCCCTGAAGTAGTAGTGGAGCAGATTGAAGATAGCAGA
*
27697100 TCTTATCTCTCTGAAGT
1 TCTTATCTCCCTGAAGT
27697117 GGCAGTAGAG
Statistics
Matches: 119, Mismatches: 23, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
43 19 0.16
44 67 0.56
45 25 0.21
46 8 0.07
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (45 bp):
TCTTATCTCCCTGAAGTAGTAGTGGAGCAGATTGAAGATAGCAGA
Found at i:27697147 original size:390 final size:388
Alignment explanation
Indices: 27696233--27697175 Score: 1026
Period size: 390 Copynumber: 2.4 Consensus size: 388
27696223 CATCATGTCT
** * * * * * * * *
27696233 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCT-GAAGTTACAGT
1 TATCTCCCTGAAGCAGTAGTAGAGCGTATT-AAACAAAAGATCCTAACTCCCTAG-AGTTGCAGT
*** * * ** * *
27696297 AGAGTAGATCGCATCAGGTCTTATCTCCCTGAAGTTG-CAGCGGAGCTGATCGAAGAATTACAGA
64 AGAGTAGATAAAATAAGATCTTATCTCCCTGAAG-TGACAGTAGAGCAGA-C-CAGAATTACAGA
* *
27696361 TCTTATCTCCCTAAGCAGTAGCGGAGCAGATCAAAGATGGCAGATCTTATCTCCCTAAGTAGTAG
126 TCTTATCTCCCTAAGCAGTAGCGGAGCAGATCAAAGATGGCAGATCTAATCTCCCTAAGCAGTAG
*
27696426 TGGAGCAAATTGTAGCCAGTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAG
191 TGGAGCAAATTGTAGCCAGTAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAAG
* * * * *
27696491 ATATTATCTCTCTGGAGTTGTAGTAGAGTAGATCGCATCATGTCTTATCTCACTGAAGTTGCAGT
256 ATATTATCCCTCTGAAGTTGCAGTAGAGTAGATCGCATCAGGTCTTATCTCACTGAAGTTGCAGC
* * * *
27696556 AGAGCAGATCGAAGATGGCAGATCTTATCTCCCTAAGCAGTAGTGGAACAGATTGTAGCCAGTAA
321 AGAGCAGATCGAAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAACAGATTGAAGACAGCAA
27696621 TCC
386 TCC
** * * * * *
27696624 TATCTCCCTGAAGTTGTAGTGGAGCGTATTAAATAAAAGATCTTAACTCTCTAGAGTTGTAGTAG
1 TATCTCCCTGAAGCAGTAGTAGAGCGTATTAAACAAAAGATCCTAACTCCCTAGAGTTGCAGTAG
* * * * * *
27696689 AGTAGATCACATCAGGTCTTATCTCCCTGAAGTTACAGTAGAGCAGACCGAAGAATTATAGATCT
66 AGTAGATAAAATAAGATCTTATCTCCCTGAAGTGACAGTAGAGCAGACC--AGAATTACAGATCT
*
27696754 TATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCAGATCTAATCTCCCTAAGCAGTAGTGG
129 TATCTCCCTAAGCAGTAGCGGAGCAGATCAAAGATGGCAGATCTAATCTCCCTAAGCAGTAGTGG
* *
27696819 AGCAGATTGTAGCCAGTAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAAGATC
194 AGCAAATTGTAGCCAGTAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAAGATA
* *
27696884 TTATCCCTCTGAAGTTGCAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAAGTTGCAGCGGA
259 TTATCCCTCTGAAGTTGCAGTAGAGTAGATCGCATCAGGTCTTATCTCACTGAAGTTGCAGCAGA
* * **
27696949 GCAGA-CTGAAGAATTAG-AGATCTTATCTCCTTAAGCAGTAGTGGAGCAGATTGAAGATGGCAG
324 GCAGATC-GAAG-A-TAGCAGATCTTATCTCCCTAAGCAGTAGTGGAACAGATTGAAGACAGCA-
*
27697012 ATCT
385 ATCC
** *
27697016 TATCTCCCT-AAGCAGTAGTAGAGCAG-ATTGAAACCAGTA-ATCCTATCTCCCT-GAAGTTGCA
1 TATCTCCCTGAAGCAGTAGTAGAGC-GTATT-AAA-CAAAAGATCCTAACTCCCTAG-AGTTGCA
* * * * * * *
27697077 GTGGAGTGGATTAAAATAAAAGATCTTATCTCTCTGAAGTGGCAGTAGAGTAGATC-GCA-T-CA
62 GTAGAGTAGA-TAAAAT--AAGATCTTATCTCCCTGAAGTGACAGTAGAGCAGACCAGAATTACA
* ** *
27697139 GGTCTTATCTCCCTAAGGTTGCAGCGGAGCAGATCAA
124 GATCTTATCTCCCTAA-GCAGTAGCGGAGCAGATCAA
27697176 GGAAGCAAGT
Statistics
Matches: 474, Mismatches: 62, Indels: 32
0.83 0.11 0.06
Matches are distributed among these distances:
389 3 0.01
390 290 0.61
391 101 0.21
392 44 0.09
393 6 0.01
395 30 0.06
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (388 bp):
TATCTCCCTGAAGCAGTAGTAGAGCGTATTAAACAAAAGATCCTAACTCCCTAGAGTTGCAGTAG
AGTAGATAAAATAAGATCTTATCTCCCTGAAGTGACAGTAGAGCAGACCAGAATTACAGATCTTA
TCTCCCTAAGCAGTAGCGGAGCAGATCAAAGATGGCAGATCTAATCTCCCTAAGCAGTAGTGGAG
CAAATTGTAGCCAGTAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAAGATATT
ATCCCTCTGAAGTTGCAGTAGAGTAGATCGCATCAGGTCTTATCTCACTGAAGTTGCAGCAGAGC
AGATCGAAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAACAGATTGAAGACAGCAATCC
Found at i:27702781 original size:49 final size:49
Alignment explanation
Indices: 27702709--27702804 Score: 174
Period size: 49 Copynumber: 2.0 Consensus size: 49
27702699 TTTGGGAACG
27702709 CAGAAATAGATAAGTTTTTGTAATGCTCCCCTACTTTCCTATTACTTGT
1 CAGAAATAGATAAGTTTTTGTAATGCTCCCCTACTTTCCTATTACTTGT
**
27702758 CAGAAATAGATAAGTTTTTGTAATGCTTGCCTACTTTCCTATTACTT
1 CAGAAATAGATAAGTTTTTGTAATGCTCCCCTACTTTCCTATTACTT
27702805 TCCTTGTTCG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (49 bp):
CAGAAATAGATAAGTTTTTGTAATGCTCCCCTACTTTCCTATTACTTGT
Found at i:27707528 original size:101 final size:102
Alignment explanation
Indices: 27707333--27707542 Score: 273
Period size: 101 Copynumber: 2.1 Consensus size: 102
27707323 CAAAAAATAT
* * *
27707333 CGATACATTTTTGGCCAAGTATCGATATATTCTGAATTATCGATACCCTCTCTTAAAAATGATGC
1 CGATACATTTTTGGCCAAGTATCGATATATTCTGAATTATCGATACCCCCTCTTAAAAACGATAC
* * *
27707398 CAAAATGGAATTTTGTTTCACAAACCCTACTAAGTAC
66 CAAAATAGAATTTTGTTTCACAAAACCTACAAAGTAC
* * * *
27707435 CGATACCTTTTT-GTCAAGTATCGATATTTTCTGAATTATCGATACCCCCTCTT-AAAGCGATAC
1 CGATACATTTTTGGCCAAGTATCGATATATTCTGAATTATCGATACCCCCTCTTAAAAACGATAC
* *
27707498 C-AAATAGCATTTTGTTTCTCACAAAACCTACAAAGTAT
66 CAAAATAGAATTTTG-TT-TCACAAAACCTACAAAGTAC
27707536 CGATACA
1 CGATACA
27707543 GCATTGATGC
Statistics
Matches: 93, Mismatches: 13, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
99 11 0.12
100 10 0.11
101 61 0.66
102 11 0.12
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (102 bp):
CGATACATTTTTGGCCAAGTATCGATATATTCTGAATTATCGATACCCCCTCTTAAAAACGATAC
CAAAATAGAATTTTGTTTCACAAAACCTACAAAGTAC
Found at i:27717502 original size:16 final size:16
Alignment explanation
Indices: 27717481--27717541 Score: 74
Period size: 16 Copynumber: 3.9 Consensus size: 16
27717471 ATATTTAGTC
27717481 ATATAATAAATTATTA
1 ATATAATAAATTATTA
27717497 ATATAATAAATTATTTA
1 ATATAATAAATTA-TTA
27717514 ATATAAT---TTATTA
1 ATATAATAAATTATTA
* *
27717527 TTTTAATAAATTATT
1 ATATAATAAATTATT
27717542 TGATATTTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
13 8 0.21
14 3 0.08
16 18 0.46
17 10 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATAATAAATTATTA
Found at i:27717534 original size:30 final size:30
Alignment explanation
Indices: 27717486--27717547 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
27717476 TAGTCATATA
27717486 ATAAATTATTAATATAATAAATTATTTAAT
1 ATAAATTATTAATATAATAAATTATTTAAT
* * * *
27717516 ATAATTTATTATTTTAATAAATTATTTGAT
1 ATAAATTATTAATATAATAAATTATTTAAT
27717546 AT
1 AT
27717548 TTCAATTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (30 bp):
ATAAATTATTAATATAATAAATTATTTAAT
Found at i:27717538 original size:17 final size:17
Alignment explanation
Indices: 27717490--27717538 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
27717480 CATATAATAA
**
27717490 ATTA-TTAATATAATAA
1 ATTATTTAATATAATTT
27717506 ATTATTTAATATAATTT
1 ATTATTTAATATAATTT
27717523 ATTATTTTAATA-AATT
1 ATTA-TTTAATATAATT
27717539 ATTTGATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 4 0.14
17 18 0.62
18 7 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTATTTAATATAATTT
Found at i:27717644 original size:15 final size:15
Alignment explanation
Indices: 27717626--27717682 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
27717616 TATCAATATT
27717626 AATATTTTAATAATA
1 AATATTTTAATAATA
*
27717641 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
27717660 AATATATTAATAATA
1 AATATTTTAATAATA
*
27717675 AATGTTTT
1 AATATTTT
27717683 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:27719167 original size:26 final size:26
Alignment explanation
Indices: 27719138--27719188 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
27719128 GGGTTTTATT
*
27719138 CTTGTAGACTAAGAAACTAAAATTAA
1 CTTGTAGAATAAGAAACTAAAATTAA
* *
27719164 CTTGTAGAATAAGAACCTATAATTA
1 CTTGTAGAATAAGAAACTAAAATTA
27719189 GGGTAACTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (26 bp):
CTTGTAGAATAAGAAACTAAAATTAA
Found at i:27719846 original size:37 final size:37
Alignment explanation
Indices: 27719805--27719891 Score: 140
Period size: 37 Copynumber: 2.4 Consensus size: 37
27719795 GAAACTAGAG
27719805 AAACTAATCCC-TATGTTGGGATTAATTTTGGAATTCT
1 AAACT-ATCCCTTATGTTGGGATTAATTTTGGAATTCT
*
27719842 AAACTCTCCCTTATGTTGGGATTAATTTTGGAATTCT
1 AAACTATCCCTTATGTTGGGATTAATTTTGGAATTCT
*
27719879 AAACTCTCCCTTA
1 AAACTATCCCTTA
27719892 AGCTAGAGGC
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
36 4 0.08
37 44 0.92
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (37 bp):
AAACTATCCCTTATGTTGGGATTAATTTTGGAATTCT
Found at i:27722414 original size:13 final size:13
Alignment explanation
Indices: 27722398--27722422 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27722388 CAAAATGTAC
27722398 AATATAAATAAAT
1 AATATAAATAAAT
27722411 AATATAAATAAA
1 AATATAAATAAA
27722423 ATAAAATAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AATATAAATAAAT
Found at i:27723791 original size:18 final size:18
Alignment explanation
Indices: 27723768--27723806 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
27723758 GGGTAAACAG
27723768 TTAA-TTAAATTATTTTAT
1 TTAATTTAAATTA-TTTAT
*
27723786 TTAATTTATATTATTTAT
1 TTAATTTAAATTATTTAT
27723804 TTA
1 TTA
27723807 TATTGTACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTAATTTAAATTATTTAT
Found at i:27723794 original size:14 final size:14
Alignment explanation
Indices: 27723772--27723810 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
27723762 AAACAGTTAA
* *
27723772 TTAAATTATTTTAT
1 TTAATTTATATTAT
27723786 TTAATTTATATTAT
1 TTAATTTATATTAT
27723800 TT-ATTTATATT
1 TTAATTTATATT
27723811 GTACATTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTAATTTATATTAT
Found at i:27729224 original size:22 final size:22
Alignment explanation
Indices: 27729196--27729299 Score: 136
Period size: 22 Copynumber: 4.7 Consensus size: 22
27729186 TTTATTGTTC
*
27729196 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
27729218 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
27729240 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
27729262 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
27729284 AAACATGAGAGCTTAG
1 AAACATGAGAGCTTAG
27729300 AGGAATACCC
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 72 1.00
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:27730086 original size:5 final size:5
Alignment explanation
Indices: 27730078--27730105 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
27730068 ATGGTATTTT
27730078 TATAA TATAA TATAA TATAA TATAA TAT
1 TATAA TATAA TATAA TATAA TATAA TAT
27730106 TTACTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:27733111 original size:67 final size:67
Alignment explanation
Indices: 27733023--27733207 Score: 280
Period size: 67 Copynumber: 2.7 Consensus size: 67
27733013 TACCTGACAT
* *
27733023 CATAGCCTAGCTATGGTCTTACACAGTATACCCCATGTTTAATGTCTTGGCGGACTTCTTTTGTT
1 CATAGCCTAGCTATGGTCTTACACAGTATACCCCATGTTTAATGTCCTGGCGGACTTCCTTTGTT
27733088 GC
66 GC
* * *
27733090 CATAGTCTAGCTATGGTCTTACACAGTATACCCTATGTTTAATGTCCTGGTGGACTTCCTTTGTT
1 CATAGCCTAGCTATGGTCTTACACAGTATACCCCATGTTTAATGTCCTGGCGGACTTCCTTTGTT
27733155 GC
66 GC
* * *
27733157 CATAGCCTAGCTATGTTCTTACATAGTATATATCCCATGTTTAATGTCCTG
1 CATAGCCTAGCTATGGTCTTACACAG--TATACCCCATGTTTAATGTCCTG
27733208 ACGGGCTCTT
Statistics
Matches: 106, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
67 85 0.80
69 21 0.20
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (67 bp):
CATAGCCTAGCTATGGTCTTACACAGTATACCCCATGTTTAATGTCCTGGCGGACTTCCTTTGTT
GC
Found at i:27740044 original size:18 final size:16
Alignment explanation
Indices: 27740012--27740058 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
27740002 GACAACCCAA
27740012 TTTTATTTTTATTTTG
1 TTTTATTTTTATTTTG
27740028 TTTTATATTTTACTTTT-
1 TTTTAT-TTTTA-TTTTG
*
27740045 TTCTA-TTTTATTTT
1 TTTTATTTTTATTTT
27740059 CTTGCATGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 4 0.14
15 5 0.18
16 6 0.21
17 9 0.32
18 4 0.14
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (16 bp):
TTTTATTTTTATTTTG
Found at i:27742648 original size:18 final size:19
Alignment explanation
Indices: 27742607--27742649 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
27742597 TAAAGATAAG
*
27742607 ATATTTTATCATCTTTTAAC
1 ATATTTTATCATC-TTTAAA
*
27742627 ATATTTTATTATC-TTAAA
1 ATATTTTATCATCTTTAAA
27742645 ATATT
1 ATATT
27742650 ATTTATTTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.43
20 12 0.57
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATTTTATCATCTTTAAA
Found at i:27743251 original size:23 final size:24
Alignment explanation
Indices: 27743224--27743274 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
27743214 TGTCAAAAAA
27743224 ATATCT-TTTT-TTATAAAAATATT
1 ATATCTATTTTATTAT-AAAATATT
*
27743247 ATATCTAATTTTATTATTAAATATT
1 ATATCT-ATTTTATTATAAAATATT
27743272 ATA
1 ATA
27743275 ATTAATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 6 0.25
25 14 0.58
26 4 0.17
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (24 bp):
ATATCTATTTTATTATAAAATATT
Found at i:27751452 original size:24 final size:24
Alignment explanation
Indices: 27751424--27751611 Score: 121
Period size: 24 Copynumber: 7.6 Consensus size: 24
27751414 ATATAATAAA
27751424 AAGCTCATAAGAGCCATAATCGGG
1 AAGCTCATAAGAGCCATAATCGGG
**
27751448 AAGCTCATGCGAGCCAATAA-CGGG
1 AAGCTCATAAGAGCC-ATAATCGGG
* ** *
27751472 TAGCTCCGAAGAGCCATTAA-CGTG
1 AAGCTCATAAGAGCCA-TAATCGGG
*
27751496 AAGCTC-TAGATAGCCATATATCGGG
1 AAGCTCATA-AGAGCCATA-ATCGGG
*** *
27751521 AAGCTCCGGAGAGCCATTAATCAGG
1 AAGCTCATAAGAGCCA-TAATCGGG
* * *
27751546 AAGCTCACAAAGAGCCTTTAATCGAG
1 AAGCTCA-TAAGAGCC-ATAATCGGG
* *
27751572 AAGCTCATGAAGAGCCATATAACGAG
1 AAGCTCAT-AAGAGCCATA-ATCGGG
*
27751598 ACGCTCATAAGAGC
1 AAGCTCATAAGAGC
27751612 TGTGGTGTGC
Statistics
Matches: 127, Mismatches: 26, Indels: 21
0.73 0.15 0.12
Matches are distributed among these distances:
23 4 0.03
24 45 0.35
25 38 0.30
26 40 0.31
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (24 bp):
AAGCTCATAAGAGCCATAATCGGG
Found at i:27751566 original size:26 final size:26
Alignment explanation
Indices: 27751480--27751604 Score: 82
Period size: 26 Copynumber: 4.9 Consensus size: 26
27751470 GGTAGCTCCG
* *
27751480 AAGAGCCATTAA-CGTGAAGCTC-TA
1 AAGAGCCATTAATCGAGAAGCTCACA
* * * *
27751504 GATAGCCA-TATATCGGGAAGCTC-CG
1 AAGAGCCATTA-ATCGAGAAGCTCACA
*
27751529 GAGAGCCATTAATC-AGGAAGCTCACA
1 AAGAGCCATTAATCGA-GAAGCTCACA
* **
27751555 AAGAGCCTTTAATCGAGAAGCTCATG
1 AAGAGCCATTAATCGAGAAGCTCACA
*
27751581 AAGAGCCATATAA-CGAGACGCTCA
1 AAGAGCCAT-TAATCGAGAAGCTCA
27751605 TAAGAGCTGT
Statistics
Matches: 80, Mismatches: 14, Indels: 12
0.75 0.13 0.11
Matches are distributed among these distances:
23 2 0.03
24 7 0.09
25 26 0.32
26 41 0.51
27 4 0.05
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.18
Consensus pattern (26 bp):
AAGAGCCATTAATCGAGAAGCTCACA
Found at i:27753303 original size:2 final size:2
Alignment explanation
Indices: 27753291--27753321 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
27753281 CAGAGACTAC
*
27753291 TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27753322 TAAAGTTTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:27754613 original size:43 final size:42
Alignment explanation
Indices: 27754517--27754742 Score: 147
Period size: 43 Copynumber: 5.3 Consensus size: 42
27754507 TACTTTGATT
* ** *
27754517 TATCCAATGATGCACTGTGTGTGCCAGTATAATTGCTTTCGCT-
1 TATCCGATGATGCACT-TACGTGCCAGTATAATTGC-TTCGGTA
* * *
27754560 TTTCTGATGATGCACTATATGTGCCAGTATAATTGCTTCGGTA
1 TATCCGATGATGCACT-TACGTGCCAGTATAATTGCTTCGGTA
* * * * *
27754603 TATCCAATGATGTACTTACG-GTCCAGTATATTTTCTTTGGTA
1 TATCCGATGATGCACTTACGTG-CCAGTATAATTGCTTCGGTA
* * * * * * * *
27754645 CATCCGTTGATGCGC-TACGTGTCAGCATAATTGCTCCGATT
1 TATCCGATGATGCACTTACGTGCCAGTATAATTGCTTCGGTA
* *
27754686 TTTCCGATGATGCAC-TACGCGTGCCAGTATAATTGCTTTTGGT-
1 TATCCGATGATGCACTTA--CGTGCCAGTATAATTGC-TTCGGTA
*
27754729 TGTCCGATGATGCA
1 TATCCGATGATGCA
27754743 TTGTGTGTTC
Statistics
Matches: 140, Mismatches: 37, Indels: 12
0.74 0.20 0.06
Matches are distributed among these distances:
41 30 0.21
42 36 0.26
43 71 0.51
44 3 0.02
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.37
Consensus pattern (42 bp):
TATCCGATGATGCACTTACGTGCCAGTATAATTGCTTCGGTA
Found at i:27760436 original size:22 final size:21
Alignment explanation
Indices: 27760411--27760473 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
27760401 GCCAGTTAAT
27760411 AGAACGGCTAAAAGCCATAAGC
1 AGAACGGCTAAAAGCCATAA-C
* * *
27760433 AGAAAGGC-AGTAAGCCTTGAAC
1 AGAACGGCTA-AAAGCCAT-AAC
*
27760455 AGAACGGCTACAAGCCATA
1 AGAACGGCTAAAAGCCATA
27760474 CACTTCCTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
21 2 0.06
22 27 0.84
23 3 0.09
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.11
Consensus pattern (21 bp):
AGAACGGCTAAAAGCCATAAC
Found at i:27760697 original size:27 final size:25
Alignment explanation
Indices: 27760644--27760699 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 25
27760634 TAAAATGGTA
* *
27760644 ATTTTACCCCAGGGGTATTTTGGTC
1 ATTTTACCCCAGGGGTATTTCGATC
*
27760669 ATTTTACCCTACGAGGGTATTTCGATC
1 ATTTTACCCCA-G-GGGTATTTCGATC
27760696 ATTT
1 ATTT
27760700 AATAACCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 10 0.38
26 1 0.04
27 15 0.58
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (25 bp):
ATTTTACCCCAGGGGTATTTCGATC
Found at i:27762811 original size:16 final size:16
Alignment explanation
Indices: 27762786--27762816 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27762776 ATCGAAGTTT
27762786 CACTACAGTTTCAGTC
1 CACTACAGTTTCAGTC
*
27762802 CACTATAGTTTCAGT
1 CACTACAGTTTCAGT
27762817 TTGCTCTATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (16 bp):
CACTACAGTTTCAGTC
Found at i:27768694 original size:85 final size:87
Alignment explanation
Indices: 27768549--27768814 Score: 292
Period size: 86 Copynumber: 3.1 Consensus size: 87
27768539 GTTTTTGGAA
* * * * *
27768549 ATAAACGCTGCTATAGACCATGACCTTTAGCGGC-ACTTTCCTCACAAACGCCGCTATAGATCAG
1 ATAAACGCCGCTATAGATCAAGACCTTTAGCGGCGATTTTCCTCACAAACGCCGCTATAGATCAA
*
27768613 GACCATTAGGGGCG-TTTTTCC
66 GACCATTAGCGGCGCTTTTTCC
* * *
27768634 ATAAACGCCGCTATAGATCAGGATCTTTAGCGGCGATTTTCC-CACAAACGCCGCTGTAGATCAA
1 ATAAACGCCGCTATAGATCAAGACCTTTAGCGGCGATTTTCCTCACAAACGCCGCTATAGATCAA
* *
27768698 GACCTTTAGCGGCGCTTTTTCT
66 GACCATTAGCGGCGCTTTTTCC
* * * *
27768720 ACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTT-ATCAAAAAACGCCGCTATAGAAT-
1 ATAAACGCCGCTATAGATCAAGACCTTTAGCGGCGATTTTCCTC-ACAAACGCCGCTATAG-ATC
* * * *
27768783 AA-ACCTTTAGCGACGCTTCTTGC
64 AAGACCATTAGCGGCGCTTTTTCC
*
27768806 AAAAACGCC
1 ATAAACGCC
27768815 ACTAAAAACT
Statistics
Matches: 154, Mismatches: 22, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
85 62 0.40
86 74 0.48
87 16 0.10
88 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.25
Consensus pattern (87 bp):
ATAAACGCCGCTATAGATCAAGACCTTTAGCGGCGATTTTCCTCACAAACGCCGCTATAGATCAA
GACCATTAGCGGCGCTTTTTCC
Found at i:27768809 original size:43 final size:42
Alignment explanation
Indices: 27768551--27768814 Score: 264
Period size: 43 Copynumber: 6.2 Consensus size: 42
27768541 TTTTGGAAAT
* * * * * *
27768551 AAACGCTGCTATAGACCATGACCTTTAGCGGCACTTTCCTCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTT-TTCAA
* * * *
27768594 AAACGCCGCTATAGATCAGGACCATTAGGGGCG-TTTTTCCAT
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTT-CAA
* * * * *
27768636 AAACGCCGCTATAGATCAGGATCTTTAGCGGCGATTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTT-TCAA
* *
27768679 AAACGCCGCTGTAGATCAAGACCTTTAGCGGCGCTTTTTCTAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTC-AA
27768722 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTATCAAA
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTT-TC-AA
* *
27768766 AAACGCCGCTATAGAAT-AA-ACCTTTAGCGACGCTTCTTGCAA
1 AAACGCCGCTATAG-ATCAAGACCTTTAGCGGCGCTT-TTTCAA
27768808 AAACGCC
1 AAACGCC
27768815 ACTAAAAACT
Statistics
Matches: 191, Mismatches: 23, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
41 1 0.01
42 45 0.24
43 122 0.64
44 21 0.11
45 2 0.01
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (42 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCAA
Found at i:27772251 original size:40 final size:40
Alignment explanation
Indices: 27772151--27772252 Score: 186
Period size: 41 Copynumber: 2.5 Consensus size: 40
27772141 TTATTTTTGT
27772151 GGCGTTTTTTATAAAAACGCCGCTATTGCTTACCTTTGGC
1 GGCGTTTTTTATAAAAACGCCGCTATTGCTTACCTTTGGC
27772191 GGCGTTTTTTTATAAAAACGCCGCTATTGCTTACCTTTGGC
1 GGCG-TTTTTTATAAAAACGCCGCTATTGCTTACCTTTGGC
*
27772232 GGCGTTTTTCATAAAAACGCC
1 GGCGTTTTTTATAAAAACGCC
27772253 ACAAAGAATT
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
40 20 0.33
41 40 0.67
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.36
Consensus pattern (40 bp):
GGCGTTTTTTATAAAAACGCCGCTATTGCTTACCTTTGGC
Found at i:27772383 original size:106 final size:104
Alignment explanation
Indices: 27772263--27772581 Score: 487
Period size: 106 Copynumber: 3.0 Consensus size: 104
27772253 ACAAAGAATT
* * *
27772263 TTTCATTTTGAACAAAATGACGCCGTTTTGCTATTCTAAAATTTTTTTATTTTTTATTTATAAAT
1 TTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTTTTTTTATAAAT
* * *
27772328 TGATTTATTTTTTGCGTCATTTTAATAAAAAAACGCCGCTA
66 TGATTTATTTTTTGCGGCGTTTT--TATAAAAACGCCGCTA
27772369 TTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTGTTTTTTATAAA
1 TTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTT-TTTTTTATAAA
* *
27772434 TTGATTTATTTTTTGCGGCGTTTTTTATAAAAATGACGCTA
65 TTGATTTATTTTTTGCGGCG-TTTTTATAAAAACGCCGCTA
* *
27772475 TTTCATTTTGAACAAAATGACACAGTTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTTATAA
1 TTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTA-TTT-TTTTTTTATAA
27772540 ATTGATTTATTTTTTGCGGCGTTTTT-TAAAAACGCCGCTA
64 ATTGATTTATTTTTTGCGGCGTTTTTATAAAAACGCCGCTA
27772580 TT
1 TT
27772582 GCTTATCTTT
Statistics
Matches: 197, Mismatches: 12, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
105 14 0.07
106 116 0.59
107 62 0.31
108 5 0.03
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (104 bp):
TTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTTTTTTTATAAAT
TGATTTATTTTTTGCGGCGTTTTTATAAAAACGCCGCTA
Found at i:27772916 original size:41 final size:41
Alignment explanation
Indices: 27772856--27772935 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 41
27772846 TAAAATATTT
* *
27772856 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCCCAGCA
1 TTAGCGGCACTTTTCCAAAAACGCCGCCAAAGCCCCCAGCA
*
27772897 TTAGCGGCACTTTTTCAAAAACGCCGCCAAAGCCCCCAG
1 TTAGCGGCACTTTTCCAAAAACGCCGCCAAAGCCCCCAG
27772936 AATTTTTGGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.28, C:0.36, G:0.19, T:0.17
Consensus pattern (41 bp):
TTAGCGGCACTTTTCCAAAAACGCCGCCAAAGCCCCCAGCA
Found at i:27773138 original size:104 final size:104
Alignment explanation
Indices: 27772971--27773348 Score: 337
Period size: 115 Copynumber: 3.4 Consensus size: 104
27772961 CATTGCGTCA
* * * *
27772971 TTGGACTTAGGTTTTTTTGCCGCGCATTCTCAAAAACGCCGCTAAAGCCCTGAGCATTGGCGGCG
1 TTGGGCTTAGG-TTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAG-CCTGAGCATTAGCGGCG
* * *
27773036 CTTTCTTAAAAACGCCTCTAAATCTCCGAAAGCT-TCATCG
64 CTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTAGCATCG
* * *
27773076 TTGGGCTTAGGTTTTTTGCGGCACTTTCTCAAAAACGGCGCTAAAGCCTTGAGTATTAGCGGCGC
1 TTGGGCTTAGGTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCC-TGAGCATTAGCGGCGC
* *
27773141 TTTAC-TAAAAATGCCGCTAAATCCCCGAAAACTCACAAAACGGCATCG
65 TTT-CTTAAAAACGCCGCTAAATCCCCGAAAGCT------A--GCATCG
* * **
27773189 TTGGGCTTAGATTTTTTTGGGGCGCTTTCTCAAAAAACGCCATTAAAGACCTGAGCATTAGCGGC
1 TTGGGCTTAG-GTTTTTTGCGGCGCTTTCTC-AAAAACGCCGCTAAAG-CCTGAGCATTAGCGGC
* * *
27773254 GCTTTCTTAAAAACACCGCTAAATCCCCAAAAGCTCAGAAAACTGCGTCG
63 GCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCT------A--GCATCG
** *
27773304 TTGGGCTTATTTTTTTTGCGGCGCTTTCTCATAAACGCCGCTAAA
1 TTGGGCTTAGGTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAA
27773349 TCCCCGAAAG
Statistics
Matches: 227, Mismatches: 31, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
103 2 0.01
104 72 0.32
105 11 0.05
113 27 0.12
114 37 0.16
115 76 0.33
116 2 0.01
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.28
Consensus pattern (104 bp):
TTGGGCTTAGGTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCTGAGCATTAGCGGCGCT
TTCTTAAAAACGCCGCTAAATCCCCGAAAGCTAGCATCG
Found at i:27773273 original size:115 final size:113
Alignment explanation
Indices: 27773071--27773348 Score: 355
Period size: 115 Copynumber: 2.4 Consensus size: 113
27773061 CCGAAAGCTT
* * * * *
27773071 CATCGTTGGGCTTAGGTTTTTTGCGGCACTTTCTCAAAAACGGCGCTAAAGCCTTGAGTATTAGC
1 CATCGTTGGGCTTAGTTTTTTTGCGGCGCTTTCTCAAAAACGCCACTAAAGCCTTGAGCATTAGC
**
27773136 GGCGCTTTACTAAAAATGCCGCTAAATCCCCGAAAA-CTCACAAAACGG
66 GGCGCTTTACTAAAAACACCGCTAAATCCCC-AAAAGCTCACAAAACGG
* *
27773184 CATCGTTGGGCTTAGATTTTTTTGGGGCGCTTTCTCAAAAAACGCCATTAAAGACC-TGAGCATT
1 CATCGTTGGGCTTAG-TTTTTTTGCGGCGCTTTCTC-AAAAACGCCACTAAAG-CCTTGAGCATT
* *
27773248 AGCGGCGCTTT-CTTAAAAACACCGCTAAATCCCCAAAAGCTCAGAAAACTG
63 AGCGGCGCTTTAC-TAAAAACACCGCTAAATCCCCAAAAGCTCACAAAACGG
* * * *
27773299 CGTCGTTGGGCTTATTTTTTTTGCGGCGCTTTCTCATAAACGCCGCTAAA
1 CATCGTTGGGCTTAGTTTTTTTGCGGCGCTTTCTCAAAAACGCCACTAAA
27773349 TCCCCGAAAG
Statistics
Matches: 143, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
113 27 0.19
114 41 0.29
115 73 0.51
116 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (113 bp):
CATCGTTGGGCTTAGTTTTTTTGCGGCGCTTTCTCAAAAACGCCACTAAAGCCTTGAGCATTAGC
GGCGCTTTACTAAAAACACCGCTAAATCCCCAAAAGCTCACAAAACGG
Found at i:27773419 original size:72 final size:72
Alignment explanation
Indices: 27773249--27773404 Score: 224
Period size: 72 Copynumber: 2.2 Consensus size: 72
27773239 CTGAGCATTA
* * * * * *
27773249 GCGGCGCTTTCTTAAAAACACCGCTAAATCCCCAAAAGCTCAGAAAACTGCGTCGTTGGGCTTAT
1 GCGGCGCTTTCTCATAAACGCCGCTAAATCCCCAAAAGCTCAGAAAACGGCGTCATTGGGCTTAG
*
27773314 TTTTTTT
66 GTTTTTT
*
27773321 GCGGCGCTTTCTCATAAACGCCGCTAAATCCCCGAAAGCTCTA-AAAACGGCGTCATTGGGCTTA
1 GCGGCGCTTTCTCATAAACGCCGCTAAATCCCCAAAAGCTC-AGAAAACGGCGTCATTGGGCTTA
27773385 GGTTTTTT
65 GGTTTTTT
27773393 GCGGCGCTTTCT
1 GCGGCGCTTTCT
27773405 GGAAAGCGTC
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
72 74 0.99
73 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.29
Consensus pattern (72 bp):
GCGGCGCTTTCTCATAAACGCCGCTAAATCCCCAAAAGCTCAGAAAACGGCGTCATTGGGCTTAG
GTTTTTT
Found at i:27776247 original size:23 final size:23
Alignment explanation
Indices: 27776221--27776269 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
27776211 GTTTAACTAC
27776221 TTGTTAGTGTCTTGGACTAGGAT
1 TTGTTAGTGTCTTGGACTAGGAT
27776244 TTGTTAGTGTCTTGGACTAGGAT
1 TTGTTAGTGTCTTGGACTAGGAT
27776267 TTG
1 TTG
27776270 CCTAATATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.16, C:0.08, G:0.31, T:0.45
Consensus pattern (23 bp):
TTGTTAGTGTCTTGGACTAGGAT
Found at i:27780068 original size:24 final size:24
Alignment explanation
Indices: 27780030--27780077 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
27780020 TTTCAAACAA
*
27780030 AAAAATAACAGAATAACAAA-AAAT
1 AAAAATAAAAGAATAA-AAACAAAT
*
27780054 AAAAATAAAATAATAAAAACAAAT
1 AAAAATAAAAGAATAAAAACAAAT
27780078 CCTAACCAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.77, C:0.06, G:0.02, T:0.15
Consensus pattern (24 bp):
AAAAATAAAAGAATAAAAACAAAT
Found at i:27781770 original size:45 final size:45
Alignment explanation
Indices: 27781716--27781825 Score: 168
Period size: 45 Copynumber: 2.4 Consensus size: 45
27781706 AAAAATGAGC
* *
27781716 AAGATCATGACTGAAAGACATTATGGCATCATGATTCTATCGAGT
1 AAGACCATGACTGAAAGACATTATGGCATCACGATTCTATCGAGT
* *
27781761 AAGACCATGACTGAAAAACATTATGGCATTACGATTCTATCGAGT
1 AAGACCATGACTGAAAGACATTATGGCATCACGATTCTATCGAGT
27781806 AAGACCAT-AGCTGAAAGACA
1 AAGACCATGA-CTGAAAGACA
27781826 CTATAGTATC
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
44 1 0.02
45 58 0.98
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (45 bp):
AAGACCATGACTGAAAGACATTATGGCATCACGATTCTATCGAGT
Found at i:27790620 original size:45 final size:46
Alignment explanation
Indices: 27790506--27790625 Score: 145
Period size: 46 Copynumber: 2.6 Consensus size: 46
27790496 ATCATGAAAC
* *
27790506 AAATGAATAAGACTATGGTTGAAAGACACTATGGCAACACAACGAA
1 AAATAAATAAGACTATGGTTAAAAGACACTATGGCAACACAACGAA
* * * *
27790552 AAATGAATAAGACCATGGTTAAAAGACACTATGGCATCA-AGACG-T
1 AAATAAATAAGACTATGGTTAAAAGACACTATGGCAACACA-ACGAA
* *
27790597 GAATAAATAATACTATGGTTAAAAGACAC
1 AAATAAATAAGACTATGGTTAAAAGACAC
27790626 CATAGCACAC
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
45 26 0.40
46 39 0.60
ACGTcount: A:0.47, C:0.14, G:0.18, T:0.20
Consensus pattern (46 bp):
AAATAAATAAGACTATGGTTAAAAGACACTATGGCAACACAACGAA
Found at i:27795686 original size:43 final size:42
Alignment explanation
Indices: 27795626--27795832 Score: 175
Period size: 42 Copynumber: 4.9 Consensus size: 42
27795616 GGCGCTTACA
**
27795626 GAAAAAAACACTACTAAAGCTCATGTTCTTTAGCGGCACTACC
1 GAAAAAAACACCGCTAAAGCTCATGTTCTTTAGCGGCACTA-C
* * *
27795669 GAAAAGAACGCCGCTAAAGCTCATGTTCTTTAGCGGCGCTAC
1 GAAAAAAACACCGCTAAAGCTCATGTTCTTTAGCGGCACTAC
* * * *
27795711 GAAAAAAACACCGCTAAAGATCATGTTCTTTAGCAGCGCTTAG
1 GAAAAAAACACCGCTAAAGCTCATGTTCTTTAGCGGCAC-TAC
* * ** * * **
27795754 GAAGAAAACGCCGCTAAAAG-AAATGTTCTGTAGCGGCGCTTG
1 GAAAAAAACACCGCT-AAAGCTCATGTTCTTTAGCGGCACTAC
* * * *
27795796 GTAAAAAACGCCGCTAAAAG-TAATGTTCTTTACCGGC
1 GAAAAAAACACCGCT-AAAGCTCATGTTCTTTAGCGGC
27795833 GCTTCATCTA
Statistics
Matches: 140, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
42 70 0.50
43 66 0.47
44 4 0.03
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (42 bp):
GAAAAAAACACCGCTAAAGCTCATGTTCTTTAGCGGCACTAC
Found at i:27795727 original size:42 final size:41
Alignment explanation
Indices: 27795614--27795878 Score: 219
Period size: 43 Copynumber: 6.2 Consensus size: 41
27795604 CTAACTTTTT
* **
27795614 GCGGCGCTTACAGAAAAAAACACTACTAAAGCTCATGTTCTTTA
1 GCGGCGC-TAC-GAAAAAAACGCCGCTAAAG-TCATGTTCTTTA
* *
27795658 GCGGCACTACCGAAAAGAACGCCGCTAAAGCTCATGTTCTTTA
1 GCGGCGCTA-CGAAAAAAACGCCGCTAAAG-TCATGTTCTTTA
*
27795701 GCGGCGCTACGAAAAAAACACCGCTAAAGATCATGTTCTTTA
1 GCGGCGCTACGAAAAAAACGCCGCTAAAG-TCATGTTCTTTA
* * * ** *
27795743 GCAGCGCTTAGGAAGAAAACGCCGCTAAAAGAAATGTTCTGTA
1 GCGGCGC-TACGAAAAAAACGCCGCT-AAAGTCATGTTCTTTA
** * *
27795786 GCGGCGCTTGGTAAAAAACGCCGCTAAAAGTAATGTTCTTTA
1 GCGGCGCTACGAAAAAAACGCCGCT-AAAGTCATGTTCTTTA
* * * *
27795828 CCGGCGCTTC-ATCTACAAACGCCGCTAAAAGT-AGTGTTCTTTA
1 GCGGCGCTACGA--AAAAAACGCCGCT-AAAGTCA-TGTTCTTTA
27795871 GCGGCGCT
1 GCGGCGCT
27795879 TATTTCACAA
Statistics
Matches: 187, Mismatches: 28, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
42 75 0.40
43 101 0.54
44 11 0.06
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.23
Consensus pattern (41 bp):
GCGGCGCTACGAAAAAAACGCCGCTAAAGTCATGTTCTTTA
Found at i:27795764 original size:85 final size:83
Alignment explanation
Indices: 27795614--27795878 Score: 250
Period size: 85 Copynumber: 3.1 Consensus size: 83
27795604 CTAACTTTTT
** * *
27795614 GCGGCGCTTACAGAAAAAAACACTACTAAAGCTCATGTTCTTTAGCGGCAC-TACCGAAAAGAAC
1 GCGGCGC-TAC-GAAAAAAACACCGCTAAAGATCATGTTCTTTAGCGGCGCTTA-CGAAAA-AAC
27795678 GCCGCT-AAAGCTCATGTTCTTTA
62 GCCGCTAAAAG-T-ATGTTCTTTA
* *
27795701 GCGGCGCTACGAAAAAAACACCGCTAAAGATCATGTTCTTTAGCAGCGCTTAGGAAGAAAACGCC
1 GCGGCGCTACGAAAAAAACACCGCTAAAGATCATGTTCTTTAGCGGCGCTTACGAA-AAAACGCC
* *
27795766 GCTAAAAGAAATGTTCTGTA
65 GCTAAAAG-TATGTTCTTTA
** * * * * * *
27795786 GCGGCGCTTGGTAAAAAACGCCGCTAAA-AGTAATGTTCTTTACCGGCGCTTCATC-TACAAACG
1 GCGGCGCTACGAAAAAAACACCGCTAAAGA-TCATGTTCTTTAGCGGCGCTT-A-CGAAAAAACG
27795849 CCGCTAAAAGTAGTGTTCTTTA
63 CCGCTAAAAGTA-TGTTCTTTA
27795871 GCGGCGCT
1 GCGGCGCT
27795879 TATTTCACAA
Statistics
Matches: 150, Mismatches: 21, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
84 2 0.01
85 128 0.85
86 13 0.09
87 7 0.05
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.23
Consensus pattern (83 bp):
GCGGCGCTACGAAAAAAACACCGCTAAAGATCATGTTCTTTAGCGGCGCTTACGAAAAAACGCCG
CTAAAAGTATGTTCTTTA
Found at i:27796371 original size:21 final size:21
Alignment explanation
Indices: 27796328--27796396 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
27796318 ACTTCTCTCG
* *
27796328 CTGCTTCTCTCGCTAC-GACCT
1 CTGCTTCCCTCGCTGCAG-CCT
* * *
27796349 CTGCTTCTCTCGTTGCAGTCT
1 CTGCTTCCCTCGCTGCAGCCT
*
27796370 CTGCTTCCCTCGCTGCCGCCT
1 CTGCTTCCCTCGCTGCAGCCT
27796391 CTGCTT
1 CTGCTT
27796397 TAAGTTGTTG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
21 39 0.98
22 1 0.03
ACGTcount: A:0.04, C:0.42, G:0.17, T:0.36
Consensus pattern (21 bp):
CTGCTTCCCTCGCTGCAGCCT
Found at i:27804753 original size:36 final size:35
Alignment explanation
Indices: 27804705--27804774 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
27804695 TACACCTGTT
* *
27804705 AAAATGTTCAATGTGGTACTTCAAATTTAATTTTTC
1 AAAATGTCCAATGT-GAACTTCAAATTTAATTTTTC
* *
27804741 AAAATGTCCAATGTGAACTTGAACTTTAATTTTT
1 AAAATGTCCAATGTGAACTTCAAATTTAATTTTT
27804775 GTATATAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 17 0.57
36 13 0.43
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (35 bp):
AAAATGTCCAATGTGAACTTCAAATTTAATTTTTC
Found at i:27805880 original size:20 final size:20
Alignment explanation
Indices: 27805852--27805900 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
27805842 ATATATCCTG
*
27805852 ATTTTATTTGATTTCAATCA
1 ATTTGATTTGATTTCAATCA
*
27805872 ATTTGATTTGATTTTAATCA
1 ATTTGATTTGATTTCAATCA
*
27805892 AATTGATTT
1 ATTTGATTT
27805901 AATTGCTCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.55
Consensus pattern (20 bp):
ATTTGATTTGATTTCAATCA
Found at i:27806375 original size:19 final size:20
Alignment explanation
Indices: 27806343--27806380 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
27806333 TATTCAATTT
27806343 ATATTTTATTTTATATATAA
1 ATATTTTATTTTATATATAA
*
27806363 ATATTTT-TTTTATTTATA
1 ATATTTTATTTTATATATA
27806381 TTTATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
ATATTTTATTTTATATATAA
Found at i:27806378 original size:23 final size:24
Alignment explanation
Indices: 27806346--27806391 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
27806336 TCAATTTATA
27806346 TTTTATTTTATATATAAATATTTT
1 TTTTATTTTATATATAAATATTTT
* *
27806370 TTTTA-TTTATATTTATATATTT
1 TTTTATTTTATATATAAATATTT
27806392 ATTCGCTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTTATTTTATATATAAATATTTT
Found at i:27808940 original size:20 final size:17
Alignment explanation
Indices: 27808899--27808932 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
27808889 GAATAAATAA
27808899 AAAAATAATAATTACAT
1 AAAAATAATAATTACAT
27808916 AAAAATAATAATTACAT
1 AAAAATAATAATTACAT
27808933 CCTAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAATAATAATTACAT
Found at i:27810399 original size:44 final size:44
Alignment explanation
Indices: 27810347--27810675 Score: 188
Period size: 44 Copynumber: 7.5 Consensus size: 44
27810337 GATATGCTCT
*
27810347 CTGCAACTTCAAAGAGATAAGATCT-AAGATTTTAATCCT-CTCCA
1 CTGCAACTTCAAGGAGATAAGAT-TGAAGATTTTAAT-CTGCTCCA
* **
27810391 CTGCAACTTC-AGGAAGATAGGATTGTCGATTTTAATCTGCTCCA
1 CTGCAACTTCAAGG-AGATAAGATTGAAGATTTTAATCTGCTCCA
* ** *
27810435 CTGCAACTTCAGGGAGATAAGATTTG-CCATCTTCAATCTGC-CTCA
1 CTGCAACTTCAAGGAGATAAGA-TTGAAGAT-TTTAATCTGCTC-CA
*** * * *
27810480 CTGCAACTTC-AGGAGGATAAGACTTGCTTA-CTTAGTCTGCCCCA
1 CTGCAACTTCAAGGA-GATAAGA-TTGAAGATTTTAATCTGCTCCA
* *** *
27810524 CTGCAACTTC-AGAGAGATAAGACT--AGA-TGCGATCTGCT-CT
1 CTGCAACTTCAAG-GAGATAAGATTGAAGATTTTAATCTGCTCCA
*
27810564 CTGCAACTTC-AGAAAGATAAGACTTG-AGATTTTAAT-TCGCTCCA
1 CTGCAACTTCAAG-GAGATAAGA-TTGAAGATTTTAATCT-GCTCCA
* ** * *
27810608 CTGCAACTTC-AGAGAGATAGGATTGTCGGTTTTAATCTGCTTCA
1 CTGCAACTTCAAG-GAGATAAGATTGAAGATTTTAATCTGCTCCA
27810652 CTGCAACTTC-AGGAAGATAAGATT
1 CTGCAACTTCAAGG-AGATAAGATT
27810676 TGCCATCTTC
Statistics
Matches: 229, Mismatches: 37, Indels: 38
0.75 0.12 0.12
Matches are distributed among these distances:
40 22 0.10
41 7 0.03
42 4 0.02
43 16 0.07
44 139 0.61
45 40 0.17
46 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (44 bp):
CTGCAACTTCAAGGAGATAAGATTGAAGATTTTAATCTGCTCCA
Found at i:27810534 original size:217 final size:217
Alignment explanation
Indices: 27810279--27810703 Score: 676
Period size: 217 Copynumber: 2.0 Consensus size: 217
27810269 GCTTAGGGAA
* * *
27810279 ATAAGACCTGCTTACTTAGTCTGCTCGACTGCAACTTCAGAGAGATAAGGCTAGATACGATATGC
1 ATAAGACCTGCTTACTTAGTCTGCCCCACTGCAACTTCAGAGAGATAAGACTAGATACGATATGC
*
27810344 TCTCTGCAACTTCA-AAGAGATAAGA-TCTAAGATTTTAATCCTCTCCACTGCAACTTCAG-GAA
66 TCTCTGCAACTTCAGAA-AGATAAGACT-TAAGATTTTAATCCGCTCCACTGCAACTTCAGAG-A
*
27810406 GATAGGATTGTCGATTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAA
128 GATAGGATTGTCGATTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAA
27810471 TCTGCCTCACTGCAACTTCAGGAGG
193 TCTGCCTCACTGCAACTTCAGGAGG
* * *
27810496 ATAAGACTTGCTTACTTAGTCTGCCCCACTGCAACTTCAGAGAGATAAGACTAGATGCGATCTGC
1 ATAAGACCTGCTTACTTAGTCTGCCCCACTGCAACTTCAGAGAGATAAGACTAGATACGATATGC
* *
27810561 TCTCTGCAACTTCAGAAAGATAAGACTTGAGATTTTAATTCGCTCCACTGCAACTTCAGAGAGAT
66 TCTCTGCAACTTCAGAAAGATAAGACTTAAGATTTTAATCCGCTCCACTGCAACTTCAGAGAGAT
* * * *
27810626 AGGATTGTCGGTTTTAATCTGCTTCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCACTTT
131 AGGATTGTCGATTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAATCT
27810691 GCCTCACTGCAAC
196 GCCTCACTGCAAC
27810704 CTACTTCAGA
Statistics
Matches: 191, Mismatches: 14, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
217 187 0.98
218 4 0.02
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (217 bp):
ATAAGACCTGCTTACTTAGTCTGCCCCACTGCAACTTCAGAGAGATAAGACTAGATACGATATGC
TCTCTGCAACTTCAGAAAGATAAGACTTAAGATTTTAATCCGCTCCACTGCAACTTCAGAGAGAT
AGGATTGTCGATTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAATCT
GCCTCACTGCAACTTCAGGAGG
Found at i:27810609 original size:84 final size:86
Alignment explanation
Indices: 27810389--27810673 Score: 260
Period size: 84 Copynumber: 3.3 Consensus size: 86
27810379 TAATCCTCTC
* *
27810389 CACTGCAACTTCAGGAAGATAGGA-TTGTCGATTTTAATCTGCTCCACTGCAACTTCAGGGAGAT
1 CACTGCAACTTCAGGAAGATAAGACTTG--GATTTTAATCTGCTCCACTGCAACTTCAGAGAGAT
* * *
27810453 AAGATTTGCCATCTTCAATCTGCCT
64 AAGACTAG-CA-CTGCAATCTGCCT
* * * *
27810478 CACTGCAACTTCAGGAGGATAAGACTT-GCTTACTTAGTCTGCCCCACTGCAACTTCAGAGAGAT
1 CACTGCAACTTCAGGAAGATAAGACTTGGATT--TTAATCTGCTCCACTGCAACTTCAGAGAGAT
*
27810542 AAGACTAG-A-TGCGATCTG-CT
64 AAGACTAGCACTGCAATCTGCCT
* *
27810562 CTCTGCAACTTCAGAAAGATAAGACTTGAGATTTTAAT-TCGCTCCACTGCAACTTCAGAGAGAT
1 CACTGCAACTTCAGGAAGATAAGACTTG-GATTTTAATCT-GCTCCACTGCAACTTCAGAGAGAT
* * ** ** *
27810626 AGGA-TTGTCGGTTTTAATCTGCTT
64 AAGACTAG-C-ACTGCAATCTGCCT
27810650 CACTGCAACTTCAGGAAGATAAGA
1 CACTGCAACTTCAGGAAGATAAGA
27810674 TTTGCCATCT
Statistics
Matches: 160, Mismatches: 25, Indels: 23
0.77 0.12 0.11
Matches are distributed among these distances:
83 3 0.02
84 56 0.35
85 7 0.04
86 3 0.02
87 10 0.06
88 23 0.14
89 56 0.35
90 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.28
Consensus pattern (86 bp):
CACTGCAACTTCAGGAAGATAAGACTTGGATTTTAATCTGCTCCACTGCAACTTCAGAGAGATAA
GACTAGCACTGCAATCTGCCT
Found at i:27810701 original size:173 final size:173
Alignment explanation
Indices: 27810391--27810703 Score: 411
Period size: 173 Copynumber: 1.8 Consensus size: 173
27810381 ATCCTCTCCA
* * * *
27810391 CTGCAACTTCAGGAAGATAGGATTGTCGATTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG
1 CTGCAACTTCAGAAAGATAAGATTGTAGATTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAG
* * *
27810456 ATTTGCCATCTTCAATCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCC
66 ATTTGCCATCTTCAATCTGCCTCACTGCAACTTCAGGAAGATAAGACTTGCATACTTACTCTGCC
27810521 CCACTGCAACTTCAGAGAGATAAGACTAGATGCGATCTGCTCT
131 CCACTGCAACTTCAGAGAGATAAGACTAGATGCGATCTGCTCT
27810564 CTGCAACTTCAGAAAGATAAGACTTG-AGATTTTAAT-TCGCTCCACTGCAACTTCAGAGAGATA
1 CTGCAACTTCAGAAAGATAAGA-TTGTAGATTTTAATCT-GCTCCACTGCAACTTCAGAGAGATA
* ** * * *
27810627 GGA-TTGTCGGT-TTTAATCTGCTTCACTGCAACTTCAGGAAGATAAGATTTGCCAT-CTTCACT
64 AGATTTG-CCATCTTCAATCTGCCTCACTGCAACTTCAGGAAGATAAGACTTG-CATACTT-ACT
* *
27810689 TTGCCTCACTGCAAC
126 CTGCCCCACTGCAAC
27810704 CTACTTCAGA
Statistics
Matches: 120, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
172 43 0.36
173 74 0.62
174 3 0.03
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (173 bp):
CTGCAACTTCAGAAAGATAAGATTGTAGATTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAG
ATTTGCCATCTTCAATCTGCCTCACTGCAACTTCAGGAAGATAAGACTTGCATACTTACTCTGCC
CCACTGCAACTTCAGAGAGATAAGACTAGATGCGATCTGCTCT
Found at i:27812220 original size:8 final size:9
Alignment explanation
Indices: 27812203--27812233 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
27812193 CCCTGGTAGA
27812203 TTTTGTTTT
1 TTTTGTTTT
27812212 TTTTGTTTT
1 TTTTGTTTT
27812221 TTTTGTTTT
1 TTTTGTTTT
27812230 TTTT
1 TTTT
27812234 TTGTCATCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (9 bp):
TTTTGTTTT
Found at i:27816852 original size:20 final size:17
Alignment explanation
Indices: 27816812--27816844 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
27816802 ATAAATAATT
27816812 AAAATAATAATTACATA
1 AAAATAATAATTACATA
27816829 AAAATAATAATTACAT
1 AAAATAATAATTACAT
27816845 CCTAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAATAATAATTACATA
Found at i:27817322 original size:11 final size:11
Alignment explanation
Indices: 27817306--27817340 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
27817296 CCCTGCTTGT
27817306 CCGGTCATCGG
1 CCGGTCATCGG
*
27817317 CCGGTCATCGT
1 CCGGTCATCGG
*
27817328 CCGATCATCGG
1 CCGGTCATCGG
27817339 CC
1 CC
27817341 ATCGTGCCGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.11, C:0.40, G:0.29, T:0.20
Consensus pattern (11 bp):
CCGGTCATCGG
Found at i:27830171 original size:33 final size:33
Alignment explanation
Indices: 27830129--27830195 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
27830119 CATACAAGAC
27830129 TTGGGTATTTCTTATGAAAGAAAAATTTGTGGT
1 TTGGGTATTTCTTATGAAAGAAAAATTTGTGGT
27830162 TTGGGTATTTCTTATGAAAGAAAAATTTGTGGT
1 TTGGGTATTTCTTATGAAAGAAAAATTTGTGGT
27830195 T
1 T
27830196 GAAAGAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.30, C:0.03, G:0.24, T:0.43
Consensus pattern (33 bp):
TTGGGTATTTCTTATGAAAGAAAAATTTGTGGT
Found at i:27830200 original size:19 final size:19
Alignment explanation
Indices: 27830176--27830244 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 19
27830166 GTATTTCTTA
27830176 TGAAAGAAAAATTTGTGGT
1 TGAAAGAAAAATTTGTGGT
* ***
27830195 TGAAAG-AATATTTCAAGT
1 TGAAAGAAAAATTTGTGGT
** *
27830213 CTTCAAGAAAAGTTTGTGGT
1 -TGAAAGAAAAATTTGTGGT
27830233 TGAAAGAAAAAT
1 TGAAAGAAAAAT
27830245 GGGGTTACAG
Statistics
Matches: 34, Mismatches: 14, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 8 0.24
19 19 0.56
20 7 0.21
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.30
Consensus pattern (19 bp):
TGAAAGAAAAATTTGTGGT
Found at i:27839472 original size:60 final size:58
Alignment explanation
Indices: 27839415--27839535 Score: 136
Period size: 60 Copynumber: 2.1 Consensus size: 58
27839405 TTAAAAAGAT
* *
27839415 AAAATAAC-ATAATTGAATGATCATTTTGTAACTTTTCATAGTTAGGTGACTAAAAAAG
1 AAAATAACAATAATTGAATGATCATTTTATAACTTTTCATAGTT-GGTGACCAAAAAAG
* * * ** * *
27839473 AAATTTACTAATTATTGGGTGATTATTTTATAACTTTTCATAGTTGGTGACCAAAAATG
1 AAAATAAC-AATAATTGAATGATCATTTTATAACTTTTCATAGTTGGTGACCAAAAAAG
27839532 AAAA
1 AAAA
27839536 AAAAAACCAT
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
58 6 0.12
59 15 0.29
60 30 0.59
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.37
Consensus pattern (58 bp):
AAAATAACAATAATTGAATGATCATTTTATAACTTTTCATAGTTGGTGACCAAAAAAG
Found at i:27842773 original size:41 final size:41
Alignment explanation
Indices: 27842717--27842801 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
27842707 TGATTCAGTA
* *
27842717 CACCGGCTTTAAGCCTGCTAGACT-TATAGTCTAAATTGTTT
1 CACCGGCTTTAAGCCTGCTAGA-TGTAAAGTCTAAATGGTTT
*
27842758 CACCGGCATTT-AGCCTGCTAGATGTAAAGTCTGAATGGTTT
1 CACCGGC-TTTAAGCCTGCTAGATGTAAAGTCTAAATGGTTT
27842799 CAC
1 CAC
27842802 TAGCAATAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
40 1 0.03
41 35 0.90
42 3 0.08
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (41 bp):
CACCGGCTTTAAGCCTGCTAGATGTAAAGTCTAAATGGTTT
Found at i:27842814 original size:41 final size:41
Alignment explanation
Indices: 27842726--27842815 Score: 101
Period size: 41 Copynumber: 2.2 Consensus size: 41
27842716 ACACCGGCTT
* * * *
27842726 TAAGCCTGCTAGACTTATAGTCTAAATTGTTTCACCGGCAT
1 TAAGCCTGCTAGACTTAAAGTCTAAATGGTTTCACCAGCAA
* * *
27842767 TTAGCCTGCTAGA-TGTAAAGTCTGAATGGTTTCACTAGCAA
1 TAAGCCTGCTAGACT-TAAAGTCTAAATGGTTTCACCAGCAA
27842808 TAAGCCTG
1 TAAGCCTG
27842816 AACAGCATAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
40 1 0.03
41 39 0.98
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (41 bp):
TAAGCCTGCTAGACTTAAAGTCTAAATGGTTTCACCAGCAA
Found at i:27844744 original size:21 final size:21
Alignment explanation
Indices: 27844718--27844773 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
27844708 AACAACGGTG
*
27844718 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
27844739 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
27844760 GCAGTGAGATTAGA
1 GCGGTGAGATTAGA
27844774 AACAATGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:27850920 original size:16 final size:16
Alignment explanation
Indices: 27850899--27850930 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
27850889 TTTTCGAGAG
27850899 AAGTGGGAAAGAAGGA
1 AAGTGGGAAAGAAGGA
*
27850915 AAGTGGGAAAGCAGGA
1 AAGTGGGAAAGAAGGA
27850931 GTTGAAGAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.44, T:0.06
Consensus pattern (16 bp):
AAGTGGGAAAGAAGGA
Found at i:27853428 original size:8 final size:8
Alignment explanation
Indices: 27853411--27853447 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
27853401 CCAAAAATAA
*
27853411 TAATATTT
1 TAATAGTT
27853419 TAATAGTT
1 TAATAGTT
*
27853427 TAATATTT
1 TAATAGTT
27853435 TAATAGTT
1 TAATAGTT
27853443 TAATA
1 TAATA
27853448 TTAAATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (8 bp):
TAATAGTT
Found at i:27853432 original size:16 final size:16
Alignment explanation
Indices: 27853411--27853449 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
27853401 CCAAAAATAA
27853411 TAATATTTTAATAGTT
1 TAATATTTTAATAGTT
27853427 TAATATTTTAATAGTT
1 TAATATTTTAATAGTT
27853443 TAATATT
1 TAATATT
27853450 AAATTAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (16 bp):
TAATATTTTAATAGTT
Found at i:27853497 original size:16 final size:16
Alignment explanation
Indices: 27853411--27853511 Score: 53
Period size: 16 Copynumber: 6.2 Consensus size: 16
27853401 CCAAAAATAA
* * *
27853411 TAATATTTTAATAGTT
1 TAATATTATATTAATT
* * *
27853427 TAATATTTTAATAGTT
1 TAATATTATATTAATT
* *
27853443 TAATATTAAATTAAATG
1 TAATATTATATT-AATT
*
27853460 TAATACTTATCTTAA--
1 TAATA-TTATATTAATT
* *
27853475 TAGTATTTTATTAATT
1 TAATATTATATTAATT
*
27853491 TAATATTAAATTAAATT
1 TAATATTATATT-AATT
27853508 TAAT
1 TAAT
27853512 GTTTATATTG
Statistics
Matches: 67, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
14 7 0.10
15 4 0.06
16 34 0.51
17 17 0.25
18 5 0.07
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (16 bp):
TAATATTATATTAATT
Found at i:27860257 original size:16 final size:16
Alignment explanation
Indices: 27860218--27860248 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
27860208 TAATAGGGCC
27860218 GAGCTCGAGAAAATCT
1 GAGCTCGAGAAAATCT
27860234 GAGCTCGAGAAAATC
1 GAGCTCGAGAAAATC
27860249 CTAGTTCGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.16
Consensus pattern (16 bp):
GAGCTCGAGAAAATCT
Found at i:27862427 original size:27 final size:27
Alignment explanation
Indices: 27862385--27862461 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
27862375 CATTTAAGAT
* **
27862385 CAAGCCATGGTCATCAACAACCT-TTG
1 CAAGCCATGGTGATCAACAACCTGTAC
* *
27862411 CAGATCCATGGTGATCAACAATCTGTAC
1 CA-AGCCATGGTGATCAACAACCTGTAC
27862439 CAAGCCATGGTGATCAACAACCT
1 CAAGCCATGGTGATCAACAACCT
27862462 ACGTCAAACC
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
26 2 0.05
27 37 0.88
28 3 0.07
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (27 bp):
CAAGCCATGGTGATCAACAACCTGTAC
Found at i:27862512 original size:171 final size:171
Alignment explanation
Indices: 27862301--27862643 Score: 632
Period size: 171 Copynumber: 2.0 Consensus size: 171
27862291 CCTGTGGCTT
27862301 ATATTACCAACTATGATTCCCATCCAGTACAAAGCAATGAGCGAGTGGCAAAACAACCTAGGAGG
1 ATATTACCAACTATGATTCCCATCCAGTACAAAGCAATGAGCGAGTGGCAAAACAACCTAGGAGG
27862366 AAGAGACCTCATTTAAGATCAAGCCATGGTCATCAACAACCTTTGCAGATCCATGGTGATCAACA
66 AAGAGACCTCATTTAAGATCAAGCCATGGTCATCAACAACCTTTGCAGATCCATGGTGATCAACA
*
27862431 ATCTGTACCAAGCCATGGTGATCAACAACCTACGTCAAACC
131 ATCTGTACCAAGCCATGGTGATCAACAACCAACGTCAAACC
*
27862472 ATATTACCAACTATGATTCCCATCCAGTACAAATCAATGAGCGAGTGGCAAAACAACCTAGGAGG
1 ATATTACCAACTATGATTCCCATCCAGTACAAAGCAATGAGCGAGTGGCAAAACAACCTAGGAGG
* *
27862537 AAGAGACCTCGTTTAAGATCAAGCCATGGTCATCAACAACCTTTGCCGATCCATGGTGATCAACA
66 AAGAGACCTCATTTAAGATCAAGCCATGGTCATCAACAACCTTTGCAGATCCATGGTGATCAACA
* *
27862602 ATCTGTACTAAGCCATGGTGATCAACAACCAATGTCAAACC
131 ATCTGTACCAAGCCATGGTGATCAACAACCAACGTCAAACC
27862643 A
1 A
27862644 CAGTGATCAA
Statistics
Matches: 166, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
171 166 1.00
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.21
Consensus pattern (171 bp):
ATATTACCAACTATGATTCCCATCCAGTACAAAGCAATGAGCGAGTGGCAAAACAACCTAGGAGG
AAGAGACCTCATTTAAGATCAAGCCATGGTCATCAACAACCTTTGCAGATCCATGGTGATCAACA
ATCTGTACCAAGCCATGGTGATCAACAACCAACGTCAAACC
Found at i:27862598 original size:27 final size:27
Alignment explanation
Indices: 27862556--27862692 Score: 125
Period size: 27 Copynumber: 5.1 Consensus size: 27
27862546 CGTTTAAGAT
* * *
27862556 CAAGCCATGGTCATCAACAACCTTTGC
1 CAAGCCATGGTGATCAACAACCTGTAC
* * *
27862583 CGATCCATGGTGATCAACAATCTGTAC
1 CAAGCCATGGTGATCAACAACCTGTAC
*
27862610 TAAGCCATGGTGATCAACAACCAATGT--
1 CAAGCCATGGTGATCAACAACC--TGTAC
* ** *
27862637 CAAACCACAGTGATCAACAATCTGTAC
1 CAAGCCATGGTGATCAACAACCTGTAC
* *
27862664 CAAGCTATGGTGATCAACAACCTGGAC
1 CAAGCCATGGTGATCAACAACCTGTAC
27862691 CA
1 CA
27862693 CGGCATTATG
Statistics
Matches: 85, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
25 3 0.04
27 79 0.93
29 3 0.04
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.21
Consensus pattern (27 bp):
CAAGCCATGGTGATCAACAACCTGTAC
Found at i:27866701 original size:7 final size:7
Alignment explanation
Indices: 27866691--27866715 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
27866681 CTTGTTTTAC
27866691 AGTGCTT
1 AGTGCTT
27866698 AGTGCTT
1 AGTGCTT
27866705 AGTGCTT
1 AGTGCTT
27866712 AGTG
1 AGTG
27866716 GGCTATTCTC
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:0.16, C:0.12, G:0.32, T:0.40
Consensus pattern (7 bp):
AGTGCTT
Found at i:27874475 original size:11 final size:11
Alignment explanation
Indices: 27874459--27874485 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
27874449 AGTTACACTC
27874459 CTACTGGGACT
1 CTACTGGGACT
27874470 CTACTGGGACT
1 CTACTGGGACT
27874481 CTACT
1 CTACT
27874486 AGAGAATTTG
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:0.19, C:0.30, G:0.22, T:0.30
Consensus pattern (11 bp):
CTACTGGGACT
Found at i:27875479 original size:2 final size:2
Alignment explanation
Indices: 27875472--27875500 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
27875462 TTAAACATTA
27875472 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27875501 CGACATTAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27878482 original size:13 final size:13
Alignment explanation
Indices: 27878464--27878488 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27878454 ACAAATGATA
27878464 AAATTTTCACACG
1 AAATTTTCACACG
27878477 AAATTTTCACAC
1 AAATTTTCACAC
27878489 ATATAAACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:27881195 original size:16 final size:16
Alignment explanation
Indices: 27881176--27881212 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
27881166 AAAAATCGGT
27881176 GAAAAGAAAAT-ACAAA
1 GAAAAGAAAATCA-AAA
27881192 GAAAAGAAAATCAAAA
1 GAAAAGAAAATCAAAA
27881208 GAAAA
1 GAAAA
27881213 AGACTGAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 19 0.95
17 1 0.05
ACGTcount: A:0.76, C:0.05, G:0.14, T:0.05
Consensus pattern (16 bp):
GAAAAGAAAATCAAAA
Found at i:27885296 original size:199 final size:196
Alignment explanation
Indices: 27884956--27885351 Score: 621
Period size: 199 Copynumber: 2.0 Consensus size: 196
27884946 ATCGTTGATG
* * **
27884956 GTAAGTTGGGTTTCTGTTCGTTCTTGGTTTTCAATTTGCTTGTAAATCAATTAAATTGATGTTGA
1 GTAAGTTGGGTTTCTATTCATTCTTGGTTGCCAATTTGCTTGTAAATCAATTAAATTGATGTTGA
*
27885021 GTATCTTGATTATAGGCTTTGGAGTGCTCAGGGACTGATTTAGCATCAAAGAGATCCAGGTGAGT
66 GTATCTTGATTATAGGCTTTGGAGTGCTCAGGGACTGATTTAGCATCAAAGAGAACCAGGTGAGT
* * *
27885086 ACCAGAAACGCAAAGAAAAAGGGATTCGGTGAAAAGCTAAAATTGCTTGTTGTTTGGACAGCAGC
131 ACCAGAAACGC-AA-AAAAA-GGATTCAGTGAAAAGCTAAAATTGCTTGCTGTTTGGACAGAAGC
27885151 AGTA
193 AGTA
**
27885155 GTAAGTTGGGTTTCTATTCATTCTTGGTTGCCAATTTGCTTGTAAATCTGTTAAATTGATGTTGA
1 GTAAGTTGGGTTTCTATTCATTCTTGGTTGCCAATTTGCTTGTAAATCAATTAAATTGATGTTGA
* * * *
27885220 GTATCTTGATTATAGGCTTTGGAGTGCTCGGGGATTGTTTTAGCATCAAAGAGAACCAGGTGTGT
66 GTATCTTGATTATAGGCTTTGGAGTGCTCAGGGACTGATTTAGCATCAAAGAGAACCAGGTGAGT
* *
27885285 ACCAGAAACGCAAAAAAAGGATTCAGTGAAAAGTTGAAATTGCTTGCTGTTTGGACAGAAGCAGT
131 ACCAGAAACGCAAAAAAAGGATTCAGTGAAAAGCTAAAATTGCTTGCTGTTTGGACAGAAGCAGT
27885350 A
196 A
27885351 G
1 G
27885352 GCTAATTGTG
Statistics
Matches: 181, Mismatches: 16, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
196 44 0.24
197 5 0.03
198 2 0.01
199 130 0.72
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (196 bp):
GTAAGTTGGGTTTCTATTCATTCTTGGTTGCCAATTTGCTTGTAAATCAATTAAATTGATGTTGA
GTATCTTGATTATAGGCTTTGGAGTGCTCAGGGACTGATTTAGCATCAAAGAGAACCAGGTGAGT
ACCAGAAACGCAAAAAAAGGATTCAGTGAAAAGCTAAAATTGCTTGCTGTTTGGACAGAAGCAGT
A
Found at i:27885640 original size:45 final size:41
Alignment explanation
Indices: 27885602--27885679 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
27885592 ATTTAAATTA
*
27885602 TTAATGAGTCTAATTACTACTTGATGCCTTATTATATTTTT
1 TTAATGAATCTAATTACTACTTGATGCCTTATTATATTTTT
*
27885643 TTAATTAATCTAATTACTACTTGATGCCTTATTATAT
1 TTAATGAATCTAATTACTACTTGATGCCTTATTATAT
27885680 ATCTAATGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (41 bp):
TTAATGAATCTAATTACTACTTGATGCCTTATTATATTTTT
Found at i:27885725 original size:36 final size:35
Alignment explanation
Indices: 27885693--27885762 Score: 104
Period size: 36 Copynumber: 2.0 Consensus size: 35
27885683 TAATGTAATT
27885693 GTTAATTAAATTGAATGGAAGTTTATGGATGTATAA
1 GTTAATTAAATTGAATGGAAG-TTATGGATGTATAA
* * *
27885729 GTTAATTCAATTGAATGTAAGTTATGGAAGTATA
1 GTTAATTAAATTGAATGGAAGTTATGGATGTATA
27885763 TGTATTTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
35 12 0.39
36 19 0.61
ACGTcount: A:0.39, C:0.01, G:0.21, T:0.39
Consensus pattern (35 bp):
GTTAATTAAATTGAATGGAAGTTATGGATGTATAA
Found at i:27886007 original size:74 final size:76
Alignment explanation
Indices: 27885914--27886076 Score: 204
Period size: 74 Copynumber: 2.2 Consensus size: 76
27885904 CAGTTATCCA
** * ** *
27885914 ACTAGCGCCGGGTGCAATAATTTTTCGACTCGTTCGACTAGTGCT-GGCACACTGTTGATCTTGT
1 ACTAGCGCTAGGTGCAATAATTTGTCGACTCGTTCGACTAGTGCTGGGCACACCATTGATCATGT
**
27885978 CG-GTTATTCG
66 CGAGTTAAACG
* * * *
27885988 GCTAGCGCTAGGTGTAATAATTTGTCGACTCGTTTGACTAGTGTTGGGCACACCATTGATCATGT
1 ACTAGCGCTAGGTGCAATAATTTGTCGACTCGTTCGACTAGTGCTGGGCACACCATTGATCATGT
27886053 CGAGTTAAACG
66 CGAGTTAAACG
27886064 ACTAGCGCTAGGT
1 ACTAGCGCTAGGT
27886077 ACAAAAACCT
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
74 38 0.51
75 18 0.24
76 18 0.24
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (76 bp):
ACTAGCGCTAGGTGCAATAATTTGTCGACTCGTTCGACTAGTGCTGGGCACACCATTGATCATGT
CGAGTTAAACG
Found at i:27890004 original size:216 final size:216
Alignment explanation
Indices: 27889627--27890062 Score: 748
Period size: 216 Copynumber: 2.0 Consensus size: 216
27889617 TCGATACTTT
* *
27889627 TCTTAAGGTATCAATATATTTCTTAAGTTATAGATATTCCTGCTTCAACGGTCACTGAAATCAAC
1 TCTTAAGGTATCAATATATTTCCTAAGGTATAGATATTCCTGCTTCAACGGTCACTGAAATCAAC
* *
27889692 ATTATTTACAAAAAATATCGATACCCTTTTAGTTGGTATCGATACTCGTTGCTGCAGGTGAAGTT
66 ATTATTTACAAAAAATATCGATACCCTTTTAGTTGGTATCGATACTCATTGCTACAGGTGAAGTT
*
27889757 AATGACCTAGTATTTCATCCCAACAGCTACATTCACTTCTACAACAACCACAACAATTGAAAATC
131 AATGACCTAGTATTTCATCCCAACAGCTACATTCACTTCTACAACAACCACAACAATTGAAAATA
27889822 AATTAGAGGGTATAAATACCA
196 AATTAGAGGGTATAAATACCA
*
27889843 TCTTAAGGTATCAATATATTTCCTAAGGTATAGATATTCCTGCTTCAACGGTCACTGAAATCAGC
1 TCTTAAGGTATCAATATATTTCCTAAGGTATAGATATTCCTGCTTCAACGGTCACTGAAATCAAC
* *
27889908 ATTATTTACAAAAAATATCGATACCTTTTTAGTTGTTATCGATACTCATTGCTACAGGTGAAGTT
66 ATTATTTACAAAAAATATCGATACCCTTTTAGTTGGTATCGATACTCATTGCTACAGGTGAAGTT
* **
27889973 AATGATCTAGTATTTCATCCCAA-AGGCTACATTCACTTCTACAACAACCACAACGGTTGAAAAT
131 AATGACCTAGTATTTCATCCCAACA-GCTACATTCACTTCTACAACAACCACAACAATTGAAAAT
*
27890037 AAATTAGAGGGTATAAATACTA
195 AAATTAGAGGGTATAAATACCA
27890059 TCTT
1 TCTT
27890063 CCAAAGGTTT
Statistics
Matches: 207, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
215 1 0.00
216 206 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (216 bp):
TCTTAAGGTATCAATATATTTCCTAAGGTATAGATATTCCTGCTTCAACGGTCACTGAAATCAAC
ATTATTTACAAAAAATATCGATACCCTTTTAGTTGGTATCGATACTCATTGCTACAGGTGAAGTT
AATGACCTAGTATTTCATCCCAACAGCTACATTCACTTCTACAACAACCACAACAATTGAAAATA
AATTAGAGGGTATAAATACCA
Found at i:27900763 original size:12 final size:12
Alignment explanation
Indices: 27900738--27900807 Score: 59
Period size: 12 Copynumber: 5.8 Consensus size: 12
27900728 CTTATTGAAC
27900738 ATAAAAATAAAA
1 ATAAAAATAAAA
**
27900750 ATAAAAATGGAA
1 ATAAAAATAAAA
* *
27900762 ATAATAATAATA
1 ATAAAAATAAAA
* *
27900774 ATAATAATAATA
1 ATAAAAATAAAA
* *
27900786 ATAATAATAATA
1 ATAAAAATAAAA
*
27900798 ATAATAATAA
1 ATAAAAATAA
27900808 TGAAAATGAA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 52 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (12 bp):
ATAAAAATAAAA
Found at i:27900769 original size:3 final size:3
Alignment explanation
Indices: 27900761--27900808 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
27900751 TAAAAATGGA
27900761 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
27900809 GAAAATGAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:27905049 original size:37 final size:37
Alignment explanation
Indices: 27904999--27905073 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
27904989 ACCAATCTCG
* * *
27904999 TTGTATTGATTAAGAGTGGAACGACGAATTTATCGAT
1 TTGTATCGATTAAGAGTGGAACAACGAATCTATCGAT
27905036 TTGTATCGATTAAGAGTGGAACAACGAATCTATCGAT
1 TTGTATCGATTAAGAGTGGAACAACGAATCTATCGAT
27905073 T
1 T
27905074 GGGAAAACTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (37 bp):
TTGTATCGATTAAGAGTGGAACAACGAATCTATCGAT
Found at i:27905851 original size:23 final size:23
Alignment explanation
Indices: 27905798--27905842 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
27905788 AAAGCAAACT
*
27905798 AATAAAA-ACAAAAACAAAACAA
1 AATAAAATAGAAAAACAAAACAA
27905820 AATAAAATAGAAAAA-AAAACAA
1 AATAAAATAGAAAAACAAAACAA
27905842 A
1 A
27905843 TAGGAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.82, C:0.09, G:0.02, T:0.07
Consensus pattern (23 bp):
AATAAAATAGAAAAACAAAACAA
Found at i:27907191 original size:17 final size:17
Alignment explanation
Indices: 27907169--27907218 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
27907159 TATCAGATTT
27907169 TGATACCCATATCTTTC
1 TGATACCCATATCTTTC
*
27907186 TGATACCTATATCTTTC
1 TGATACCCATATCTTTC
27907203 TGATACCCATATCTTT
1 TGATACCCATATCTTT
27907219 GACTTTCTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.24, C:0.26, G:0.06, T:0.44
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:27911830 original size:17 final size:17
Alignment explanation
Indices: 27911808--27911857 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
27911798 TCTCATATTT
27911808 TGATACCCATATCTTTC
1 TGATACCCATATCTTTC
* *
27911825 TGATACCTATATATTTC
1 TGATACCCATATCTTTC
27911842 TGATACCCATATCTTT
1 TGATACCCATATCTTT
27911858 GACTTTCTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:27919237 original size:9 final size:9
Alignment explanation
Indices: 27919225--27919250 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
27919215 TAAAAATTAA
27919225 AAATAAAAT
1 AAATAAAAT
27919234 AAATAAAAT
1 AAATAAAAT
27919243 AAATAAAA
1 AAATAAAA
27919251 ATATCGTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:27921208 original size:24 final size:24
Alignment explanation
Indices: 27921180--27921253 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
27921170 TTATAAATTA
27921180 AATTATAATTATTTTTAAATGTTT
1 AATTATAATTATTTTTAAATGTTT
* ** *
27921204 AATTATCACAACTTTT--A---TT
1 AATTATAATTATTTTTAAATGTTT
27921223 AAGTTATAATTATTTTTAAATGTTT
1 AA-TTATAATTATTTTTAAATGTTT
27921248 AATTAT
1 AATTAT
27921254 TACAACTTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 12
0.64 0.14 0.21
Matches are distributed among these distances:
19 4 0.11
20 10 0.28
22 2 0.06
24 16 0.44
25 4 0.11
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (24 bp):
AATTATAATTATTTTTAAATGTTT
Found at i:27921230 original size:44 final size:44
Alignment explanation
Indices: 27921176--27921266 Score: 164
Period size: 44 Copynumber: 2.1 Consensus size: 44
27921166 ATAATTATAA
27921176 ATTAAATTATAATTATTTTTAAATGTTTAATTATCACAACTTTT
1 ATTAAATTATAATTATTTTTAAATGTTTAATTATCACAACTTTT
* *
27921220 ATTAAGTTATAATTATTTTTAAATGTTTAATTATTACAACTTTT
1 ATTAAATTATAATTATTTTTAAATGTTTAATTATCACAACTTTT
27921264 ATT
1 ATT
27921267 TTAATTCAAC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.54
Consensus pattern (44 bp):
ATTAAATTATAATTATTTTTAAATGTTTAATTATCACAACTTTT
Found at i:27921263 original size:24 final size:24
Alignment explanation
Indices: 27921192--27921264 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
27921182 TTATAATTAT
*
27921192 TTTTAAATGTTTAATTATCACAAC
1 TTTTAAATGTTTAATTATTACAAC
27921216 TTTTATTAA-GTTATAATTA-T-----
1 TTTTA--AATGTT-TAATTATTACAAC
27921236 TTTTAAATGTTTAATTATTACAAC
1 TTTTAAATGTTTAATTATTACAAC
27921260 TTTTA
1 TTTTA
27921265 TTTTAATTCA
Statistics
Matches: 38, Mismatches: 1, Indels: 20
0.64 0.02 0.34
Matches are distributed among these distances:
18 8 0.21
19 4 0.11
20 5 0.13
24 10 0.26
25 3 0.08
26 8 0.21
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.53
Consensus pattern (24 bp):
TTTTAAATGTTTAATTATTACAAC
Found at i:27923774 original size:16 final size:16
Alignment explanation
Indices: 27923753--27923784 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
27923743 TGGTTACTTA
27923753 GCTTGAGAATACCTCT
1 GCTTGAGAATACCTCT
27923769 GCTTGAGAATACCTCT
1 GCTTGAGAATACCTCT
27923785 TTCTTCACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (16 bp):
GCTTGAGAATACCTCT
Found at i:27925024 original size:14 final size:16
Alignment explanation
Indices: 27925002--27925036 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
27924992 GTAATATAGT
27925002 AATATATATCAAATTA
1 AATATATATCAAATTA
27925018 AATATATATCAAATTA
1 AATATATATCAAATTA
27925034 AAT
1 AAT
27925037 GTGCAAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (16 bp):
AATATATATCAAATTA
Found at i:27929802 original size:17 final size:17
Alignment explanation
Indices: 27929780--27929823 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
27929770 ATATAGCTCT
27929780 AACAAGCTTCCAACCCA
1 AACAAGCTTCCAACCCA
*
27929797 AACAAGCTTCCAACCCG
1 AACAAGCTTCCAACCCA
*
27929814 AACGAGCTTC
1 AACAAGCTTC
27929824 TGATTCACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.36, C:0.39, G:0.11, T:0.14
Consensus pattern (17 bp):
AACAAGCTTCCAACCCA
Found at i:27930372 original size:24 final size:24
Alignment explanation
Indices: 27930300--27930373 Score: 60
Period size: 24 Copynumber: 3.0 Consensus size: 24
27930290 TCATGAATTG
* * *
27930300 GAAATCGATAAGCTTATATGAGTT
1 GAAATCGATAAGCTCATACGAGCT
* * * *
27930324 GAGAATCGGTAAACTC-TCCCAAGCT
1 GA-AATCGATAAGCTCAT-ACGAGCT
27930349 GAAATCGATAAGCTCATACGAGCT
1 GAAATCGATAAGCTCATACGAGCT
27930373 G
1 G
27930374 TGGTGTGTCC
Statistics
Matches: 36, Mismatches: 11, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
24 20 0.56
25 16 0.44
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (24 bp):
GAAATCGATAAGCTCATACGAGCT
Found at i:27937226 original size:17 final size:17
Alignment explanation
Indices: 27937204--27937239 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
27937194 GTTGGGGCTC
27937204 TAATGACTGAGTTTTCT
1 TAATGACTGAGTTTTCT
27937221 TAATGACTGAGTTTTCT
1 TAATGACTGAGTTTTCT
27937238 TA
1 TA
27937240 CTTTTGTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.25, C:0.11, G:0.17, T:0.47
Consensus pattern (17 bp):
TAATGACTGAGTTTTCT
Found at i:27940336 original size:28 final size:28
Alignment explanation
Indices: 27940283--27940348 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
27940273 AGTACAATGA
**
27940283 GGGCCTTAGCCCAATTCAATAGCAGTCT
1 GGGCCTTAGCCCAACACAATAGCAGTCT
* * *
27940311 GGGCCTTAGCCCAACACAGTATCAGTGT
1 GGGCCTTAGCCCAACACAATAGCAGTCT
*
27940339 GGACCTTAGC
1 GGGCCTTAGC
27940349 GTAATACAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.23
Consensus pattern (28 bp):
GGGCCTTAGCCCAACACAATAGCAGTCT
Found at i:27941311 original size:27 final size:27
Alignment explanation
Indices: 27940713--27941314 Score: 484
Period size: 27 Copynumber: 22.5 Consensus size: 27
27940703 TCATCTCCTA
* **
27940713 GGTATTTCAGTCATTTTACCCTTC-AA
1 GGTATTTCGGTCATTTTACCCTTCGGG
** * *
27940739 GGTATTTCAATTATTTTA-CCTTCGAG
1 GGTATTTCGGTCATTTTACCCTTCGGG
* *
27940765 GGTATTTCGATCATTTTACCCTTCGAG
1 GGTATTTCGGTCATTTTACCCTTCGGG
* * **
27940792 GGTATTTTGATCATTTTACCCTTCAAG
1 GGTATTTCGGTCATTTTACCCTTCGGG
* *
27940819 GGTATTTCGGTCATATTACCCTTC-GA
1 GGTATTTCGGTCATTTTACCCTTCGGG
*
27940845 GGTATTTCAGTCATTTTACCCTAT-GGG
1 GGTATTTCGGTCATTTTACCCT-TCGGG
* *
27940872 GGTAATTCGGTCATTTTTCCCTGT-GGG
1 GGTATTTCGGTCATTTTACCCT-TCGGG
** **
27940899 GGTATTTCATTCATTTCCCCCTT-GGG
1 GGTATTTCGGTCATTTTACCCTTCGGG
* * *
27940925 GGTATTTCGGTTATTTCACCCTTTGGG
1 GGTATTTCGGTCATTTTACCCTTCGGG
* * *
27940952 GGTATTTCGATCATTTTACTCTTCGAG
1 GGTATTTCGGTCATTTTACCCTTCGGG
* *
27940979 GG-ATTTCAGTCATTTTACCCTTCGAG
1 GGTATTTCGGTCATTTTACCCTTCGGG
* * * *
27941005 GGTATTTCGGTGATCTTACCTTTTGGG
1 GGTATTTCGGTCATTTTACCCTTCGGG
* *
27941032 GGTATTTCGATCATTTTATCCTTCGGG
1 GGTATTTCGGTCATTTTACCCTTCGGG
* *** *
27941059 AGTATTTTAATCATTTTACCCTTCGGA
1 GGTATTTCGGTCATTTTACCCTTCGGG
* * *
27941086 GGTAATTCGGTCATTTTACCCTTTGTG
1 GGTATTTCGGTCATTTTACCCTTCGGG
* * * **
27941113 AGTGA-TTCAGTCATTTTAACCTTTTGG
1 GGT-ATTTCGGTCATTTTACCCTTCGGG
* * *
27941140 GGTAATCCGATCATTTTACCCTTCGGG
1 GGTATTTCGGTCATTTTACCCTTCGGG
* * **
27941167 GGTAATTCGATCATTTTACCCTTCAAG
1 GGTATTTCGGTCATTTTACCCTTCGGG
**
27941194 GGTATTTCAATCATTTTACCCTTCGGG
1 GGTATTTCGGTCATTTTACCCTTCGGG
* **
27941221 GGTAATTCGGTCATTTTACCCATT-AAG
1 GGTATTTCGGTCATTTTACCC-TTCGGG
* **
27941248 GGTATTTCGGTTATTTTACCCTTCAAG
1 GGTATTTCGGTCATTTTACCCTTCGGG
* * * *
27941275 AGTAATTCGGTCATTTTATCCTACGGG
1 GGTATTTCGGTCATTTTACCCTTCGGG
*
27941302 GGTAATTCGGTCA
1 GGTATTTCGGTCA
27941315 ATTTCCCATA
Statistics
Matches: 470, Mismatches: 96, Indels: 19
0.80 0.16 0.03
Matches are distributed among these distances:
25 5 0.01
26 102 0.22
27 360 0.77
28 3 0.01
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.41
Consensus pattern (27 bp):
GGTATTTCGGTCATTTTACCCTTCGGG
Found at i:27944325 original size:359 final size:359
Alignment explanation
Indices: 27943656--27944347 Score: 1222
Period size: 359 Copynumber: 1.9 Consensus size: 359
27943646 GGCCCTAACA
* *
27943656 TTCGACGATTGCCTCTTATTACTTACCAATCTTGGTATACCTCTTAACTGTCACAAGGCCGTTTG
1 TTCGACGATTGCCTCTTATTACTTACCAATCTTGGTATACCTCTTAACTGTCACAAGGCCATTCG
* *
27943721 GCAAGGTCCAAAATCAGTATGCACAATTAATCACATGCATAAAATATACCATTTCTTAAACACTA
66 GCAAGGTCCAAAATCAGTATGAAAAATTAATCACATGCATAAAATATACCATTTCTTAAACACTA
*
27943786 ATACACACAAAAGGTTAGACCCACACCTTATTTACATGAATCTGATGCACTAAAATCATCGCAAC
131 ATACACACAAAAGGTTAAACCCACACCTTATTTACATGAATCTGATGCACTAAAATCATCGCAAC
*
27943851 TTCTACAACTTAAATCTAGACAGCTCTAGACCAGATCTGTACACAACATGAATGAAACTCGATTA
196 TTCTACAACTTAAATATAGACAGCTCTAGACCAGATCTGTACACAACATGAATGAAACTCGATTA
* *
27943916 AAACTAGCCTTTAGAAACACCTATAAGGTTCAAACAGAACAAGGATTAACAATGTCAAATCAAAT
261 AAACAAGCCTTTAGAAACACCTATAAGGTTCAAACAGAACAAGAATTAACAATGTCAAATCAAAT
27943981 TCAATTTTACCAATCTTGGTATACCTCTTAACTG
326 TCAATTTTACCAATCTTGGTATACCTCTTAACTG
* *
27944015 TTCGATGATTGCCTCTTATTACTTACCAATCTTGGTATACCTCTTAACTGTCACAATGCCATTCG
1 TTCGACGATTGCCTCTTATTACTTACCAATCTTGGTATACCTCTTAACTGTCACAAGGCCATTCG
27944080 GCAAGGTCCAAAATCAGTATGAAAAATTAATCACATGCATAAAATATACCATTTCTTAAACACTA
66 GCAAGGTCCAAAATCAGTATGAAAAATTAATCACATGCATAAAATATACCATTTCTTAAACACTA
* * **
27944145 ATACACACAAAAGGTTAAATCCACACCTTATTTACATGAATCTGATGTACTAACGTCATCGCAAC
131 ATACACACAAAAGGTTAAACCCACACCTTATTTACATGAATCTGATGCACTAAAATCATCGCAAC
* *
27944210 TTCTATAACTTAAATATAGACAGCTCTAGACCAGATTTGTACACAACATGAATGAAACTCGATTA
196 TTCTACAACTTAAATATAGACAGCTCTAGACCAGATCTGTACACAACATGAATGAAACTCGATTA
* *
27944275 AAACAAGCCTTTAGAAACCCCTATAAGGTTCGAACAGAACAAGAATTAACAATGTCAAATCAAAT
261 AAACAAGCCTTTAGAAACACCTATAAGGTTCAAACAGAACAAGAATTAACAATGTCAAATCAAAT
27944340 TCAATTTT
326 TCAATTTT
27944348 TGATCACTTA
Statistics
Matches: 315, Mismatches: 18, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
359 315 1.00
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.28
Consensus pattern (359 bp):
TTCGACGATTGCCTCTTATTACTTACCAATCTTGGTATACCTCTTAACTGTCACAAGGCCATTCG
GCAAGGTCCAAAATCAGTATGAAAAATTAATCACATGCATAAAATATACCATTTCTTAAACACTA
ATACACACAAAAGGTTAAACCCACACCTTATTTACATGAATCTGATGCACTAAAATCATCGCAAC
TTCTACAACTTAAATATAGACAGCTCTAGACCAGATCTGTACACAACATGAATGAAACTCGATTA
AAACAAGCCTTTAGAAACACCTATAAGGTTCAAACAGAACAAGAATTAACAATGTCAAATCAAAT
TCAATTTTACCAATCTTGGTATACCTCTTAACTG
Found at i:27945149 original size:528 final size:524
Alignment explanation
Indices: 27944095--27945675 Score: 2082
Period size: 528 Copynumber: 3.0 Consensus size: 524
27944085 GTCCAAAATC
* *
27944095 AGTATGAAAAATTAATCACATGCATAAAATATACCATTTCTTAAACACTAATACACACAAAAGGT
1 AGTA-GAATAATTAATCACATGCATAAAATATACCATTTTTTAAACACTAATACACA-AAAAGGT
* * ** * * *
27944160 TAAATCCACACCTTATTTACATGAATCTGATGTACTAACGTC-ATCGCAACTTCTATAACTTAAA
64 TAAACCCACACCTAATTTATGTGAATCTGATGCACTAACG-CAATCGCAACTTCTACAACTTAGA
* * * *
27944224 TATAGACAGCTCTAGACCAGATTTGTACACAACATGAATGAAACTCGATTAAAACAAGCCTTTAG
128 TCTAGACAGCTCTAGACCGGATTTGTACACAACATGAATGAAACTCAATTAAAACCAGCCTTTAG
* * * *
27944289 AAACCCCTATAAGGTTCGAACAGAACAAGAATTAACAATGTCAAATCAAATTCAATTTTTGATCA
193 AAACCCCTATAAGGTTCGACCAGAACAAGGATTAACAGTGTCAAATCGAATTCAA-TTTTG-TCA
* * * * * **
27944354 CTTACTTACTGTATTTTGATATATAACGAAGACATGAATGAGTTTTGATGTCACTACTGATCCAT
256 CTTACTTACTATATTCT-ATATATAACAAAGACACGAATGAGTTTAGATGTCACTGTTGATCCAT
*
27944419 GACATTCGGATTAGGTCCTTCAATCAAAATAACACTCAAAAGTTAGTATAGAATATTTGACTATG
320 GACGTTCGGATTAGGTCCTTCAATCAAAATAACACTCAAAAGTTAGTATAGAATATTTGACTATG
** * * *
27944484 CCACCAGTAACATTCAACCAAAGTAGAAAAGAAAGGAAGAAGGAAACGAGATAAGATCTGATTGA
385 CCACCAGTAACATT-TGCCAAAGCAGAAAATAAAGGAAGAAGGAAACGAGATAAGATCTGATCGA
* *
27944549 AAGAAAAACTACTTACTCCACATGAACGACAGATTCGAAGAACCAATCAAAAATCCAAGCAGTAC
449 AAGAAAAACTACTTACTCCACATGAACAACAGATTCGAAGAACCAATCAAAAATCCAAGCAATAC
27944614 AGATGAATTC-
514 AGATGAATTCG
* *
27944624 AGCTAGAATAATTAATCACATGTATAAAATATACCATTTTTTAAACACTAATACACAAAAAGGTC
1 AG-TAGAATAATTAATCACATGCATAAAATATACCATTTTTTAAACACTAATACACAAAAAGGTT
* *
27944689 AAACCCACACCTAATTTATGTGAATAC-GATACACTAACGCAATTGCAACTTCTACAACTTAGAT
65 AAACCCACACCTAATTTATGTGAAT-CTGATGCACTAACGCAATCGCAACTTCTACAACTTAGAT
*
27944753 CTAGACAGCTCTAGACCGGATTTGTACACAACATGAATGAAACTCAATTAAAACCAGCCATTAGA
129 CTAGACAGCTCTAGACCGGATTTGTACACAACATGAATGAAACTCAATTAAAACCAGCCTTTAGA
*
27944818 AACCCCTATAAGGTTTGACCAGAACAAGGATTAACAGTGTCAAATCGAATTCAATATTTCGTCAC
194 AACCCCTATAAGGTTCGACCAGAACAAGGATTAACAGTGTCAAATCGAATTCAAT-TTT-GTCAC
* * * *
27944883 TTACTTACTCTATCTCTATTTATACCAAAGACACAAATGAGTTTAGATGTCACTGTTGATCCATG
257 TTACTTACTATAT-TCTATATATAACAAAGACACGAATGAGTTTAGATGTCACTGTTGATCCATG
* * *
27944948 ACGTTCGGATTAGGTCCTTCAATCAAAATAACAATCAAAAGCTAGTAAAGAATATTTGACTATGC
321 ACGTTCGGATTAGGTCCTTCAATCAAAATAACACTCAAAAGTTAGTATAGAATATTTGACTATGC
* * * * *
27945013 CACCAGTAACATTTGCCCAAAGCAAAAAATCAAGGGAGAAGGAACCGAGATCAGATCTGATCGAA
386 CACCAGTAACATTTG-CCAAAGCAGAAAATAAAGGAAGAAGGAAACGAGATAAGATCTGATCGAA
* * * *
27945078 AGAAAAATTACTTACTCTAC-TAGAACAACAGATTCGAAGAACCAATGAAAAATCTAAGCAATAT
450 AGAAAAACTACTTACTCCACAT-GAACAACAGATTCGAAGAACCAATCAAAAATCCAAGCAATA-
27945142 C-GATGAATTCG
513 CAGATGAATTCG
* *
27945153 AGTAGAATAATTAATCACATGCATAAAATATACCATTTTTTAAACACTAATACACACAAATGTTA
1 AGTAGAATAATTAATCACATGCATAAAATATACCATTTTTTAAACACTAATACACAAAAAGGTTA
* * **
27945218 GACCCACACCTAATTTATGTCAATCTGATGCACTAACATAATCGCAACTTCTACAACTTAGATCT
66 AACCCACACCTAATTTATGTGAATCTGATGCACTAACGCAATCGCAACTTCTACAACTTAGATCT
* * *
27945283 AGACAGCTCTAGATCGGATCTGTACACAACATGAATGAAACTTAATTAAAACCAGCCTTTAGAAA
131 AGACAGCTCTAGACCGGATTTGTACACAACATGAATGAAACTCAATTAAAACCAGCCTTTAGAAA
* * * * *
27945348 CCCCTATAAGGTTCGGCCAGAACAAGGACTAACAGTGTCAAATCGGATTCAATTTT-T-AATCAC
196 CCCCTATAAGGTTCGACCAGAACAAGGATTAACAGTGTCAAATCGAATTCAATTTTGTCACTTAC
* * * *
27945411 TTACTATATTTCGATATAGAACAAAGACACGAATGAGTCTCGATGTCACTGTTGATCCATGACGT
261 TTACTATA-TTCTATATATAACAAAGACACGAATGAGTTTAGATGTCACTGTTGATCCATGACGT
* * * *
27945476 TTGGATTAGGTCCTTCAATCAAAATAACACTCAAAAGTTAGTATAGAACATTCGGCTATGCCACC
325 TCGGATTAGGTCCTTCAATCAAAATAACACTCAAAAGTTAGTATAGAATATTTGACTATGCCACC
* * * * * * *
27945541 AATAACTTTTAGACAAATCAGAAAATAAAGGAAGAAGGAAACAAGATAAGATTTTGATCAAAAGA
390 AGTAACATTT-GCCAAAGCAGAAAATAAAGGAAGAAGGAAACGAGATAAGA-TCTGATCGAAAGA
* * * * * * * * * *
27945606 AAAACTATTTATTCAAC-CGAAACGACAAATTTGAAGCACCAAGT-AAAAATCGAAGCAGTACAG
453 AAAACTACTTACTCCACATG-AACAACAGATTCGAAGAACCAA-TCAAAAATCCAAGCAATACAG
27945669 ATGAATT
516 ATGAATT
27945676 TAGCCAGAAT
Statistics
Matches: 924, Mismatches: 111, Indels: 38
0.86 0.10 0.04
Matches are distributed among these distances:
524 158 0.17
525 67 0.07
526 1 0.00
527 7 0.01
528 631 0.68
529 58 0.06
530 2 0.00
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (524 bp):
AGTAGAATAATTAATCACATGCATAAAATATACCATTTTTTAAACACTAATACACAAAAAGGTTA
AACCCACACCTAATTTATGTGAATCTGATGCACTAACGCAATCGCAACTTCTACAACTTAGATCT
AGACAGCTCTAGACCGGATTTGTACACAACATGAATGAAACTCAATTAAAACCAGCCTTTAGAAA
CCCCTATAAGGTTCGACCAGAACAAGGATTAACAGTGTCAAATCGAATTCAATTTTGTCACTTAC
TTACTATATTCTATATATAACAAAGACACGAATGAGTTTAGATGTCACTGTTGATCCATGACGTT
CGGATTAGGTCCTTCAATCAAAATAACACTCAAAAGTTAGTATAGAATATTTGACTATGCCACCA
GTAACATTTGCCAAAGCAGAAAATAAAGGAAGAAGGAAACGAGATAAGATCTGATCGAAAGAAAA
ACTACTTACTCCACATGAACAACAGATTCGAAGAACCAATCAAAAATCCAAGCAATACAGATGAA
TTCG
Found at i:27952048 original size:18 final size:18
Alignment explanation
Indices: 27952020--27952057 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
27952010 TGCTTGTTTG
27952020 TTATTTTTTCTTTT-CTT
1 TTATTTTTTCTTTTGCTT
27952037 TTATTATTTTCTTTTGCTT
1 TTATT-TTTTCTTTTGCTT
27952056 TT
1 TT
27952058 CTTGTGTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.26
18 9 0.47
19 5 0.26
ACGTcount: A:0.08, C:0.11, G:0.03, T:0.79
Consensus pattern (18 bp):
TTATTTTTTCTTTTGCTT
Found at i:27955846 original size:41 final size:42
Alignment explanation
Indices: 27955788--27955906 Score: 206
Period size: 41 Copynumber: 2.9 Consensus size: 42
27955778 ATTTACTAGC
* *
27955788 GATACAATTTAAGCCATCACAACTATTCTTAAAATA-CTTGT
1 GATACAATTTAAACCATCACAACTATTGTTAAAATAGCTTGT
27955829 GATACAATTTAAACCATCACAACTATTGTTAAAA-AGCTTGT
1 GATACAATTTAAACCATCACAACTATTGTTAAAATAGCTTGT
27955870 GATACAATTTAAACCATCACAACTATTGTTAAAATAG
1 GATACAATTTAAACCATCACAACTATTGTTAAAATAG
27955907 TAACCAAGTA
Statistics
Matches: 74, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
40 1 0.01
41 71 0.96
42 2 0.03
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (42 bp):
GATACAATTTAAACCATCACAACTATTGTTAAAATAGCTTGT
Found at i:27969742 original size:22 final size:22
Alignment explanation
Indices: 27969677--27969756 Score: 76
Period size: 22 Copynumber: 3.7 Consensus size: 22
27969667 TACTATTTTC
*
27969677 TCTTTTAAACAGTAATTTATCTGA
1 TCTTTTAAACA-T-ATTTATTTGA
**
27969701 TCTTTTCTACATA---ATTTGA
1 TCTTTTAAACATATTTATTTGA
27969720 TCTTTTAAACATATTTATTTGA
1 TCTTTTAAACATATTTATTTGA
**
27969742 TCTTTTCTACATATT
1 TCTTTTAAACATATT
27969757 AAGTCACTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
19 16 0.35
22 20 0.43
23 1 0.02
24 9 0.20
ACGTcount: A:0.29, C:0.14, G:0.05, T:0.53
Consensus pattern (22 bp):
TCTTTTAAACATATTTATTTGA
Found at i:27974014 original size:23 final size:23
Alignment explanation
Indices: 27973988--27974033 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
27973978 ACTACTTGTA
27973988 TCCATTCTTCAACTCTTAAATAG
1 TCCATTCTTCAACTCTTAAATAG
*
27974011 TCCATTCTTCAATTCTTAAATAG
1 TCCATTCTTCAACTCTTAAATAG
27974034 AATGATAAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.30, C:0.24, G:0.04, T:0.41
Consensus pattern (23 bp):
TCCATTCTTCAACTCTTAAATAG
Done.