Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 121 of 135
Found at i:40192796 original size:95 final size:93
Alignment explanation
Indices: 40192608--40192785 Score: 252
Period size: 95 Copynumber: 1.9 Consensus size: 93
40192598 ACCTTTAAGT
*
40192608 CAAGATGAAGTTTCAAATGTCAAAATTTTATCCTCTTAAAGTTATAGTAAAGTTGGATAATGAAT
1 CAAGATGAAGTTTCAAATGTCAAAATTTTATCCTCTTAAAGTTATAGTAAAGTTAGATAATGAAT
* *
40192673 CTTCATCTCTCTGGAGTTATAATAAGAG
66 CTTCATCTCTCTGAAATTATAATAAGAG
* *
40192701 CAAGATGAATTTTCAAATGTCAAATTTTTTTATCCTCTTAAAGTTATAGTAAAGTTAGAT-A-GC
1 CAAGATGAAGTTTCAAATGTCAAA--ATTTTATCCTCTTAAAGTTATAGTAAAGTTAGATAATG-
*
40192764 AAGTCTTTATCTCTCTGAAATT
63 AA-TCTTCATCTCTCTGAAATT
40192786 GAAGTAAGAG
Statistics
Matches: 75, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
93 24 0.32
94 3 0.04
95 48 0.64
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.38
Consensus pattern (93 bp):
CAAGATGAAGTTTCAAATGTCAAAATTTTATCCTCTTAAAGTTATAGTAAAGTTAGATAATGAAT
CTTCATCTCTCTGAAATTATAATAAGAG
Found at i:40192872 original size:38 final size:38
Alignment explanation
Indices: 40192829--40193044 Score: 158
Period size: 38 Copynumber: 5.6 Consensus size: 38
40192819 CCTATCCTCT
40192829 TGAAATTGAAGTAA-AGCTGGATATCAAGTCTTCATCTC
1 TGAAATTGAAGTAAGAGCTGGATATCAAGTCTT-ATCTC
* * * ** *
40192867 TGAAATTGAAGTAAGAAC--AAGATCATTTCCTATCCTC
1 TGAAATTGAAGTAAGAGCTGGATATCAAGTCTTAT-CTC
* *
40192904 TTGAAATTGAAGT-AGAGTTGGATAACAAGTCTTCATCTC
1 -TGAAATTGAAGTAAGAGCTGGATATCAAGTCTT-ATCTC
* * ** *
40192943 TGAAATTGAAGTAAGAGC--AAGATCATTTCCTATCCTC
1 TGAAATTGAAGTAAGAGCTGGATATCAAGTCTTAT-CTC
* *
40192980 TTGAAATTGAAGTAA-AGCTGGATAGCAAGTTTTTATCTCTC
1 -TGAAATTGAAGTAAGAGCTGGATATCAAG-TCTTA--TCTC
*
40193021 TGAAATTGAAGTAAGAGCTAGATA
1 TGAAATTGAAGTAAGAGCTGGATA
40193045 AAGCATCCAA
Statistics
Matches: 134, Mismatches: 29, Indels: 27
0.71 0.15 0.14
Matches are distributed among these distances:
36 4 0.03
37 27 0.20
38 52 0.39
39 20 0.15
40 19 0.14
41 11 0.08
42 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (38 bp):
TGAAATTGAAGTAAGAGCTGGATATCAAGTCTTATCTC
Found at i:40192936 original size:76 final size:76
Alignment explanation
Indices: 40192810--40193687 Score: 716
Period size: 76 Copynumber: 10.9 Consensus size: 76
40192800 ATAAAGCATC
* * *
40192810 AGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTCATCTCTGAAATTG
1 AGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGAAATTG
*
40192875 AAGTAAGAACA
66 AAGTAAGAGCA
* *
40192886 AGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTG
1 AGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGAAATTG
40192951 AAGTAAGAGCA
66 AAGTAAGAGCA
* * *
40192962 AGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAGCAAGTTTTTATCTCTCTGAAAT
1 AGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTA--TCTCTGAAAT
*
40193027 TGAAGTAAGAGCT
64 TGAAGTAAGAGCA
* ** **** * *
40193040 AGATAAAGCA-TCCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGCC
1 AGAT----CATTTC--C-T-ATCCT-CT-TGAAATT------GAAGTAGAGCTGGATAACAAGTC
** *
40193104 TTCGTCCCTCTGAAATTGAAGTAAGAGTA
50 TT--TATCTCTGAAATTGAAGTAAGAGCA
** * * **** * * * *
40193133 AGATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTTTT
1 AGAT-------C-ATTTC-CTATCC--T-CTTGAAAT--TGAAGTAGAGCTGGATAACAAGTCTT
40193198 TATCTCTGAAATTGAAGTAAGAGCA
52 TATCTCTGAAATTGAAGTAAGAGCA
* * *
40193223 AGATCATCTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTTTTTATCTCTGAAATTG
1 AGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGAAATTG
* *
40193288 GAGTAAGAGTA
66 AAGTAAGAGCA
** * * **** * * * *
40193299 AGATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTTTT
1 AGAT-------C-ATTTC-CTATCC--T-CTTGAAAT--TGAAGTAGAGCTGGATAACAAGTCTT
40193364 TATCTCTGAAATTGAAGTAAGAGCA
52 TATCTCTGAAATTGAAGTAAGAGCA
* *
40193389 AGATCATCTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTG
1 AGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGAAATTG
* *
40193454 AAGTAGGAACA
66 AAGTAAGAGCA
* * * *
40193465 AGATCATTTTCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTTTTTATCTCTGAAATTG
1 AGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGAAATTG
40193530 AAGTAAGAGCA
66 AAGTAAGAGCA
* *
40193541 AGATCATCTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGAT-TTTATCTCTGAAATT
1 AGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAG-TCTTTATCTCTGAAATT
40193605 GAAGTAAGAGCA
65 GAAGTAAGAGCA
* * * *
40193617 ATATCATCTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTAAAATTG
1 AGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGAAATTG
40193682 AAGTAA
66 AAGTAA
40193688 AGTAGGATAG
Statistics
Matches: 653, Mismatches: 104, Indels: 90
0.77 0.12 0.11
Matches are distributed among these distances:
75 1 0.00
76 419 0.64
77 1 0.00
78 32 0.05
79 2 0.00
81 10 0.02
82 8 0.01
83 4 0.01
84 4 0.01
85 7 0.01
86 2 0.00
87 4 0.01
88 3 0.00
90 76 0.12
92 22 0.03
93 45 0.07
95 2 0.00
96 3 0.00
97 6 0.01
98 2 0.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Consensus pattern (76 bp):
AGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGAAATTG
AAGTAAGAGCA
Found at i:40193184 original size:92 final size:91
Alignment explanation
Indices: 40192964--40193226 Score: 379
Period size: 93 Copynumber: 2.9 Consensus size: 91
40192954 TAAGAGCAAG
*
40192964 ATCA-TTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAGCAAGTTTTTATCTCTCTGAAATT
1 ATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAG--TTTATCTCTCTGAAATT
40193028 GAAGTAAGAGCT-AGATAAAGCATCCAAC
64 GAAGTAAGAG-TAAGATAAAGCATCCAAC
* ** *
40193056 ATCATTTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGCCTTCGTCCCTCTGAAATT
1 ATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAG--TTTATCTCTCTGAAATT
*
40193121 GAAGTAAGAGTAAGATGAAGCA-CCAAC
64 GAAGTAAGAGTAAGATAAAGCATCCAAC
* *
40193148 ATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTTTTTATCTCTGAAATTGA
1 ATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTTTATCTCTCTGAAATTGA
*
40193213 AGTAAGAGCAAGAT
66 AGTAAGAGTAAGAT
40193227 CATCTCCTAT
Statistics
Matches: 155, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
90 28 0.18
92 55 0.35
93 72 0.46
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (91 bp):
ATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTTTATCTCTCTGAAATTGA
AGTAAGAGTAAGATAAAGCATCCAAC
Found at i:40193208 original size:38 final size:38
Alignment explanation
Indices: 40193166--40193293 Score: 120
Period size: 38 Copynumber: 3.4 Consensus size: 38
40193156 CCTATCCTCT
40193166 TGAAATTGAAGTAAAGCTGGATATCAAGTTTTTATCTC
1 TGAAATTGAAGTAAAGCTGGATATCAAGTTTTTATCTC
* * **
40193204 TGAAATTGAAGTAAGAGC--AAGATC-A-TCTCCTATCCTC
1 TGAAATTGAAGTAA-AGCTGGATATCAAGT-TTTTAT-CTC
* * *
40193241 TTGAAATTGAAGTAGAGTTGGATAACAAGTTTTTATCTC
1 -TGAAATTGAAGTAAAGCTGGATATCAAGTTTTTATCTC
*
40193280 TGAAATTGGAGTAA
1 TGAAATTGAAGTAA
40193294 GAGTAAGATG
Statistics
Matches: 69, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
35 1 0.01
36 5 0.07
37 9 0.13
38 39 0.57
39 9 0.13
40 5 0.07
41 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.34
Consensus pattern (38 bp):
TGAAATTGAAGTAAAGCTGGATATCAAGTTTTTATCTC
Found at i:40193339 original size:166 final size:166
Alignment explanation
Indices: 40192731--40193614 Score: 1096
Period size: 166 Copynumber: 5.4 Consensus size: 166
40192721 CAAATTTTTT
* * * *
40192731 TATCCTCTT-AAAGTT-ATAGTAAAGTTAGATAGCAAGTCTTTATCTCTCTGAAATTGAAGTAAG
1 TATCCTCTTGAAA-TTGA-AGTAGAGTTGGATAACAAGT-TTT-TATCTCTGAAATTGAAGTAAG
* * *
40192794 AGCT-AGATAAAGCATC-AGATCA-TTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAA
62 AG-TAAGATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAA
* * * *
40192856 GTCTTCATCTCTGAAATTGAAGTAAGAACAAGATCATTTCC
126 GTTTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATCTCC
* *
40192897 TATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATT---G--A-AGT-
1 TATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTTTTTATCTCTGAAATTGAAGTAAGAGTA
* *
40192955 A-A-G-AG---CAAGATCA-TTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAGCAAGTTTT
66 AGATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTTTT
40193013 TATCTCTCTGAAATTGAAGTAAGAGCTAGATAAAGCATCCAACATCATTTTCC
131 TA--TCTCTGAAATTGAAGTAAGAGC------AAG-AT----CATC----TCC
* * ** **
40193066 TATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGCCTTCGTCCCTCTGAAATTGAAGTAAGAG
1 TATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAG--TTTTTATCTCTGAAATTGAAGTAAGAG
40193131 TAAGATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTT
64 TAAGATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTT
40193196 TTTATCTCTGAAATTGAAGTAAGAGCAAGATCATCTCC
129 TTTATCTCTGAAATTGAAGTAAGAGCAAGATCATCTCC
*
40193234 TATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTTTTTATCTCTGAAATTGGAGTAAGAGTA
1 TATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTTTTTATCTCTGAAATTGAAGTAAGAGTA
40193299 AGATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTTTT
66 AGATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTTTT
40193364 TATCTCTGAAATTGAAGTAAGAGCAAGATCATCTCC
131 TATCTCTGAAATTGAAGTAAGAGCAAGATCATCTCC
*
40193400 TATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATT---G--A-AGT-
1 TATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTTTTTATCTCTGAAATTGAAGTAAGAGTA
*
40193458 AG--G-A--A-CAAGATCATTTT-CTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTTTT
66 AGATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTTTT
40193516 TATCTCTGAAATTGAAGTAAGAGCAAGATCATCTCC
131 TATCTCTGAAATTGAAGTAAGAGCAAGATCATCTCC
*
40193552 TATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGATTTTATCTCTGAAATTGAAGTAAGAG
1 TATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTTTTTATCTCTGAAATTGAAGTAAGAG
40193615 CAATATCATC
Statistics
Matches: 643, Mismatches: 33, Indels: 92
0.84 0.04 0.12
Matches are distributed among these distances:
151 1 0.00
152 178 0.28
153 11 0.02
154 24 0.04
155 1 0.00
156 2 0.00
157 4 0.01
158 4 0.01
159 3 0.00
160 6 0.01
161 4 0.01
163 1 0.00
164 11 0.02
165 5 0.01
166 205 0.32
167 4 0.01
168 37 0.06
169 37 0.06
171 11 0.02
172 4 0.01
174 1 0.00
176 3 0.00
177 6 0.01
178 1 0.00
179 1 0.00
180 1 0.00
181 2 0.00
183 22 0.03
184 7 0.01
185 46 0.07
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Consensus pattern (166 bp):
TATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTTTTTATCTCTGAAATTGAAGTAAGAGTA
AGATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTTTT
TATCTCTGAAATTGAAGTAAGAGCAAGATCATCTCC
Found at i:40193374 original size:38 final size:38
Alignment explanation
Indices: 40193332--40193727 Score: 225
Period size: 38 Copynumber: 10.4 Consensus size: 38
40193322 CCTATCCTCT
40193332 TGAAATTGAAGTAAAGCTGGATATCAAGTTTTTATCTC
1 TGAAATTGAAGTAAAGCTGGATATCAAGTTTTTATCTC
* * **
40193370 TGAAATTGAAGTAAGAGC--AAGATC-A-TCTCCTATCCTC
1 TGAAATTGAAGTAA-AGCTGGATATCAAGT-TTTTAT-CTC
* * * *
40193407 TTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTC
1 -TGAAATTGAAGTAAAGCTGGATATCAAGTTTTTATCTC
* *
40193446 TGAAATTGAAGTAGGAA-C--AAGATC-A-TTTTCTATCCTC
1 TGAAATTGAAGTA--AAGCTGGATATCAAGTTTT-TAT-CTC
40193483 TTGAAATTGAAGTAAAGCTGGATATCAAGTTTTTATCTC
1 -TGAAATTGAAGTAAAGCTGGATATCAAGTTTTTATCTC
* * **
40193522 TGAAATTGAAGTAAGAGC--AAGATC-A-TCTCCTATCCTC
1 TGAAATTGAAGTAA-AGCTGGATATCAAGT-TTTTAT-CTC
* * * *
40193559 TTGAAATTGAAGTAGAGTTGGATAACAAGATTTTATCTC
1 -TGAAATTGAAGTAAAGCTGGATATCAAGTTTTTATCTC
* **
40193598 TGAAATTGAAGTAAGAGC--AATATC-A-TCTCCTATCCTC
1 TGAAATTGAAGTAA-AGCTGGATATCAAGT-TTTTAT-CTC
* * * *
40193635 TTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTC
1 -TGAAATTGAAGTAAAGCTGGATATCAAGTTTTTATCTC
* * *
40193674 TAAAATTGAAGTAAAG-TAGGATAGCAAGTCTTTATCTCTC
1 TGAAATTGAAGTAAAGCT-GGATATCAAGT-TTT-TATCTC
*
40193714 TGAAATTAAAGTAA
1 TGAAATTGAAGTAA
40193728 GAGCAAGATG
Statistics
Matches: 268, Mismatches: 53, Indels: 72
0.68 0.13 0.18
Matches are distributed among these distances:
35 5 0.02
36 21 0.08
37 35 0.13
38 130 0.49
39 36 0.13
40 35 0.13
41 6 0.02
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.33
Consensus pattern (38 bp):
TGAAATTGAAGTAAAGCTGGATATCAAGTTTTTATCTC
Found at i:40194060 original size:17 final size:17
Alignment explanation
Indices: 40194022--40194065 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
40194012 TTTGAACAAG
40194022 ATTTAAATTTATGGTTAA
1 ATTTAAATTTAT-GTTAA
40194040 ATTTAAATTTAT-TTAAA
1 ATTTAAATTTATGTT-AA
40194057 ATTTAAATT
1 ATTTAAATT
40194066 AATAATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.08
17 11 0.44
18 12 0.48
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (17 bp):
ATTTAAATTTATGTTAA
Found at i:40194260 original size:20 final size:20
Alignment explanation
Indices: 40194237--40194283 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
40194227 GTCAAGAAGG
40194237 TCACAGCCAACTTGCTCTGC
1 TCACAGCCAACTTGCTCTGC
*
40194257 TCACCAG-TAACTTGCTCTGC
1 TCA-CAGCCAACTTGCTCTGC
40194277 -CACAGCC
1 TCACAGCC
40194284 GGTTGCCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
18 3 0.13
19 2 0.09
20 15 0.65
21 3 0.13
ACGTcount: A:0.21, C:0.40, G:0.15, T:0.23
Consensus pattern (20 bp):
TCACAGCCAACTTGCTCTGC
Found at i:40195977 original size:29 final size:29
Alignment explanation
Indices: 40195915--40195995 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 29
40195905 ATAGGTCCCT
* * *
40195915 AAACTATCAAAAAATTACATTTTGACCTCG
1 AAACT-TCCAAAAATTACATTTTGACCCCC
40195945 AAACTTCCAAAAATTACCATTTT-ACCCCC
1 AAACTTCCAAAAATTA-CATTTTGACCCCC
*
40195974 AAACTTTCC-AAAATTTCATTTT
1 AAAC-TTCCAAAAATTACATTTT
40195996 TAACCCTGAT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
28 6 0.13
29 24 0.53
30 15 0.33
ACGTcount: A:0.40, C:0.25, G:0.02, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTGACCCCC
Found at i:40196016 original size:59 final size:59
Alignment explanation
Indices: 40195951--40196289 Score: 425
Period size: 59 Copynumber: 5.8 Consensus size: 59
40195941 CTCGAAACTT
* * * *
40195951 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTTCATTTTTAACCCTGATTTCA
1 CCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * *
40196010 CCAAAAATTATCGTTTTACCCTTGAACTTTCTAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
40196069 -CACAAAATTACCATTTTACCCCCGAACTTTCTAAAATTCCATTTTTAACCCCGGTTTCA
1 CCA-AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* *
40196128 CC-AAAATTACCATTTTACCCTCGAACTTTCCTAAATTCCATTTTTAA-CCCGATTTCG
1 CCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * * *
40196185 CTAAAAATCACCATTTTACCCTCGAGCTTTCC-AAATCCCATTTTTAACCTCGATTTTCA
1 CCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGA-TTTCA
* * * * *
40196244 CCAAAAATTACCGTTTTACCCTAGAACCTTCCAAGATCCCATTTTT
1 CCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTT
40196290 TTAACCCTAA
Statistics
Matches: 243, Mismatches: 31, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
57 23 0.09
58 75 0.31
59 132 0.54
60 13 0.05
ACGTcount: A:0.30, C:0.29, G:0.05, T:0.36
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:40196055 original size:29 final size:29
Alignment explanation
Indices: 40195925--40196230 Score: 123
Period size: 29 Copynumber: 10.5 Consensus size: 29
40195915 AAACTATCAA
* * * *
40195925 AAAATTACATTTTGACCTCGAAAC-TTCCA
1 AAAATTCCATTTTTACCCCG-AACTTTCCT
*
40195954 AAAATTACCA-TTTTACCCCCAAACTTTCC-
1 AAAATT-CCATTTTTA-CCCCGAACTTTCCT
* * *
40195983 AAAATTTCATTTTTAACCCTG-A-TTTCACCA
1 AAAATTCCATTTTT-ACCCCGAACTTT--CCT
*
40196013 AAAATT--ATCGTTTTACCCTTGAACTTT-CT
1 AAAATTCCAT--TTTTACCC-CGAACTTTCCT
*
40196042 AAAATTCCATTTTTAACCCCG-A-TTTCACAC
1 AAAATTCCATTTTT-ACCCCGAACTTTC-C-T
40196072 AAAATTACCA-TTTTACCCCCGAACTTT-CT
1 AAAATT-CCATTTTTA-CCCCGAACTTTCCT
* *
40196101 AAAATTCCATTTTTAACCCCG--GTTTCACC
1 AAAATTCCATTTTT-ACCCCGAACTTTC-CT
40196130 AAAATTACCA-TTTTACCCTCGAACTTTCCT
1 AAAATT-CCATTTTTACCC-CGAACTTTCCT
*
40196160 -AAATTCCATTTTTAACCCG-A-TTTCGCT
1 AAAATTCCATTTTTACCCCGAACTTTC-CT
* *
40196187 AAAAATCACCA-TTTTACCCTCGAGCTTTCC-
1 -AAAAT-TCCATTTTTACCC-CGAACTTTCCT
*
40196217 -AAATCCCATTTTTA
1 AAAATTCCATTTTTA
40196231 ACCTCGATTT
Statistics
Matches: 217, Mismatches: 20, Indels: 81
0.68 0.06 0.25
Matches are distributed among these distances:
26 4 0.02
27 15 0.07
28 27 0.12
29 97 0.45
30 52 0.24
31 12 0.06
32 10 0.05
ACGTcount: A:0.31, C:0.28, G:0.05, T:0.36
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCCGAACTTTCCT
Found at i:40196251 original size:117 final size:115
Alignment explanation
Indices: 40195952--40196289 Score: 423
Period size: 117 Copynumber: 2.9 Consensus size: 115
40195942 TCGAAACTTC
* *
40195952 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTTCATTTTTAACCCTGATTTCACCAAAAA
1 CAAAAATTACCATTTTACCCCCGAACTTTCC-AAATTCCATTTTTAACCC-GATTTCACCAAAAA
* *
40196017 TTATCGTTTTACCCTTGAACTTT-CTAAAATTCCATTTTTAACCCCGATTTCA
64 TTACCGTTTTACCCTAGAACTTTCCT-AAATTCCATTTTTAACCCCGATTTCA
* *
40196069 CACAAAATTACCATTTTACCCCCGAACTTTCTAAAATTCCATTTTTAACCCCGGTTTCACC-AAA
1 CA-AAAATTACCATTTTACCCCCGAACTTTC-CAAATTCCATTTTTAA-CCCGATTTCACCAAAA
* * *
40196133 ATTACCATTTTACCCTCGAACTTTCCTAAATTCCATTTTTAA-CCCGATTTCG
63 ATTACCGTTTTACCCTAGAACTTTCCTAAATTCCATTTTTAACCCCGATTTCA
* * * *
40196185 CTAAAAATCACCATTTTACCCTCGAGCTTTCCAAATCCCATTTTTAACCTCGATTTTCACCAAAA
1 C-AAAAATTACCATTTTACCCCCGAACTTTCCAAATTCCATTTTTAACC-CGA-TTTCACCAAAA
* *
40196250 ATTACCGTTTTACCCTAGAACCTTCC-AAGATCCCATTTTT
63 ATTACCGTTTTACCCTAGAACTTTCCTAA-ATTCCATTTTT
40196290 TTAACCCTAA
Statistics
Matches: 194, Mismatches: 18, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
114 2 0.01
115 16 0.08
116 44 0.23
117 78 0.40
118 51 0.26
119 3 0.02
ACGTcount: A:0.30, C:0.29, G:0.05, T:0.36
Consensus pattern (115 bp):
CAAAAATTACCATTTTACCCCCGAACTTTCCAAATTCCATTTTTAACCCGATTTCACCAAAAATT
ACCGTTTTACCCTAGAACTTTCCTAAATTCCATTTTTAACCCCGATTTCA
Found at i:40198536 original size:394 final size:394
Alignment explanation
Indices: 40197556--40198819 Score: 2390
Period size: 392 Copynumber: 3.2 Consensus size: 394
40197546 GGTTTCGACA
*
40197556 ACTAATATCAACCAAGACAATTTTAGAGACCAAGATAAAGTTACCAAATTTAGATATAAGTTTTG
1 ACTAATATCAACCAAGACGATTTTAGAGACCAAGATAAAGTTACCAAATTTAGATATAAGTTTTG
40197621 CTTTTATATTATTTGTTTGATGATTTCAAATGTTTCAAGTGTGATAAATTCCTTAAGTTGCCCCT
66 CTTTTATATTATTTGTTTGATGATTTCAAATGTTTCAAGTGTGATAAATTCCTTAAGTTGCCCCT
40197686 TACTCCCCTTAAGTATTGAATAGTGATGAATGTTCCAATAAAACCTTTGAGTCAAGATTTTTTAT
131 TACTCCCCTTAAGTATTGAATAGTGATGAATGTTCCAATAAAACCTTTGAGTCAAGATTTTTTAT
* * *
40197751 CTTTATCGTTGTAATAGGGGTTTTTAACGTGATTTGTGGCGACTTTTTTTGTTGTTGTCAAATAG
196 CTCTATCGTTGTAATAGGGGTTTTTAACGTGATTTGTGGCGACTTTTTTTGTTGTTGTTAAAGAG
40197816 TCTGTATCGAACTCTTGTTTCTTAATCCACTTTGAAAATGTTCTGACAAAAAATAAAATTTCAGT
261 TCTGTATCGAACTCTTGTTTCTTAATCCACTTTGAAAATGTTCTGACAAAAAATAAAATTTCAGT
40197881 GTCATATTATCTCATTTTAATGGAATTCAAATTTAAAGACCAAATTT--AAAAATTATCGAACCC
326 GTCATATTATCTCATTTTAATGGAATTCAAATTTAAAGACCAAATTTAAAAAAATTATCGAACCC
40197944 CAAT
391 CAAT
40197948 ACTAATATCAACCAAGACGATTTTAGAGACCAAGATAAAGTTACCAAATTTAGATATAAGTTTTG
1 ACTAATATCAACCAAGACGATTTTAGAGACCAAGATAAAGTTACCAAATTTAGATATAAGTTTTG
40198013 CTTTTATATTATTTGTTTGATGATTTCAAATGTTTCAAGTGTGATAAATTCCTTAAGTTGCCCCT
66 CTTTTATATTATTTGTTTGATGATTTCAAATGTTTCAAGTGTGATAAATTCCTTAAGTTGCCCCT
40198078 TACTCCCCTTAAGTATTGAATAGTGATGAATGTTCCAATAAAACCTTTGAGTCAAGATTTTTTAT
131 TACTCCCCTTAAGTATTGAATAGTGATGAATGTTCCAATAAAACCTTTGAGTCAAGATTTTTTAT
40198143 CTCTATCGTTGTAATAGGGGTTTTTAACGTGATTTGTGGCGACTTTTTTTGTTGTTGTTAAAGAG
196 CTCTATCGTTGTAATAGGGGTTTTTAACGTGATTTGTGGCGACTTTTTTTGTTGTTGTTAAAGAG
40198208 TCTGTATCGAACTCTTGTTTCTTAATCCACTTTGAAAATGTTCTGACAAAAAATAAAATTTCAGT
261 TCTGTATCGAACTCTTGTTTCTTAATCCACTTTGAAAATGTTCTGACAAAAAATAAAATTTCAGT
40198273 GTCATATTATCTCATTTTAATGGAATTCAAATTTAAAGACCAAATTTAAAAAAATTATCGAACCC
326 GTCATATTATCTCATTTTAATGGAATTCAAATTTAAAGACCAAATTTAAAAAAATTATCGAACCC
40198338 CAAT
391 CAAT
*
40198342 ACTAATATCAACCAAGACGATTTTAGAGACCAAAATAAAGTTACCAAATTTAGATATAAGTTTTG
1 ACTAATATCAACCAAGACGATTTTAGAGACCAAGATAAAGTTACCAAATTTAGATATAAGTTTTG
*
40198407 CTTTTATATTATTTGTTTGATGATTTCAAATGTTTCAAGTGTGATAAATTCCTTAAGTTGTCCCT
66 CTTTTATATTATTTGTTTGATGATTTCAAATGTTTCAAGTGTGATAAATTCCTTAAGTTGCCCCT
40198472 TACTCCCCTTAAGTATTGAATAGTGATGAATGTTCCAATAAAACCTTTGAGTCAAGATTTTTTAT
131 TACTCCCCTTAAGTATTGAATAGTGATGAATGTTCCAATAAAACCTTTGAGTCAAGATTTTTTAT
40198537 CTCTATCGTTGTAATAGGGGTTTTTAACGTGATTTGTGGCGACTTTTTTTGTTGTTGTTAAAGAG
196 CTCTATCGTTGTAATAGGGGTTTTTAACGTGATTTGTGGCGACTTTTTTTGTTGTTGTTAAAGAG
* *
40198602 TCTATATCGAACTCTTGTTTCTTAATCCACTTTG-AAATGTTCTGACAAAAACTAAAATTTCAGT
261 TCTGTATCGAACTCTTGTTTCTTAATCCACTTTGAAAATGTTCTGACAAAAAATAAAATTTCAGT
* * *
40198666 GTCATATTATCTCATTTTAATGAAATTAAAATTTAAAGATCAAATTTAAAAAAATTATCGAACCC
326 GTCATATTATCTCATTTTAATGGAATTCAAATTTAAAGACCAAATTTAAAAAAATTATCGAACCC
40198731 CAAT
391 CAAT
* *
40198735 ACTAATATCAACCAAGATGGTTTTAGAGACCAAGATAAAGTTACCAAATTTAGATATAAGTTTTG
1 ACTAATATCAACCAAGACGATTTTAGAGACCAAGATAAAGTTACCAAATTTAGATATAAGTTTTG
40198800 CTTTTATATTATTTGTTTGA
66 CTTTTATATTATTTGTTTGA
40198820 CAAAAAATAA
Statistics
Matches: 856, Mismatches: 14, Indels: 3
0.98 0.02 0.00
Matches are distributed among these distances:
392 368 0.43
393 177 0.21
394 311 0.36
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (394 bp):
ACTAATATCAACCAAGACGATTTTAGAGACCAAGATAAAGTTACCAAATTTAGATATAAGTTTTG
CTTTTATATTATTTGTTTGATGATTTCAAATGTTTCAAGTGTGATAAATTCCTTAAGTTGCCCCT
TACTCCCCTTAAGTATTGAATAGTGATGAATGTTCCAATAAAACCTTTGAGTCAAGATTTTTTAT
CTCTATCGTTGTAATAGGGGTTTTTAACGTGATTTGTGGCGACTTTTTTTGTTGTTGTTAAAGAG
TCTGTATCGAACTCTTGTTTCTTAATCCACTTTGAAAATGTTCTGACAAAAAATAAAATTTCAGT
GTCATATTATCTCATTTTAATGGAATTCAAATTTAAAGACCAAATTTAAAAAAATTATCGAACCC
CAAT
Found at i:40198934 original size:173 final size:173
Alignment explanation
Indices: 40198639--40198993 Score: 620
Period size: 173 Copynumber: 2.0 Consensus size: 173
40198629 CACTTTGAAA
* *
40198639 TGTTCTGACAAAAACTAAAATTTCAGTGTCATATTATCTCATTTTAATGAAATTAAAATTTAAAG
1 TGTT-TGACAAAAAATAAAACTTCAGTGTCATATTATCTCATTTTAATGAAATTAAAATTTAAAG
***
40198704 ATCAAATTTAAAAAAATTATCGAACCCCAATACTAATATCAACCAAGATGGTTTTAGAGACCAAG
65 ATCAAATTTAAAAAAATTATCGAACCCCAATACTAATATCAACCAAGACAATTTTAGAGACCAAG
40198769 ATAAAGTTACCAAATTTAGATATAAGTTTTGCTTTTATATTATT
130 ATAAAGTTACCAAATTTAGATATAAGTTTTGCTTTTATATTATT
* *
40198813 TGTTTGACAAAAAATAAAACTTCAGTGTCATATTATCTCATTTTAATGGAATTCAAATTTAAAGA
1 TGTTTGACAAAAAATAAAACTTCAGTGTCATATTATCTCATTTTAATGAAATTAAAATTTAAAGA
* *
40198878 TTAAATTTAAAAAAATTATCGAACCCCAATACTAATATCAAGCAAGACAATTTTAGAGACCAAGA
66 TCAAATTTAAAAAAATTATCGAACCCCAATACTAATATCAACCAAGACAATTTTAGAGACCAAGA
40198943 TAAAGTTACCAAATTTAGATATAAGTTTTGCTTTTATATTATT
131 TAAAGTTACCAAATTTAGATATAAGTTTTGCTTTTATATTATT
40198986 TGTTTGAC
1 TGTTTGAC
40198994 GATTTCAAAT
Statistics
Matches: 172, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
173 168 0.98
174 4 0.02
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (173 bp):
TGTTTGACAAAAAATAAAACTTCAGTGTCATATTATCTCATTTTAATGAAATTAAAATTTAAAGA
TCAAATTTAAAAAAATTATCGAACCCCAATACTAATATCAACCAAGACAATTTTAGAGACCAAGA
TAAAGTTACCAAATTTAGATATAAGTTTTGCTTTTATATTATT
Found at i:40199762 original size:24 final size:24
Alignment explanation
Indices: 40199735--40199799 Score: 67
Period size: 28 Copynumber: 2.5 Consensus size: 24
40199725 TACAATAACA
*
40199735 AATGATATTTAAATAATTTATTAT
1 AATGATATTTAAATAATTTAATAT
*
40199759 AATGATACTTATGTAAATTATTTAATAT
1 AATGATA--T-T-TAAATAATTTAATAT
*
40199787 AATGATACTTAAA
1 AATGATATTTAAA
40199800 ATATAAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
24 11 0.32
25 1 0.03
26 1 0.03
27 1 0.03
28 20 0.59
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (24 bp):
AATGATATTTAAATAATTTAATAT
Found at i:40199776 original size:28 final size:28
Alignment explanation
Indices: 40199744--40199797 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
40199734 AAATGATATT
*
40199744 TAAATAATTTATTATAATGATACTTATG
1 TAAATAATTTAATATAATGATACTTATG
*
40199772 TAAATTATTTAATATAATGATACTTA
1 TAAATAATTTAATATAATGATACTTA
40199798 AAATATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (28 bp):
TAAATAATTTAATATAATGATACTTATG
Found at i:40206948 original size:19 final size:19
Alignment explanation
Indices: 40206919--40206955 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
40206909 GTAGACAATA
40206919 TAAAAAATATTT-AAATGC
1 TAAAAAATATTTCAAATGC
40206937 TAAAATAATATTTCAAATG
1 TAAAA-AATATTTCAAATG
40206956 TTATTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 7 0.41
20 5 0.29
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (19 bp):
TAAAAAATATTTCAAATGC
Found at i:40207942 original size:12 final size:12
Alignment explanation
Indices: 40207910--40207943 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
40207900 TAAATCGCTG
*
40207910 CTAACAACCTAC
1 CTAACAACTTAC
40207922 CTAACAACTTAC
1 CTAACAACTTAC
40207934 CTAACAACTT
1 CTAACAACTT
40207944 TCCATTCTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.41, C:0.35, G:0.00, T:0.24
Consensus pattern (12 bp):
CTAACAACTTAC
Found at i:40217195 original size:29 final size:29
Alignment explanation
Indices: 40217153--40217322 Score: 146
Period size: 29 Copynumber: 5.8 Consensus size: 29
40217143 AAAATTATGT
*
40217153 TTTGACCCTTAAACTATCTAAAAATTTAGA
1 TTTGACCC-TAAACTTTCTAAAAATTTAGA
* * *
40217183 TTTGACCCTAAACTTT-TCATAAATTCAAA
1 TTTGACCCTAAACTTTCT-AAAAATTTAGA
* * *
40217212 TTTGACCCTAAACTTTCCAAAAATTAAGT
1 TTTGACCCTAAACTTTCTAAAAATTTAGA
* * *
40217241 TTTAACCCCCAAACTTTC-AAAAATTTGGA
1 TTTGA-CCCTAAACTTTCTAAAAATTTAGA
* * *
40217270 TTTAACCCTCGAACTTTCTAAAAATTTAAA
1 TTTGACCCT-AAACTTTCTAAAAATTTAGA
* *
40217300 TTTGGCCCCTAAACTTTTTAAAA
1 TTT-GACCCTAAACTTTCTAAAA
40217323 TTTCATTTTT
Statistics
Matches: 112, Mismatches: 22, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
28 4 0.04
29 62 0.55
30 42 0.38
31 4 0.04
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.36
Consensus pattern (29 bp):
TTTGACCCTAAACTTTCTAAAAATTTAGA
Found at i:40217314 original size:59 final size:57
Alignment explanation
Indices: 40217157--40217325 Score: 142
Period size: 59 Copynumber: 2.9 Consensus size: 57
40217147 TTATGTTTTG
* * * * * *
40217157 ACCCTTAAACTATCTAAAAATTTAGATTTGACCCTAAACTTTTCATAAATTCAAATTTG
1 ACCC-TAAACTTTCTAAAAATTTAAATTTGCCCCTAAAC-TTTCAAAAATTTAAATTTA
* * * * **
40217216 ACCCTAAACTTTCCAAAAA-TTAAGTTTTAACCCCCAAACTTTCAAAAATTTGGATTTA
1 ACCCTAAACTTTCTAAAAATTTAA-ATTT-GCCCCTAAACTTTCAAAAATTTAAATTTA
* **
40217274 ACCCTCGAACTTTCTAAAAATTTAAATTTGGCCCCTAAACTTTTTAAAATTT
1 ACCCT-AAACTTTCTAAAAATTTAAATTT-GCCCCTAAACTTTCAAAAATTT
40217326 CATTTTTGAC
Statistics
Matches: 86, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
57 3 0.03
58 35 0.41
59 44 0.51
60 4 0.05
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (57 bp):
ACCCTAAACTTTCTAAAAATTTAAATTTGCCCCTAAACTTTCAAAAATTTAAATTTA
Found at i:40221571 original size:5 final size:5
Alignment explanation
Indices: 40221561--40221606 Score: 56
Period size: 5 Copynumber: 8.8 Consensus size: 5
40221551 GCAGATTAAA
* *
40221561 AAAAG AAAAG AAAAG AAAAG AAGAAG TAAAGG AGAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AA-AAG -AAAAG AAAAG AAAAG AAAA
40221607 AGGAAGAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
5 28 0.80
6 5 0.14
7 2 0.06
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:40221591 original size:11 final size:11
Alignment explanation
Indices: 40221563--40221604 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
40221553 AGATTAAAAA
40221563 AAGAAAAGAA-
1 AAGAAAAGAAG
40221573 AAGAAAAGAAG
1 AAGAAAAGAAG
* *
40221584 AAGTAAAGGAG
1 AAGAAAAGAAG
40221595 AAGAAAAGAA
1 AAGAAAAGAA
40221605 AAAGGAAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
10 10 0.37
11 17 0.63
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.02
Consensus pattern (11 bp):
AAGAAAAGAAG
Found at i:40221614 original size:32 final size:31
Alignment explanation
Indices: 40221563--40221622 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
40221553 AGATTAAAAA
*
40221563 AAGAAAAGAAAAGAAAAGAAGAAGTAAAGGAG
1 AAGAAAAGAAAAGAAAAGAAAAAG-AAAGGAG
*
40221595 AAGAAAAGAAAA-AGGAAGAAAAAGAAAG
1 AAGAAAAGAAAAGA-AAAGAAAAAGAAAG
40221623 TCAAGATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 5 0.20
32 20 0.80
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.02
Consensus pattern (31 bp):
AAGAAAAGAAAAGAAAAGAAAAAGAAAGGAG
Found at i:40222997 original size:104 final size:104
Alignment explanation
Indices: 40222809--40223001 Score: 314
Period size: 104 Copynumber: 1.9 Consensus size: 104
40222799 AATGTTTGTC
*
40222809 ATTTTTAATCTTTTTATTCATGCGAGCTTTGCCTTCAATAAAATTCAATTTTATCCACCTTACAA
1 ATTTTTAATCTTTTTATTCACGCGAGCTTTGCCTTCAATAAAATTCAATTTTATCCACCTTACAA
*
40222874 CCTTGTTCAAGCACATTTGCATTAGTTAGTAGACTAATG
66 CCCTGTTCAAGCACATTTGCATTAGTTAGTAGACTAATG
* * *
40222913 ATTTTTAATCTTTTTATTCACGTGAGCTTTGCCTTCAATAAAATTTAATTTTATTCACCTTACAA
1 ATTTTTAATCTTTTTATTCACGCGAGCTTTGCCTTCAATAAAATTCAATTTTATCCACCTTACAA
* **
40222978 CCCTGTTCACGCATTTTTGCATTA
66 CCCTGTTCAAGCACATTTGCATTA
40223002 AAATGACGGT
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
104 81 1.00
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.44
Consensus pattern (104 bp):
ATTTTTAATCTTTTTATTCACGCGAGCTTTGCCTTCAATAAAATTCAATTTTATCCACCTTACAA
CCCTGTTCAAGCACATTTGCATTAGTTAGTAGACTAATG
Found at i:40223710 original size:49 final size:49
Alignment explanation
Indices: 40223324--40223713 Score: 207
Period size: 49 Copynumber: 7.9 Consensus size: 49
40223314 CAGGTTTAAA
* * ** * *
40223324 GGAAAAGATTGAAGCCGCAATGGCAAATCTAATACCCTGGAGATATGGAG
1 GGAAAAG-TTGAAGCCGCAACGGCGAATCTTGTACCTTAGAGATATGGAG
* * * * * *
40223374 GGAAAGGTTAAAGCCACAATGGCGAATCTTGTACCTTAGAGACAT-TA-
1 GGAAAAGTTGAAGCCGCAACGGCGAATCTTGTACCTTAGAGATATGGAG
** * * * * * *
40223421 TTAGAAAGATTGAAGTCGTAACGACGAATCTTGTACCATGGAGATATGGAA
1 GGA-AAAG-TTGAAGCCGCAACGGCGAATCTTGTACCTTAGAGATATGGAG
* * * ** * **
40223472 GGAAATGTTGAGGTCATAACGACGAA-CTTTGTACCTTAGAGACGT-GATG
1 GGAAAAGTTGAAGCCGCAACGGCGAATC-TTGTACCTTAGAGATATGGA-G
* * * * * * * *
40223521 GGAAAAATTGAAGCTGCAACAGTGAATCTTGTATCATGGAGATATGAAG
1 GGAAAAGTTGAAGCCGCAACGGCGAATCTTGTACCTTAGAGATATGGAG
* * * * * * * *
40223570 GGAAAAATTAAAGTCACAATGGCGAACCTTATACCTTAGAGATGT-GA-
1 GGAAAAGTTGAAGCCGCAACGGCGAATCTTGTACCTTAGAGATATGGAG
* * * * * *
40223617 TGAGAAAGATTGAAGTCGCAACGACGAATCTTGTATCATGGAGATATGGAG
1 GGA-AAAG-TTGAAGCCGCAACGGCGAATCTTGTACCTTAGAGATATGGAG
* *
40223668 GGAAAAGTTGAAGCCGCAACGGCGAACCTTATACCTTAGAGATATG
1 GGAAAAGTTGAAGCCGCAACGGCGAATCTTGTACCTTAGAGATATG
40223714 AAACGAAAGA
Statistics
Matches: 245, Mismatches: 83, Indels: 25
0.69 0.24 0.07
Matches are distributed among these distances:
47 3 0.01
48 11 0.04
49 210 0.86
50 18 0.07
51 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.23
Consensus pattern (49 bp):
GGAAAAGTTGAAGCCGCAACGGCGAATCTTGTACCTTAGAGATATGGAG
Found at i:40223710 original size:98 final size:98
Alignment explanation
Indices: 40223361--40223727 Score: 407
Period size: 98 Copynumber: 3.7 Consensus size: 98
40223351 TCTAATACCC
* * * * * *
40223361 TGGAGATATGGAGGGAAAGGTTAAAGCCACAATGGCGAATCTTGTACCTTAGAGACATTATTAGA
1 TGGAGATATGGAGGGAAAAGTTAAAGCCACAACGGCGAACCTTATACCTTAGAGACATGATGAGA
* *
40223426 AAGATTGAAGTCGTAACGACGAATCTTGTACCA
66 AAGATTGAAGTCGCAACGACGAATCTTGTATCA
* * * * * * * * * * *
40223459 TGGAGATATGGAAGGAAATGTTGAGGTCATAACGACGAACTTTGTACCTTAGAGACGTGATGGGA
1 TGGAGATATGGAGGGAAAAGTTAAAGCCACAACGGCGAACCTTATACCTTAGAGACATGATGAGA
* *
40223524 AAAATTGAAG-CTGCAAC-AGTGAATCTTGTATCA
66 AAGATTGAAGTC-GCAACGA-CGAATCTTGTATCA
* * * * **
40223557 TGGAGATATGAAGGGAAAAATTAAAGTCACAATGGCGAACCTTATACCTTAGAGATGTGATGAGA
1 TGGAGATATGGAGGGAAAAGTTAAAGCCACAACGGCGAACCTTATACCTTAGAGACATGATGAGA
40223622 AAGATTGAAGTCGCAACGACGAATCTTGTATCA
66 AAGATTGAAGTCGCAACGACGAATCTTGTATCA
* * * *
40223655 TGGAGATATGGAGGGAAAAGTTGAAGCCGCAACGGCGAACCTTATACCTTAGAGATATGA-AACG
1 TGGAGATATGGAGGGAAAAGTTAAAGCCACAACGGCGAACCTTATACCTTAGAGACATGATGA-G
40223719 AAAGATTGA
65 AAAGATTGA
40223728 GGCAGCAACG
Statistics
Matches: 223, Mismatches: 41, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
97 3 0.01
98 218 0.98
99 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.23
Consensus pattern (98 bp):
TGGAGATATGGAGGGAAAAGTTAAAGCCACAACGGCGAACCTTATACCTTAGAGACATGATGAGA
AAGATTGAAGTCGCAACGACGAATCTTGTATCA
Found at i:40223736 original size:49 final size:47
Alignment explanation
Indices: 40223590--40223738 Score: 120
Period size: 49 Copynumber: 3.0 Consensus size: 47
40223580 AAGTCACAAT
* * *
40223590 GGCGAACCTTATACCTTAGAGATGTGATGAGAAAGATTGAAGTCGCAAC
1 GGCGAACCTTATACCTTAGAGATATGA-AAGAAAGATTG-AGGCGCAAC
* * * * * * ** *
40223639 GACGAATCTTGTATCATGGAGATATGGAGGGAAA-AGTTGAAGCCGCAAC
1 GGCGAACCTTATACCTTAGAGATAT-GAAAGAAAGA-TTG-AGGCGCAAC
40223688 GGCGAACCTTATACCTTAGAGATATGAAACGAAAGATTGAGGCAGCAAC
1 GGCGAACCTTATACCTTAGAGATATGAAA-GAAAGATTGAGGC-GCAAC
40223737 GG
1 GG
40223739 TGAATCTCAT
Statistics
Matches: 77, Mismatches: 18, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
48 6 0.08
49 68 0.88
50 3 0.04
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.20
Consensus pattern (47 bp):
GGCGAACCTTATACCTTAGAGATATGAAAGAAAGATTGAGGCGCAAC
Found at i:40223744 original size:196 final size:196
Alignment explanation
Indices: 40223361--40223745 Score: 500
Period size: 196 Copynumber: 2.0 Consensus size: 196
40223351 TCTAATACCC
* ** * * * *
40223361 TGGAGATATGGAGGGAAAGGTTAAAGCCACAATGGCGAATCTTGTACCTTAGAGACATTATTAGA
1 TGGAGATATGAAGGGAAAAATTAAAGCCACAATGGCGAACCTTATACCTTAGAGACATGATGAGA
* * * * *
40223426 AAGATTGAAGTCGTAACGACGAATCTTGTACCATGGAGATATGGAAGGAAATGTTGAGGTCATAA
66 AAGATTGAAGTCGCAACGACGAATCTTGTACCATGGAGATATGGAAGGAAAAGTTGAAGCCACAA
* * * *** *
40223491 CGACGAACTTTGTACCTTAGAGACGTGATGGGAAAAATTGAAGCTGCAACAGTGAATCTTGTATC
131 CGACGAACCTTATACCTTAGAGACATGAAACGAAAAATTGAAGCAGCAACAGTGAATCTTGTATC
40223556 A
196 A
* **
40223557 TGGAGATATGAAGGGAAAAATTAAAGTCACAATGGCGAACCTTATACCTTAGAGATGTGATGAGA
1 TGGAGATATGAAGGGAAAAATTAAAGCCACAATGGCGAACCTTATACCTTAGAGACATGATGAGA
* * *
40223622 AAGATTGAAGTCGCAACGACGAATCTTGTATCATGGAGATATGGAGGGAAAAGTTGAAGCCGCAA
66 AAGATTGAAGTCGCAACGACGAATCTTGTACCATGGAGATATGGAAGGAAAAGTTGAAGCCACAA
* * * * *
40223687 CGGCGAACCTTATACCTTAGAGATATGAAACGAAAGATTGAGGCAGCAACGGTGAATCT
131 CGACGAACCTTATACCTTAGAGACATGAAACGAAAAATTGAAGCAGCAACAGTGAATCT
40223746 CATACCCTGA
Statistics
Matches: 159, Mismatches: 30, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
196 159 1.00
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.23
Consensus pattern (196 bp):
TGGAGATATGAAGGGAAAAATTAAAGCCACAATGGCGAACCTTATACCTTAGAGACATGATGAGA
AAGATTGAAGTCGCAACGACGAATCTTGTACCATGGAGATATGGAAGGAAAAGTTGAAGCCACAA
CGACGAACCTTATACCTTAGAGACATGAAACGAAAAATTGAAGCAGCAACAGTGAATCTTGTATC
A
Found at i:40224074 original size:78 final size:78
Alignment explanation
Indices: 40223979--40225069 Score: 1244
Period size: 78 Copynumber: 13.9 Consensus size: 78
40223969 AGGTACCATA
* * * *
40223979 CAATCTCTTACCCCGATCATGGGACAGATTGAAGCATCCAATCTATTATCTTAATCAGAGGGCAG
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAG
*
40224044 ATTAAAGACAATC
66 ATTGAAGACAATC
* *
40224057 CAATCTTTTACCCCGATCATGGGGCAGATTAAAGCATCCAATCTTTTACCCTAATCAGAGGGCAG
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAG
* *
40224122 ATTGAAGATAATT
66 ATTGAAGACAATC
* ** * * * *
40224135 CAATCTCTTACCTCGATCATGAAGCAAATTG-AGACATCCAATATTTTACCTTAATCAGAAGGCA
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAG-CATCCAATCTTTTACCCTAATCAGAGGGCA
*
40224199 GATTAAAGACAATC
65 GATTGAAGACAATC
* * *
40224213 CAATCTCTTACCCTGATCATGTGACAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAG
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAG
40224278 ATTGAAGACAATC
66 ATTGAAGACAATC
* * ** * ** * * *
40224291 AAATCTTTTACCTTGATCATGAGAAAGATTGAAGTATCTAATCTTTTACCCTAATCAGAGGGTAG
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAG
*
40224356 ATTGAAGATACA-C
66 ATTGAAGACA-ATC
** * * *
40224369 CAATCTCTTACCTTGATCATGGGGCGGATTGAAGCATCCGATCTTTTACCCTAATCAGAAGGCAG
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAG
*
40224434 ATAGAAGACACA-C
66 ATTGAAGACA-ATC
* *
40224447 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCGATCTTTTACCCTAATCAGAGGACAG
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAG
*
40224512 ATTAAAGACACA-C
66 ATTGAAGACA-ATC
* * ** ** * *
40224525 CAATCTCTTACCCCGATCATGGGGTAAATAAAAGCATCTGATCTTTTACCCTAATCAGAAGGCAA
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAG
*
40224590 ATTGAAGATATCATC
66 ATTGAAGACA--ATC
* * * * * *
40224605 CAATCTCTTACCCCGATCATAGGGCAGATTGAAGCATCTAATCTCTTACCTTAATCAGAAGACAG
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAG
*
40224670 ATTGAAGATAATC
66 ATTGAAGACAATC
* * * * * * *
40224683 CAATCTCTTAGCTCGATCATGGGGCAGATTGAAACATCTAATCTCTTACCTTAATCAGAAGGCAG
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAG
*
40224748 ATTGAAGATAATC
66 ATTGAAGACAATC
* * * * * * *
40224761 CAATCTCTTACCCTGATCATAGGGTAGATTGAAGCATCCAATCTCTTACCTTAATCAGAAGGAAG
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAG
* *
40224826 ATTGAAAAAAATC
66 ATTGAAGACAATC
* * * *
40224839 CAATCTCTTACCCCGATCATGGGACAGATTGAAGCATCAAATCGTTTACCCTAATCAAAGGGCAG
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAG
*
40224904 ATTAAAGACACAT-
66 ATTGAAGACA-ATC
* * * *
40224917 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCC-ATTTTTTACCCTAATTAGAGGGAAA
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAG
40224981 ATTGAAGACACA-C
66 ATTGAAGACA-ATC
* *
40224994 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGATACCATCCAATCTTTTACCAC-GATCATAG
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAG----CATCCAATCTTTTACC-CTAATCAGAG
*
40225058 GGCAAATTGAAG
61 GGCAGATTGAAG
40225070 CTACCAGAAG
Statistics
Matches: 877, Mismatches: 123, Indels: 22
0.86 0.12 0.02
Matches are distributed among these distances:
77 66 0.08
78 707 0.81
79 7 0.01
80 66 0.08
81 5 0.01
82 25 0.03
83 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (78 bp):
CAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAG
ATTGAAGACAATC
Found at i:40225075 original size:42 final size:42
Alignment explanation
Indices: 40224585--40225075 Score: 183
Period size: 40 Copynumber: 12.4 Consensus size: 42
40224575 CTAATCAGAA
* *
40224585 GGCAAATTGAAGATATCATCCAATCTCTTACCCCGATCATAG
1 GGCAAATTGAAGATACCATCCAATCTCTTACCACGATCATAG
* * *** * *
40224627 GGCAGATTGAAG----CATCTAATCTCTTACCTTAATCAGAA
1 GGCAAATTGAAGATACCATCCAATCTCTTACCACGATCATAG
* * * * *
40224665 GACAGATTGAAGATA--ATCCAATCTCTTAGCTCGATCATGG
1 GGCAAATTGAAGATACCATCCAATCTCTTACCACGATCATAG
* * *** * *
40224705 GGCAGATTG-A-A-A-CATCTAATCTCTTACCTTAATCAGAA
1 GGCAAATTGAAGATACCATCCAATCTCTTACCACGATCATAG
*
40224743 GGCAGATTGAAGATA--ATCCAATCTCTTACC-CTGATCATAG
1 GGCAAATTGAAGATACCATCCAATCTCTTACCAC-GATCATAG
* * *** * *
40224783 GGTAGATTGAAG----CATCCAATCTCTTACCTTAATCAGAA
1 GGCAAATTGAAGATACCATCCAATCTCTTACCACGATCATAG
** *
40224821 GG-AAGATTGAA-A-AAAATCCAATCTCTTACCCCGATCAT-G
1 GGCAA-ATTGAAGATACCATCCAATCTCTTACCACGATCATAG
* * * *
40224860 GGACAGATTGAAG----CATCAAATCGT-TTACC-CTAATCAAAG
1 GG-CAAATTGAAGATACCATCCAATC-TCTTACCAC-GATCATAG
* * * * *
40224899 GGCAGATTAAAGACA-CAT-CAATCTCTTACCCCGATCATGG
1 GGCAAATTGAAGATACCATCCAATCTCTTACCACGATCATAG
* * * * * *
40224939 GGCAGATTGAAG----CATCC-ATTTTTTACC-CTAATTAGAG
1 GGCAAATTGAAGATACCATCCAATCTCTTACCAC-GATCATAG
* * * *
40224976 GGAAAATTGAAGACA-CA-CCAATCTCTTACCCCGATCATGG
1 GGCAAATTGAAGATACCATCCAATCTCTTACCACGATCATAG
* *
40225016 GGCAGATTGAAGATACCATCCAATCTTTTACCACGATCATAG
1 GGCAAATTGAAGATACCATCCAATCTCTTACCACGATCATAG
*
40225058 GGCAAATTGAAGCTACCA
1 GGCAAATTGAAGATACCA
40225076 GAAGTGAATC
Statistics
Matches: 342, Mismatches: 73, Indels: 68
0.71 0.15 0.14
Matches are distributed among these distances:
36 1 0.00
37 28 0.08
38 113 0.33
39 11 0.03
40 133 0.39
41 9 0.03
42 47 0.14
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (42 bp):
GGCAAATTGAAGATACCATCCAATCTCTTACCACGATCATAG
Found at i:40226835 original size:29 final size:30
Alignment explanation
Indices: 40226772--40226840 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
40226762 AAAAATTATG
*
40226772 TTTTGACCCCTAAACTTTCCAGAAATTTAA
1 TTTTGACCCTTAAACTTTCCAGAAATTTAA
* * * *
40226802 ATTTGGCCCTTAAACTTTTCA-AAATTTCA
1 TTTTGACCCTTAAACTTTCCAGAAATTTAA
40226831 TTTTGACCCT
1 TTTTGACCCT
40226841 GTTTTTCCTT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.29, C:0.23, G:0.07, T:0.41
Consensus pattern (30 bp):
TTTTGACCCTTAAACTTTCCAGAAATTTAA
Found at i:40227006 original size:14 final size:14
Alignment explanation
Indices: 40226989--40227036 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
40226979 TTGCATTGCA
40226989 TATTTTTTTATTTT
1 TATTTTTTTATTTT
* *
40227003 TATTTTTATATATT
1 TATTTTTTTATTTT
*
40227017 TGTTTTTTGTATTTAT
1 TATTTTTT-TATTT-T
40227033 TATT
1 TATT
40227037 CATGTAATTG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 18 0.69
15 4 0.15
16 4 0.15
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.77
Consensus pattern (14 bp):
TATTTTTTTATTTT
Found at i:40227035 original size:24 final size:24
Alignment explanation
Indices: 40226988--40227035 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
40226978 TTTGCATTGC
* *
40226988 ATATTTTTTTATTTTTATTTTTAT
1 ATATTTGTTTATTTGTATTTTTAT
40227012 ATATTTGTTT-TTTGTATTTATTAT
1 ATATTTGTTTATTTGTATTT-TTAT
40227036 TCATGTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (24 bp):
ATATTTGTTTATTTGTATTTTTAT
Found at i:40229191 original size:14 final size:15
Alignment explanation
Indices: 40229164--40229196 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
40229154 AAAAAAATAA
40229164 TTTGGTTAATATTAT
1 TTTGGTTAATATTAT
*
40229179 TTTGGTTCA-ATTAT
1 TTTGGTTAATATTAT
40229193 TTTG
1 TTTG
40229197 CCCGGATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.21, C:0.03, G:0.15, T:0.61
Consensus pattern (15 bp):
TTTGGTTAATATTAT
Found at i:40230950 original size:33 final size:30
Alignment explanation
Indices: 40230899--40230970 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 30
40230889 AATTTAAGCA
* *
40230899 AAATCAAAGTTT--TATGTATGCATTCGAACC
1 AAATCAAATTTTCATATGTAT-AATT-GAACC
*
40230929 ATAATCAAATTTTCATATGTATAATTGTACC
1 A-AATCAAATTTTCATATGTATAATTGAACC
40230960 AAATCAAATTT
1 AAATCAAATTT
40230971 CAAGTATCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
30 11 0.31
31 15 0.42
32 3 0.08
33 7 0.19
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (30 bp):
AAATCAAATTTTCATATGTATAATTGAACC
Found at i:40231667 original size:19 final size:19
Alignment explanation
Indices: 40231635--40231673 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
40231625 TAAAAATTAA
40231635 AAAAAATTCAAAATATTTAT
1 AAAAAATTCAAAAT-TTTAT
*
40231655 AAAAATTTC-AAATTTTAT
1 AAAAAATTCAAAATTTTAT
40231673 A
1 A
40231674 TTTTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
20 8 0.44
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAAATTCAAAATTTTAT
Found at i:40231719 original size:25 final size:25
Alignment explanation
Indices: 40231649--40231720 Score: 67
Period size: 27 Copynumber: 2.8 Consensus size: 25
40231639 AATTCAAAAT
* *
40231649 ATTTATAAAAAT-TTC-AAATTTTAT
1 ATTT-TAAAAATATTCTAAAATTTAA
* *
40231673 ATTTTAAAAAAATATATAAAAATTTAA
1 ATTTTAAAAATAT-TCT-AAAATTTAA
40231700 ATTTTAAAAATATTCTAAAAT
1 ATTTTAAAAATATTCTAAAAT
40231721 AATAATTTTG
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
23 6 0.16
24 5 0.13
25 6 0.16
26 2 0.05
27 19 0.50
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (25 bp):
ATTTTAAAAATATTCTAAAATTTAA
Found at i:40238887 original size:21 final size:21
Alignment explanation
Indices: 40238862--40238902 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
40238852 AGCATATGGC
40238862 TGGAGGGGAGCAGAAAAAGGG
1 TGGAGGGGAGCAGAAAAAGGG
40238883 TGGAGGGGAGCAGAAAAAGG
1 TGGAGGGGAGCAGAAAAAGG
40238903 CTGGTGGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.51, T:0.05
Consensus pattern (21 bp):
TGGAGGGGAGCAGAAAAAGGG
Found at i:40240255 original size:26 final size:26
Alignment explanation
Indices: 40240226--40240278 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
40240216 GCAGTCTTAA
40240226 AATTTTTACTTTTGAGAAGTATTTAT
1 AATTTTTACTTTTGAGAAGTATTTAT
40240252 AATTTTTACTTTTGAGAAGTATTTAT
1 AATTTTTACTTTTGAGAAGTATTTAT
40240278 A
1 A
40240279 CTTAGAGAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.53
Consensus pattern (26 bp):
AATTTTTACTTTTGAGAAGTATTTAT
Found at i:40244048 original size:18 final size:19
Alignment explanation
Indices: 40244017--40244062 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
40244007 GATATATACG
* *
40244017 TAAAAATTATTTAAAAAA-C
1 TAAAAA-TAATTAAAAAATA
40244036 TAAAAATAATTAAAAAATA
1 TAAAAATAATTAAAAAATA
40244055 TAAAAATA
1 TAAAAATA
40244063 TTTTTAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (19 bp):
TAAAAATAATTAAAAAATA
Found at i:40254922 original size:28 final size:28
Alignment explanation
Indices: 40254830--40254931 Score: 104
Period size: 28 Copynumber: 3.6 Consensus size: 28
40254820 GGATACCCGA
** *
40254830 GGGTAAAATGGTAATTTGG-GTTTTTAG
1 GGGTAAAATGGTAATTTGGAAATTTTGG
40254857 GGGTAAAATGGTAATTTTGTGAAA--TTGG
1 GGGTAAAATGGTAA-TTTG-GAAATTTTGG
40254885 GGGCTAAAAATGG-AATTTGGAAATTTTGG
1 GGG-T-AAAATGGTAATTTGGAAATTTTGG
40254914 GGAGTAAAATGGTAATTT
1 GG-GTAAAATGGTAATTT
40254932 TGGTAAAAAC
Statistics
Matches: 63, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
27 18 0.29
28 21 0.33
29 16 0.25
30 8 0.13
ACGTcount: A:0.32, C:0.01, G:0.31, T:0.35
Consensus pattern (28 bp):
GGGTAAAATGGTAATTTGGAAATTTTGG
Found at i:40255051 original size:59 final size:56
Alignment explanation
Indices: 40254856--40255049 Score: 167
Period size: 59 Copynumber: 3.3 Consensus size: 56
40254846 TGGGTTTTTA
* * *
40254856 GGGGTAAAATGGTAATTTT-GTGAAATTGGGGGCTAAAAATGGAATTTGGAAATTTTG
1 GGGGTAAAATGGTAATTTTGGTGAAA-T-CGGGTTAAAAATGGAATTTGGAAAGTTTG
* * * * * *
40254913 GGGAGTAAAATGGTAATTTTGGTAAAAACAAGGTCAAAAATGAAATTTTGGAAAGTTCG
1 GGG-GTAAAATGGTAATTTTGGTGAAATC-GGGTTAAAAATGGAA-TTTGGAAAGTTTG
** * * *
40254972 AAGGCAAAACGGTAAGTTTTGGTGAAATCGGGATTAAAAATGGGATTTAAGG-AAGTTTG
1 GGGGTAAAATGGTAA-TTTTGGTGAAATCGGG-TTAAAAATGGAATTT--GGAAAGTTTG
40255031 GGGGTAAAATGGTAATTTT
1 GGGGTAAAATGGTAATTTT
40255050 TGAAAGTTTC
Statistics
Matches: 105, Mismatches: 24, Indels: 15
0.73 0.17 0.10
Matches are distributed among these distances:
57 3 0.03
58 46 0.44
59 54 0.51
60 2 0.02
ACGTcount: A:0.37, C:0.04, G:0.29, T:0.30
Consensus pattern (56 bp):
GGGGTAAAATGGTAATTTTGGTGAAATCGGGTTAAAAATGGAATTTGGAAAGTTTG
Found at i:40255094 original size:30 final size:30
Alignment explanation
Indices: 40255032--40255409 Score: 510
Period size: 30 Copynumber: 12.6 Consensus size: 30
40255022 GGAAGTTTGG
* **
40255032 GGGT-AAAATGGTAATTTTTG-AAAGTTTCG
1 GGGTCAAAAT-GTAATTTTGGAAAAGTTTTA
* * * *
40255061 GGGTCAAAATATAATTTTAGAAAAATTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTA
40255091 GGGTCAAAATGTAATTTTGGAAAAGTTTTA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTA
* * * * *
40255121 GGGTTAAAATGTAGTTTTAGAATAGTTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTA
40255151 GGGTCAAAATGTAATTTTGGAAAAGTTTTA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTA
40255181 GGGTCAAAATGTAATTTTGGAAAAGTTTTA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTA
* * *
40255211 GGGTCAAAATATAATTTAGGAAAAGTTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTA
*
40255241 GGGTTAAAATGTAATTTTGGAAAAGTTTTA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTA
40255271 GGGTCAAAATGTAATTTTGGAAAAGTTTT-
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTA
* * *
40255300 GAGGTTAAAATATAATTTAGGAAAAGTTTTA
1 G-GGTCAAAATGTAATTTTGGAAAAGTTTTA
40255331 GGGTCAAAATGTAATTTTGGAAAAGTTTTA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTA
** *
40255361 GGGTCAAAATACAATTTTGGAAAAGTTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTA
40255391 GGGATCAAAATGTAATTTT
1 GGG-TCAAAATGTAATTTT
40255410 TGGACAATTT
Statistics
Matches: 307, Mismatches: 37, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
29 13 0.04
30 280 0.91
31 14 0.05
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (30 bp):
GGGTCAAAATGTAATTTTGGAAAAGTTTTA
Found at i:40257103 original size:27 final size:27
Alignment explanation
Indices: 40257068--40257120 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
40257058 CATTGGGCCT
40257068 ATTTGGGCCATTGTAATTGGGCCTTTG
1 ATTTGGGCCATTGTAATTGGGCCTTTG
*
40257095 ATTTGGGCCTTTGTAATTGGGCCTTT
1 ATTTGGGCCATTGTAATTGGGCCTTT
40257121 TGTAATTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.13, C:0.15, G:0.28, T:0.43
Consensus pattern (27 bp):
ATTTGGGCCATTGTAATTGGGCCTTTG
Found at i:40257124 original size:15 final size:14
Alignment explanation
Indices: 40257070--40257129 Score: 86
Period size: 14 Copynumber: 4.3 Consensus size: 14
40257060 TTGGGCCTAT
*
40257070 TTGGGCCATTGTAA
1 TTGGGCCTTTGTAA
*
40257084 TTGGGCCTTTG-AT
1 TTGGGCCTTTGTAA
40257097 TTGGGCCTTTGTAA
1 TTGGGCCTTTGTAA
40257111 TTGGGCCTTTTGTAA
1 TTGGGCC-TTTGTAA
40257126 TTGG
1 TTGG
40257130 ACTTTAGACT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
13 12 0.29
14 18 0.44
15 11 0.27
ACGTcount: A:0.13, C:0.13, G:0.30, T:0.43
Consensus pattern (14 bp):
TTGGGCCTTTGTAA
Found at i:40257825 original size:38 final size:36
Alignment explanation
Indices: 40257774--40257969 Score: 106
Period size: 38 Copynumber: 5.4 Consensus size: 36
40257764 TATCTTACTC
40257774 TTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCT
1 TTACTTCAATTTCAGAGATAAAGAC-TG-TATCCAGCT
**
40257812 TTACTTCAATTTCAAGAGGATAGGAA-AC-G-ATCTTGCT
1 TTACTTCAATTTC-AGA-GATA--AAGACTGTATCCAGCT
* * *
40257849 CTTGCTTCAATTTCGGAGATAAAGACTTGTTATCCAACT
1 -TTACTTCAATTTCAGAGATAAAGAC-TG-TATCCAGCT
* * ** *
40257888 CTACTTTAATTTCA-AGAGGATGAC-GT-T---GCT
1 TTACTTCAATTTCAGAGATAAAGACTGTATCCAGCT
*
40257918 CTTATTTCAATTTCAGAGATAAAGACGTGTTATCCA-CT
1 -TTACTTCAATTTCAGAGATAAAGAC-TG-TATCCAGCT
*
40257956 CTACTTCAATTTCA
1 TTACTTCAATTTCA
40257970 AAGGGGTGAC
Statistics
Matches: 116, Mismatches: 23, Indels: 39
0.65 0.13 0.22
Matches are distributed among these distances:
30 2 0.02
31 11 0.09
32 7 0.06
33 1 0.01
34 4 0.03
35 4 0.03
36 5 0.04
37 28 0.24
38 37 0.32
39 9 0.08
40 4 0.03
41 2 0.02
42 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.36
Consensus pattern (36 bp):
TTACTTCAATTTCAGAGATAAAGACTGTATCCAGCT
Found at i:40257893 original size:76 final size:71
Alignment explanation
Indices: 40257766--40258033 Score: 334
Period size: 68 Copynumber: 3.8 Consensus size: 71
40257756 TGGTGCTTTA
* * * *
40257766 TCTTACTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGG
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA-CTCTACTTCAATTTCAAGAGG
40257831 ATAGGAAACG
65 AT-GG--ACG
* * * *
40257841 ATCTTGCTCTTGCTTCAATTTCGGAGATAAAGACTTGTTATCCAACTCTACTTTAATTTCAAGAG
1 -TCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAG
40257906 GAT-GACG
64 GATGGACG
*
40257913 --TTGCTCTTATTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAA-AGG-
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGA
*
40257974 GGTGACG
66 TG-GACG
40257981 TC--GCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAAT
1 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAAT
40258034 GACATTGCTC
Statistics
Matches: 174, Mismatches: 13, Indels: 18
0.85 0.06 0.09
Matches are distributed among these distances:
67 3 0.02
68 71 0.41
69 36 0.21
72 3 0.02
74 1 0.01
76 59 0.34
77 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.35
Consensus pattern (71 bp):
TCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGA
TGGACG
Found at i:40257989 original size:68 final size:68
Alignment explanation
Indices: 40257844--40258578 Score: 1107
Period size: 68 Copynumber: 10.9 Consensus size: 68
40257834 GGAAACGATC
* * * *
40257844 TTGCTCTTGCTTCAATTTCGGAGATAAAGACTTGTTATCCAACTCTACTTTAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGAT
40257909 GACG
65 GACG
* *
40257913 TTGCTCTTATTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAA-AGGGGT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGA-GGAT
40257977 GACG
65 GACG
*
40257981 TCGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTA---C---TTC---A--ATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATG
*
40258035 ACA
66 ACG
* * * * *
40258038 TTGCTCTTACTTCAATTTCAGAGATAAGGACTTGATATCCACTCTACTTCAATTTCAAGGGGCTG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATG
*
40258103 ACA
66 ACG
* *
40258106 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGCGGACT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGA-T
40258171 GACG
65 GACG
*
40258175 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATG
40258240 ACG
66 ACG
*
40258243 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATG
*
40258308 ACA
66 ACG
* *
40258311 TTGTTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATG
40258376 ACG
66 ACG
* *
40258379 TTGCTCTTACTTCAATTTCAGAGGTAAAGACATGTTATCCACTCTACTTCAATTTCAAGAGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATG
40258444 ACG
66 ACG
* *
40258447 TTGGTCTTACTTCAATTTCAGAGGTAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATG
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATG
40258512 ACG
66 ACG
* * *
40258515 TTACTCTTACTTCAATTTCAGAGGTAAAGACGTGTTATCCACTCTACTTCAATTTCAAGCGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGAT
40258579 TGGTAATGAT
Statistics
Matches: 617, Mismatches: 36, Indels: 27
0.91 0.05 0.04
Matches are distributed among these distances:
57 46 0.07
60 2 0.00
62 3 0.00
63 3 0.00
65 1 0.00
67 1 0.00
68 459 0.74
69 102 0.17
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (68 bp):
TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATG
ACG
Found at i:40259257 original size:22 final size:22
Alignment explanation
Indices: 40259229--40259271 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
40259219 CAGCTATGAG
40259229 TTTCCTCGATCCAAAGATCATT
1 TTTCCTCGATCCAAAGATCATT
40259251 TTTCCTCGATCCAAAGATCAT
1 TTTCCTCGATCCAAAGATCAT
40259272 CGATGCCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.35
Consensus pattern (22 bp):
TTTCCTCGATCCAAAGATCATT
Found at i:40270512 original size:30 final size:30
Alignment explanation
Indices: 40270448--40270803 Score: 423
Period size: 30 Copynumber: 11.9 Consensus size: 30
40270438 GGATTTAAGG
*
40270448 AAGTTTTGGGGT-AAAATGGTAATTTTTG-A
1 AAGTTTTGGGGTCAAAAT-GTAATTTTAGAA
* *
40270477 AAGTTTCGGGGTCGAAATAG-AATTTTAGAA
1 AAGTTTTGGGGTCAAAAT-GTAATTTTAGAA
*** *
40270507 AAGTTTCAAGGTCGAAATGTAATTTTAGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
** * * *
40270537 AAGTTTTAAGGTTAAAATGTAGTTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
*
40270567 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
40270597 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
* *
40270627 AAGTTTTGGGGTTAAAATATAA-TTTAGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTA-GAA
* *
40270657 AAGTTTTAGGGTCAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
* *
40270687 AAGTTTTGGGGTTAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
*
40270717 AAGTTTTGAGGTCAAAATGTAATTTTAGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
* * ** *
40270747 AAGTTTTAGGGTTAAAATACAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
40270777 AAGTTTTGGGGATCAAAATGTAATTTT
1 AAGTTTTGGGG-TCAAAATGTAATTTT
40270804 TGGATAATTT
Statistics
Matches: 284, Mismatches: 37, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
29 23 0.08
30 246 0.87
31 15 0.05
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.37
Consensus pattern (30 bp):
AAGTTTTGGGGTCAAAATGTAATTTTAGAA
Found at i:40272502 original size:27 final size:27
Alignment explanation
Indices: 40272467--40272518 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
40272457 CATTGGGCCT
40272467 ATTTGGGCCATTGTAATTGGGCCTTCG
1 ATTTGGGCCATTGTAATTGGGCCTTCG
*
40272494 ATTTGGGCCTTTGTAATTGGGCCTT
1 ATTTGGGCCATTGTAATTGGGCCTT
40272519 TTGTAATTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.13, C:0.17, G:0.29, T:0.40
Consensus pattern (27 bp):
ATTTGGGCCATTGTAATTGGGCCTTCG
Found at i:40272523 original size:15 final size:14
Alignment explanation
Indices: 40272469--40272528 Score: 77
Period size: 14 Copynumber: 4.3 Consensus size: 14
40272459 TTGGGCCTAT
*
40272469 TTGGGCCATTGTAA
1 TTGGGCCTTTGTAA
* *
40272483 TTGGGCCTTCG-AT
1 TTGGGCCTTTGTAA
40272496 TTGGGCCTTTGTAA
1 TTGGGCCTTTGTAA
40272510 TTGGGCCTTTTGTAA
1 TTGGGCC-TTTGTAA
40272525 TTGG
1 TTGG
40272529 ACTCTGGACT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
13 11 0.28
14 17 0.44
15 11 0.28
ACGTcount: A:0.13, C:0.15, G:0.30, T:0.42
Consensus pattern (14 bp):
TTGGGCCTTTGTAA
Found at i:40272623 original size:18 final size:18
Alignment explanation
Indices: 40272602--40272650 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
40272592 AAAATTGATT
40272602 TAAATTTAAATTT-TAAGA
1 TAAATTTAAATTTGTAA-A
**
40272620 TAAATCCAAATTTGTAAA
1 TAAATTTAAATTTGTAAA
40272638 TAAATTTAGAATT
1 TAAATTTA-AATT
40272651 AACTTAAACC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (18 bp):
TAAATTTAAATTTGTAAA
Found at i:40274531 original size:16 final size:15
Alignment explanation
Indices: 40274512--40274559 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
40274502 TCAAATTATT
40274512 TTTGAATCATTTTAAA
1 TTTGAAT-ATTTTAAA
40274528 TTTGAATTATTTTAAAA
1 TTTGAA-TATTTT-AAA
40274545 TTTGAAT-TTTTAAA
1 TTTGAATATTTTAAA
40274559 T
1 T
40274560 CAAAATCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.13
15 4 0.13
16 12 0.40
17 10 0.33
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (15 bp):
TTTGAATATTTTAAA
Found at i:40274547 original size:17 final size:16
Alignment explanation
Indices: 40274512--40274552 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
40274502 TCAAATTATT
*
40274512 TTTGAATCATTTTAAA
1 TTTGAATTATTTTAAA
40274528 TTTGAATTATTTTAAAA
1 TTTGAATTATTTT-AAA
40274545 TTTGAATT
1 TTTGAATT
40274553 TTTAAATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (16 bp):
TTTGAATTATTTTAAA
Found at i:40286719 original size:27 final size:27
Alignment explanation
Indices: 40286689--40286748 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
40286679 ATGATCCAAA
* *
40286689 AAATTTAACGACCATATTGTAACGATC
1 AAATTTAACGACCATATCGTAACAATC
** *
40286716 AAATTCCATGACCATATCGTAACAATC
1 AAATTTAACGACCATATCGTAACAATC
40286743 AAATTT
1 AAATTT
40286749 TAACAGTCAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (27 bp):
AAATTTAACGACCATATCGTAACAATC
Found at i:40297947 original size:18 final size:18
Alignment explanation
Indices: 40297926--40297960 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
40297916 ATCTTGGGGC
*
40297926 GACATTATAACTTGCAGT
1 GACATTACAACTTGCAGT
40297944 GACATTACAACTTGCAG
1 GACATTACAACTTGCAG
40297961 ATAGATCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (18 bp):
GACATTACAACTTGCAGT
Found at i:40301041 original size:6 final size:6
Alignment explanation
Indices: 40301007--40301056 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
40300997 TAATAAGGAT
* * *
40301007 TTTCAA TTTACAA -TTC-A TATCAC TTTCAA TTTCAA TTTCAC TTTCAA
1 TTTCAA TTT-CAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
40301054 TTT
1 TTT
40301057 TGATCACAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
4 1 0.03
5 3 0.09
6 28 0.80
7 3 0.09
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTCAA
Found at i:40305779 original size:3 final size:3
Alignment explanation
Indices: 40305771--40305797 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
40305761 GCACAAGGAT
40305771 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
40305798 CACCATGACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:40311910 original size:205 final size:208
Alignment explanation
Indices: 40311526--40311927 Score: 575
Period size: 208 Copynumber: 1.9 Consensus size: 208
40311516 CGATAAAACG
** *
40311526 AAGCTCAATGTGAGTGAAACTTTTAAACCCCATCTTCTTGATGAGATACAGAGAAGTGGGTCAAA
1 AAGCTCAATGTGAGTGAAACTTCCAAACCCCATCTTCTTGATGAGATACAGAAAAGTGGGTCAAA
* * *
40311591 GCAATAAAATGGTTATCTTCTTGATGAGATGTGGAGAAGTGAACCAAATCTGCCTTTCTGATGAG
66 GCAATAAAATGGTTATCTTCTTAACGAGA-GTGGAGAAGTGAACCAAATCCGCCTTTCTGATGAG
* * *
40311656 GTACAGAGAAGTGGATTAAAACAATGAAGTGGTCATCTTCCTGATGAGATCA-A-AAAAGTAGAC
130 ATACAGAGAAGTGGATTAAAACAATGAAATGGTCATCTTCCTAATGAGAT-ATAGAAAAGTAGAC
40311719 CAATTCAACGAAGCA
194 CAATTCAACGAAGCA
**
40311734 AAGCTCAATGTGAGTGAAACTTCCAAACCCCATCTTCTTGATGAGATACAGAAAAGTGGGTTGAA
1 AAGCTCAATGTGAGTGAAACTTCCAAACCCCATCTTCTTGATGAGATACAGAAAAGTGGGTCAAA
* *
40311799 GCAATAAAGT-GTTCATCTT-TCTAACGAGA-T-GAGAAGTGAACCAAATCCGTC-TTCTTGATG
66 GCAATAAAATGGTT-ATCTTCT-TAACGAGAGTGGAGAAGTGAACCAAATCCGCCTTTC-TGATG
* *
40311859 AGATAGAGAGAAGTGGATTAAAACAATGAAATGGTCATCTTCCTAATGAGATATAGAGAAGTAGA
128 AGATACAGAGAAGTGGATTAAAACAATGAAATGGTCATCTTCCTAATGAGATATAGAAAAGTAGA
40311924 CCAA
193 CCAA
40311928 GAGATGAAGC
Statistics
Matches: 174, Mismatches: 15, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
204 4 0.02
205 73 0.42
206 13 0.07
207 4 0.02
208 80 0.46
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.25
Consensus pattern (208 bp):
AAGCTCAATGTGAGTGAAACTTCCAAACCCCATCTTCTTGATGAGATACAGAAAAGTGGGTCAAA
GCAATAAAATGGTTATCTTCTTAACGAGAGTGGAGAAGTGAACCAAATCCGCCTTTCTGATGAGA
TACAGAGAAGTGGATTAAAACAATGAAATGGTCATCTTCCTAATGAGATATAGAAAAGTAGACCA
ATTCAACGAAGCA
Found at i:40313311 original size:30 final size:29
Alignment explanation
Indices: 40313255--40313513 Score: 208
Period size: 30 Copynumber: 8.8 Consensus size: 29
40313245 GCTCGAGGGC
*
40313255 AAAATGGTAATTTTT-AGAAGTTTGGGGCA
1 AAAAT-GTAATTTTTGAGAAGTTTGGGGTA
40313284 AAAATGTAATTTTTGAGAAGTTTTGGGGTA
1 AAAATGTAATTTTTGAGAAG-TTTGGGGTA
* ***
40313314 AAAATGTGATTTTTG-GAAGCACGGGAGTA
1 AAAATGTAATTTTTGAGAAGTTTGGG-GTA
* *
40313343 AAAATGTGATTTTTG-GAAGTTCGAGGGT-
1 AAAATGTAATTTTTGAGAAGTTTG-GGGTA
**
40313371 AAAATGTAATTTTTGAGAAGTTCAAGGGTA
1 AAAATGTAATTTTTGAGAAGTT-TGGGGTA
* *
40313401 AAAATGTAAATTTT-ATGAAGTTTGAGGGTT
1 AAAATGTAATTTTTGA-GAAGTTTG-GGGTA
* * *
40313431 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
1 AAAATGTAATTTTTGAGAAGTTT-GGGGTA
* *
40313461 AAAATGTAATTTTAGA-AATGTTTAGGGGTC
1 AAAATGTAATTTTTGAGAA-GTTT-GGGGTA
* *
40313491 AAAATATGATTTTT-AGAATGTTT
1 AAAATGTAATTTTTGAGAA-GTTT
40313514 AGGGACCTTT
Statistics
Matches: 195, Mismatches: 22, Indels: 25
0.81 0.09 0.10
Matches are distributed among these distances:
28 26 0.13
29 54 0.28
30 113 0.58
31 2 0.01
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (29 bp):
AAAATGTAATTTTTGAGAAGTTTGGGGTA
Found at i:40314687 original size:14 final size:14
Alignment explanation
Indices: 40314661--40314694 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
40314651 TAATAATGGT
40314661 AATATA-ATAAATA
1 AATATATATAAATA
*
40314674 AATATATATTAATA
1 AATATATATAAATA
40314688 AATATAT
1 AATATAT
40314695 GTATAGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATATATATAAATA
Found at i:40315317 original size:17 final size:16
Alignment explanation
Indices: 40315297--40315397 Score: 112
Period size: 17 Copynumber: 5.9 Consensus size: 16
40315287 TAAATTTTAT
40315297 ATTTAAATTCAAAATAA
1 ATTTAAATT-AAAATAA
40315314 ATTTAAATTTAAAATAA
1 ATTTAAA-TTAAAATAA
*
40315331 ATTTAAACTCAAAAATAA
1 ATTTAAA-T-TAAAATAA
*
40315349 GTTTAAAGTTAAAATAA
1 ATTTAAA-TTAAAATAA
40315366 ATTTAAACTTAAAATAA
1 ATTTAAA-TTAAAATAA
*
40315383 ATTAAAATTTAAAAT
1 ATTTAAA-TTAAAAT
40315398 TTAAAATTAG
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
17 57 0.78
18 16 0.22
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (16 bp):
ATTTAAATTAAAATAA
Found at i:40315328 original size:7 final size:6
Alignment explanation
Indices: 40315286--40315402 Score: 62
Period size: 6 Copynumber: 19.8 Consensus size: 6
40315276 GGACTTTTAA
* * * *
40315286 TTAAATT TTATAT TTAAAT TCAAA- ATAAAT TTAAAT TTAAA- ATAAAT
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * * * * * * *
40315333 TTAAAC TCAAAA ATAAGT TTAAAG TTAAA- ATAAAT TTAAAC TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
40315379 ATAAAT TAAAAT TTAAAAT TTAAA
1 TTAAAT TTAAAT TT-AAAT TTAAA
40315403 ATTAGGTTCA
Statistics
Matches: 80, Mismatches: 25, Indels: 11
0.69 0.22 0.09
Matches are distributed among these distances:
5 15 0.19
6 55 0.69
7 10 0.12
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.38
Consensus pattern (6 bp):
TTAAAT
Found at i:40315354 original size:35 final size:34
Alignment explanation
Indices: 40315297--40315397 Score: 148
Period size: 35 Copynumber: 2.9 Consensus size: 34
40315287 TAAATTTTAT
*
40315297 ATTTAAATTCAAAATAAATTTAAATTTAAAATAA
1 ATTTAAACTCAAAATAAATTTAAATTTAAAATAA
* *
40315331 ATTTAAACTCAAAAATAAGTTTAAAGTTAAAATAA
1 ATTTAAACTC-AAAATAAATTTAAATTTAAAATAA
* *
40315366 ATTTAAACTTAAAATAAATTAAAATTTAAAAT
1 ATTTAAACTCAAAATAAATTTAAATTTAAAAT
40315398 TTAAAATTAG
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
34 28 0.47
35 31 0.53
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (34 bp):
ATTTAAACTCAAAATAAATTTAAATTTAAAATAA
Found at i:40317036 original size:28 final size:28
Alignment explanation
Indices: 40316996--40317050 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
40316986 AATATCCGAT
40316996 TTACTCCCTGTTGACCCAAAGGTCATGC
1 TTACTCCCTGTTGACCCAAAGGTCATGC
40317024 TTACTCCCTGTTGACCCAAAGGTCATG
1 TTACTCCCTGTTGACCCAAAGGTCATG
40317051 ATGCTCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.22, C:0.31, G:0.18, T:0.29
Consensus pattern (28 bp):
TTACTCCCTGTTGACCCAAAGGTCATGC
Found at i:40320272 original size:39 final size:39
Alignment explanation
Indices: 40320228--40320362 Score: 162
Period size: 39 Copynumber: 3.5 Consensus size: 39
40320218 TTTGCCTCAA
* *
40320228 GCTCGGGGTAAAAGATTGGATGGCTGCAATCTGTCCCAG
1 GCTCGGGATAAAAGATTGGATGGTTGCAATCTGTCCCAG
* * * * **
40320267 ACTCGGGATAAAAGATCGAATGGTTGCAATTTGTCCTGG
1 GCTCGGGATAAAAGATTGGATGGTTGCAATCTGTCCCAG
* * *
40320306 GCTCGGGGTAAAAGATTGGATGTTTGCAATCTGCCCCAG
1 GCTCGGGATAAAAGATTGGATGGTTGCAATCTGTCCCAG
*
40320345 GCTCGGGATAAGAGATTG
1 GCTCGGGATAAAAGATTG
40320363 ATTGATGGTG
Statistics
Matches: 77, Mismatches: 19, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
39 77 1.00
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (39 bp):
GCTCGGGATAAAAGATTGGATGGTTGCAATCTGTCCCAG
Found at i:40320388 original size:78 final size:78
Alignment explanation
Indices: 40320189--40320397 Score: 231
Period size: 78 Copynumber: 2.7 Consensus size: 78
40320179 TAGTCCTTTC
** *
40320189 ACTCTGGG-TAAGAGATTGGCTGATGGTGATTTGCCTCAAGCTCGGGGTAAAAGATTGGATGGCT
1 ACTC-GGGATAAGAGATTGAATGATGGTGATTTGCCCCAAGCTCGGGGTAAAAGATTGGATGGCT
*
40320253 GCAATCTGTCCCAG
65 GCAATCTGCCCCAG
* * * * ** * *** **
40320267 ACTCGGGATAAAAGATCGAATGGTTGCAATTTGTCCTGGGCTCGGGGTAAAAGATTGGATGTTTG
1 ACTCGGGATAAGAGATTGAATGATGGTGATTTGCCCCAAGCTCGGGGTAAAAGATTGGATGGCTG
40320332 CAATCTGCCCCAG
66 CAATCTGCCCCAG
* * *
40320345 GCTCGGGATAAGAGATTGATTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAG
1 ACTCGGGATAAGAGATTGAATGATGGTGATTTGCCCCAAGCTCGGGGTAAAAG
40320398 GTCAGAATCT
Statistics
Matches: 101, Mismatches: 29, Indels: 2
0.77 0.22 0.02
Matches are distributed among these distances:
77 3 0.03
78 98 0.97
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.26
Consensus pattern (78 bp):
ACTCGGGATAAGAGATTGAATGATGGTGATTTGCCCCAAGCTCGGGGTAAAAGATTGGATGGCTG
CAATCTGCCCCAG
Found at i:40332814 original size:30 final size:29
Alignment explanation
Indices: 40332736--40332905 Score: 159
Period size: 29 Copynumber: 5.7 Consensus size: 29
40332726 ATTTGAAGGC
*
40332736 AAAATGGTAATTTTTGGATGCTT-G-GGAGT-
1 AAAAT-GTAATTTTTGGAAG-TTCGAGG-GTA
* *
40332765 AAAATGGTAATTTTTGGAAGTTCGCGGGCA
1 AAAAT-GTAATTTTTGGAAGTTCGAGGGTA
40332795 AAAATGTAATTTTTAGGAAGTTCGAGGGTA
1 AAAATGTAATTTTT-GGAAGTTCGAGGGTA
* * * *
40332825 AAAATGTGATTTTTGAAAGCTCAAGGGTA
1 AAAATGTAATTTTTGGAAGTTCGAGGGTA
* *
40332854 AAAATGTGATTTTTGAGAAGTTCGGGGGTA
1 AAAATGTAATTTTTG-GAAGTTCGAGGGTA
40332884 AAAATGTAAATTTTAT-GAAGTT
1 AAAATGT-AATTTT-TGGAAGTT
40332906 TAGGGGTTAA
Statistics
Matches: 121, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
28 2 0.02
29 57 0.47
30 56 0.46
31 5 0.04
32 1 0.01
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAGTTCGAGGGTA
Found at i:40332839 original size:59 final size:59
Alignment explanation
Indices: 40332765--40332902 Score: 161
Period size: 59 Copynumber: 2.3 Consensus size: 59
40332755 GCTTGGGAGT
* * **
40332765 AAAATGGTAATTTTTGGAAGTTCGCGGGCAAAAATGTAATTTTT-AGGAAGTTCGAGGGTA
1 AAAAT-GTAATTTTTGAAAGCTCAAGGGCAAAAATGTAATTTTTGA-GAAGTTCGAGGGTA
* * * *
40332825 AAAATGTGATTTTTGAAAGCTCAAGGGTAAAAATGTGATTTTTGAGAAGTTCGGGGGTA
1 AAAATGTAATTTTTGAAAGCTCAAGGGCAAAAATGTAATTTTTGAGAAGTTCGAGGGTA
40332884 AAAATGTAAATTTTATGAA
1 AAAATGT-AATTTT-TGAA
40332903 GTTTAGGGGT
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
59 51 0.77
60 11 0.17
61 4 0.06
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.33
Consensus pattern (59 bp):
AAAATGTAATTTTTGAAAGCTCAAGGGCAAAAATGTAATTTTTGAGAAGTTCGAGGGTA
Found at i:40332886 original size:29 final size:29
Alignment explanation
Indices: 40332763--40332905 Score: 123
Period size: 30 Copynumber: 4.8 Consensus size: 29
40332753 ATGCTTGGGA
*
40332763 GTAAAATGGTAATTTTTG-GAAGTTCGCGG
1 GTAAAAT-GTAATTTTTGAGAAGTTCGAGG
*
40332792 GCAAAAATGTAATTTTT-AGGAAGTTCGAGG
1 G-TAAAATGTAATTTTTGA-GAAGTTCGAGG
* * *
40332822 GTAAAAATGTGATTTTTGA-AAGCTCAAGG
1 GT-AAAATGTAATTTTTGAGAAGTTCGAGG
* *
40332851 GTAAAAATGTGATTTTTGAGAAGTTCGGGG
1 GT-AAAATGTAATTTTTGAGAAGTTCGAGG
*
40332881 GTAAAAATGTAAATTTT-ATGAAGTT
1 GT-AAAATGTAATTTTTGA-GAAGTT
40332906 TAGGGGTTAA
Statistics
Matches: 96, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
29 38 0.40
30 57 0.59
31 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.34
Consensus pattern (29 bp):
GTAAAATGTAATTTTTGAGAAGTTCGAGG
Found at i:40332912 original size:30 final size:30
Alignment explanation
Indices: 40332794--40332977 Score: 101
Period size: 30 Copynumber: 6.2 Consensus size: 30
40332784 GTTCGCGGGC
* *
40332794 AAAAATGTAATTTTTAGGAAG-TTCGAGGGT
1 AAAAATGTAAATTTTAGGAAGTTTAG-GGGT
* * * * * *
40332824 AAAAATGT-GATTTTTGAAAGCTCAAGGGT
1 AAAAATGTAAATTTTAGGAAGTTTAGGGGT
* * **
40332853 AAAAATGT-GATTTTTGAGAAGTTCGGGGGT
1 AAAAATGTAAATTTTAG-GAAGTTTAGGGGT
*
40332883 AAAAATGTAAATTTTATGAAGTTTAGGGGT
1 AAAAATGTAAATTTTAGGAAGTTTAGGGGT
* * ** *
40332913 TAAAATAT-AATTTTAAAAAAGTTCTA-GTGT
1 AAAAATGTAAATTTT-AGGAAGTT-TAGGGGT
* *
40332943 TAAAATGTAAA-TTTGGGAAGTTTAGGGGT
1 AAAAATGTAAATTTTAGGAAGTTTAGGGGT
*
40332972 CAAAAT
1 AAAAAT
40332978 ATGATTTCTA
Statistics
Matches: 120, Mismatches: 27, Indels: 15
0.74 0.17 0.09
Matches are distributed among these distances:
28 2 0.02
29 47 0.39
30 62 0.52
31 9 0.08
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (30 bp):
AAAAATGTAAATTTTAGGAAGTTTAGGGGT
Found at i:40332935 original size:60 final size:60
Alignment explanation
Indices: 40332871--40332991 Score: 154
Period size: 59 Copynumber: 2.0 Consensus size: 60
40332861 GATTTTTGAG
* * *
40332871 AAGTTCGGGGGTAAAAATGTAAATTTTATGAAGTTTAGGGGTTAAAATATAATTT-TAAAA
1 AAGTTCGAGGGTAAAAATGTAAA-TTTAGGAAGTTTAGGGGTCAAAATATAATTTCTAAAA
* * * * *
40332931 AAGTTCTAGTGTTAAAATGTAAATTTGGGAAGTTTAGGGGTCAAAATATGATTTCTAAAA
1 AAGTTCGAGGGTAAAAATGTAAATTTAGGAAGTTTAGGGGTCAAAATATAATTTCTAAAA
40332991 A
1 A
40332992 GTTTAAGGAC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
59 27 0.52
60 25 0.48
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.35
Consensus pattern (60 bp):
AAGTTCGAGGGTAAAAATGTAAATTTAGGAAGTTTAGGGGTCAAAATATAATTTCTAAAA
Found at i:40334381 original size:6 final size:6
Alignment explanation
Indices: 40334364--40334467 Score: 63
Period size: 6 Copynumber: 17.7 Consensus size: 6
40334354 GGACTTTTAA
** * * *
40334364 TTAAATT TTAAAT TTAAAT TTAAA- AAAAAT TTAAAT TTAAAC TCAAAA
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * * * *
40334412 ATAAGT TTAAAT TTAACA- -TAAAT TTAAAC TTAAA- ATAAAT TAAAAT
1 TTAAAT TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
40334458 TTAAAA TTAA
1 TTAAAT TTAA
40334468 GTTCAATTTG
Statistics
Matches: 73, Mismatches: 19, Indels: 11
0.71 0.18 0.11
Matches are distributed among these distances:
4 1 0.01
5 10 0.14
6 56 0.77
7 6 0.08
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (6 bp):
TTAAAT
Found at i:40334396 original size:23 final size:24
Alignment explanation
Indices: 40334365--40334427 Score: 83
Period size: 23 Copynumber: 2.6 Consensus size: 24
40334355 GACTTTTAAT
* *
40334365 TAAATTTTAAATTTAAATTTAAAAA
1 TAAA-TTTAAATTTAAACTCAAAAA
40334390 -AAATTTAAATTTAAACTCAAAAA
1 TAAATTTAAATTTAAACTCAAAAA
*
40334413 TAAGTTTAAATTTAA
1 TAAATTTAAATTTAA
40334428 CATAAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 18 0.53
24 16 0.47
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.40
Consensus pattern (24 bp):
TAAATTTAAATTTAAACTCAAAAA
Found at i:40334412 original size:24 final size:23
Alignment explanation
Indices: 40334370--40334427 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 23
40334360 TTAATTAAAT
**
40334370 TTTAAATTTAAATTTAAAAAAAA
1 TTTAAATTTAAATCAAAAAAAAA
* *
40334393 TTTAAATTTAAACTCAAAAATAAG
1 TTTAAATTTAAA-TCAAAAAAAAA
40334417 TTTAAATTTAA
1 TTTAAATTTAA
40334428 CATAAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 12 0.40
24 18 0.60
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (23 bp):
TTTAAATTTAAATCAAAAAAAAA
Found at i:40334464 original size:17 final size:17
Alignment explanation
Indices: 40334372--40334464 Score: 78
Period size: 17 Copynumber: 5.1 Consensus size: 17
40334362 AATTAAATTT
40334372 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
40334389 AAAATTTAAATTTAAACTCAAAAA
1 TAAATTTAAA-TT----T--AAAA
* *
40334413 TAAGTTTAAATTTAACA
1 TAAATTTAAATTTAAAA
*
40334430 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
40334447 TAAATTAAAATTTAAAA
1 TAAATTTAAATTTAAAA
40334464 T
1 T
40334465 TAAGTTCAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
17 42 0.70
18 2 0.03
19 1 0.02
22 1 0.02
23 2 0.03
24 12 0.20
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:40334860 original size:14 final size:14
Alignment explanation
Indices: 40334837--40334866 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
40334827 AACAAATAAT
*
40334837 AATTTTTTTAATTA
1 AATTTATTTAATTA
40334851 AATTTATTTAATTA
1 AATTTATTTAATTA
40334865 AA
1 AA
40334867 AAAATGTCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
AATTTATTTAATTA
Found at i:40340207 original size:5 final size:5
Alignment explanation
Indices: 40340176--40340236 Score: 50
Period size: 5 Copynumber: 11.8 Consensus size: 5
40340166 TACATAATAA
* * * * * *
40340176 AAAAT AATAT ATACAT AAAAT ACAAT AAAAT AAAAT AATAT ACATAT AAGAT
1 AAAAT AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT AAAAT
40340228 AAAAT AAAA
1 AAAAT AAAA
40340237 AAATACATTA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
5 37 0.80
6 9 0.20
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.25
Consensus pattern (5 bp):
AAAAT
Found at i:40340214 original size:31 final size:31
Alignment explanation
Indices: 40340176--40340236 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
40340166 TACATAATAA
* *
40340176 AAAATAATATATACATAAAATACAATAAAAT
1 AAAATAATATACACATAAAATAAAATAAAAT
* *
40340207 AAAATAATATACATATAAGATAAAATAAAA
1 AAAATAATATACACATAAAATAAAATAAAA
40340237 AAATACATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.25
Consensus pattern (31 bp):
AAAATAATATACACATAAAATAAAATAAAAT
Found at i:40340286 original size:30 final size:29
Alignment explanation
Indices: 40340252--40340347 Score: 104
Period size: 30 Copynumber: 3.3 Consensus size: 29
40340242 CATTAAAATC
**
40340252 GGGTCAAATTTGAATTTTTGAAAGCTTCAG
1 GGGTCAAATTAAAATTTTTGAAAG-TTCAG
*
40340282 GGGTCAAATCAAAATTTTTAGAAAGTTCAG
1 GGGTCAAATTAAAATTTTT-GAAAGTTCAG
* * * *
40340312 GGGTTAAATTCAAATTTTAGAAAGTT-TG
1 GGGTCAAATTAAAATTTTTGAAAGTTCAG
40340340 GGGTCAAA
1 GGGTCAAA
40340348 AATAATTTTA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
28 8 0.14
29 7 0.12
30 36 0.64
31 5 0.09
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.33
Consensus pattern (29 bp):
GGGTCAAATTAAAATTTTTGAAAGTTCAG
Found at i:40341341 original size:8 final size:9
Alignment explanation
Indices: 40341329--40341360 Score: 50
Period size: 8 Copynumber: 3.8 Consensus size: 9
40341319 AATAATAAAG
40341329 TTTATTTTA
1 TTTATTTTA
40341338 -TTATTTTA
1 TTTATTTTA
40341346 TTTA-TTTA
1 TTTATTTTA
40341354 TTTATTT
1 TTTATTT
40341361 ACATTTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTATTTTA
Found at i:40341383 original size:4 final size:4
Alignment explanation
Indices: 40341370--40341399 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
40341360 TACATTTATA
40341370 AAAT -AAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
40341400 ATGGGTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:40344878 original size:30 final size:30
Alignment explanation
Indices: 40344815--40345019 Score: 191
Period size: 30 Copynumber: 6.9 Consensus size: 30
40344805 TGAAATTTCA
40344815 GAGAA-TTT-GGGGTTAAAATGTGA-TTTT
1 GAGAAGTTTGGGGGTTAAAATGTGATTTTT
*
40344842 GGGAAGTTTGGGGGTTAAAATGTGATTTTT
1 GAGAAGTTTGGGGGTTAAAATGTGATTTTT
* * *
40344872 GAGAAGTTTAGAGGCTAAAATGTGATTTTT
1 GAGAAGTTTGGGGGTTAAAATGTGATTTTT
* * **
40344902 GAGGAGTTCGGGGGCCAAAATGTGATTTTT
1 GAGAAGTTTGGGGGTTAAAATGTGATTTTT
* * * * *
40344932 GTGGAGTTCGAGGGTTAAAATGTAATTTTT
1 GAGAAGTTTGGGGGTTAAAATGTGATTTTT
* * * *
40344962 AAAAAGTTTGAGGGTTAAAATGTAATTTTT
1 GAGAAGTTTGGGGGTTAAAATGTGATTTTT
* * * * *
40344992 AAAAAGTTCGAGGGTTAAAATGTAATTT
1 GAGAAGTTTGGGGGTTAAAATGTGATTT
40345020 ATACAAAGTT
Statistics
Matches: 154, Mismatches: 21, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
27 4 0.03
28 3 0.02
29 15 0.10
30 132 0.86
ACGTcount: A:0.31, C:0.03, G:0.29, T:0.37
Consensus pattern (30 bp):
GAGAAGTTTGGGGGTTAAAATGTGATTTTT
Found at i:40344953 original size:90 final size:89
Alignment explanation
Indices: 40344829--40344991 Score: 222
Period size: 90 Copynumber: 1.8 Consensus size: 89
40344819 ATTTGGGGTT
* * * * *
40344829 AAAATGTGATTTTGGGAAGTTTGGGGGTTAAAATGTGATTTTTGAGAAGTTT-AGAGGCTAAAAT
1 AAAATGTGATTTTGGGAAGTTCGAGGGTTAAAATGTAATTTTTAAAAAGTTTGAG-GGCTAAAAT
*
40344893 GTGATTTTTGAGGAGTTCGGGGGCC
65 GTAATTTTTGAGGAGTTCGGGGGCC
*
40344918 AAAATGTGATTTTTGTGG-AGTTCGAGGGTTAAAATGTAATTTTTAAAAAGTTTGAGGGTTAAAA
1 AAAATGTGA-TTTTG-GGAAGTTCGAGGGTTAAAATGTAATTTTTAAAAAGTTTGAGGGCTAAAA
40344982 TGTAATTTTT
64 TGTAATTTTT
40344992 AAAAAGTTCG
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
89 9 0.14
90 51 0.80
91 4 0.06
ACGTcount: A:0.30, C:0.03, G:0.29, T:0.38
Consensus pattern (89 bp):
AAAATGTGATTTTGGGAAGTTCGAGGGTTAAAATGTAATTTTTAAAAAGTTTGAGGGCTAAAATG
TAATTTTTGAGGAGTTCGGGGGCC
Found at i:40345000 original size:90 final size:90
Alignment explanation
Indices: 40344829--40345019 Score: 217
Period size: 90 Copynumber: 2.1 Consensus size: 90
40344819 ATTTGGGGTT
* * * * *
40344829 AAAATGTGA-TTTTGGGAAGTTTGGGGGTTAAAATGTGATTTTTGAGAAGTTTAGAGGCTAAAAT
1 AAAATGTGATTTTTGGGAAGTTCGAGGGTTAAAATGTAATTTTTAAAAAGTTTAGAGGCTAAAAT
* * ** *
40344893 GTGATTTTTGAGGAGTTCGGGGGCC
66 GTAATTTTTAAAAAGTTCGAGGGCC
*
40344918 AAAATGTGATTTTTGTGG-AGTTCGAGGGTTAAAATGTAATTTTTAAAAAGTTT-GAGGGTTAAA
1 AAAATGTGATTTTTG-GGAAGTTCGAGGGTTAAAATGTAATTTTTAAAAAGTTTAGA-GGCTAAA
**
40344981 ATGTAATTTTTAAAAAGTTCGAGGGTT
64 ATGTAATTTTTAAAAAGTTCGAGGGCC
*
40345008 AAAATGTAATTT
1 AAAATGTGATTT
40345020 ATACAAAGTT
Statistics
Matches: 85, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
89 11 0.13
90 72 0.85
91 2 0.02
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.37
Consensus pattern (90 bp):
AAAATGTGATTTTTGGGAAGTTCGAGGGTTAAAATGTAATTTTTAAAAAGTTTAGAGGCTAAAAT
GTAATTTTTAAAAAGTTCGAGGGCC
Found at i:40345028 original size:30 final size:30
Alignment explanation
Indices: 40344936--40345035 Score: 173
Period size: 30 Copynumber: 3.3 Consensus size: 30
40344926 ATTTTTGTGG
40344936 AGTTCGAGGGTTAAAATGTAATTTTTAAAA
1 AGTTCGAGGGTTAAAATGTAATTTTTAAAA
*
40344966 AGTTTGAGGGTTAAAATGTAATTTTTAAAA
1 AGTTCGAGGGTTAAAATGTAATTTTTAAAA
* *
40344996 AGTTCGAGGGTTAAAATGTAATTTATACAA
1 AGTTCGAGGGTTAAAATGTAATTTTTAAAA
40345026 AGTTCGAGGG
1 AGTTCGAGGG
40345036 CCTCTTAAGA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 66 1.00
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (30 bp):
AGTTCGAGGGTTAAAATGTAATTTTTAAAA
Found at i:40346042 original size:3 final size:3
Alignment explanation
Indices: 40346034--40346059 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40346024 ATTTATTTAT
40346034 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
40346060 TTAAAACCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:40352930 original size:18 final size:19
Alignment explanation
Indices: 40352907--40352943 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
40352897 AACATTTATA
*
40352907 TTTTTTTTGTT-AATTTGG
1 TTTTTTTAGTTAAATTTGG
40352925 TTTTTTTAGTTAAATTTGG
1 TTTTTTTAGTTAAATTTGG
40352944 CCTCAATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (19 bp):
TTTTTTTAGTTAAATTTGG
Found at i:40353127 original size:26 final size:27
Alignment explanation
Indices: 40353091--40353147 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
40353081 ATGCTAATCT
40353091 TTTTGAATTTTTTAGAA-A-TTTTAGAA
1 TTTTGAATTTTTT-GAATATTTTTAGAA
* *
40353117 TTTTGATTTTTTTGAATATTTTTATAA
1 TTTTGAATTTTTTGAATATTTTTAGAA
40353144 TTTT
1 TTTT
40353148 TAAATTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 3 0.11
26 13 0.48
27 11 0.41
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (27 bp):
TTTTGAATTTTTTGAATATTTTTAGAA
Found at i:40354337 original size:28 final size:27
Alignment explanation
Indices: 40354283--40354342 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
40354273 GAAATGGTAG
*
40354283 CAAAATAGTGAAAAAAAACAACAACAA
1 CAAAATAGTGAAAAAAAACAAAAACAA
* *
40354310 GAAAATAGT-AACAAAACAATAAAAACAA
1 CAAAATAGTGAA-AAAA-AACAAAAACAA
40354338 CAAAA
1 CAAAA
40354343 AAAAGTAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 2 0.07
27 12 0.44
28 13 0.48
ACGTcount: A:0.72, C:0.13, G:0.07, T:0.08
Consensus pattern (27 bp):
CAAAATAGTGAAAAAAAACAAAAACAA
Found at i:40362330 original size:3 final size:3
Alignment explanation
Indices: 40362322--40362348 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
40362312 CTTGCTGTCT
40362322 TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA
40362349 GTAGAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:40365148 original size:2 final size:2
Alignment explanation
Indices: 40365141--40365167 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40365131 AATTGTTTGA
40365141 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 A
40365168 AATGAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40374896 original size:16 final size:16
Alignment explanation
Indices: 40374877--40374907 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40374867 TTTTAAATTA
40374877 TTTAAAATATATATTT
1 TTTAAAATATATATTT
*
40374893 TTTATAATATATATT
1 TTTAAAATATATATT
40374908 AAATATCATA
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTAAAATATATATTT
Found at i:40375243 original size:45 final size:45
Alignment explanation
Indices: 40375179--40375267 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
40375169 TAGTTGAAAC
* * *
40375179 CACGGGAGTTAAGTGAGATGTCAATGATCTCT-CTTACATTAACCT
1 CACGGGAGTTAAGTAAGATGGCAAAGATCTCTCCTT-CATTAACCT
*
40375224 CACGGGAGTTAAGTAAGATGGCAAAGGTCTCTCCTTCATTAACC
1 CACGGGAGTTAAGTAAGATGGCAAAGATCTCTCCTTCATTAACC
40375268 AGTGATCGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 36 0.92
46 3 0.08
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.28
Consensus pattern (45 bp):
CACGGGAGTTAAGTAAGATGGCAAAGATCTCTCCTTCATTAACCT
Found at i:40377448 original size:29 final size:28
Alignment explanation
Indices: 40377411--40377476 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 28
40377401 ATCTTACATT
* *
40377411 TATTAAAAT-AAT-ATTTA-TTTCATAT
1 TATTTAAATAAATAATTTATTTTCATAA
* *
40377436 TATTTAAGTAAATAATTTATTTTTATAA
1 TATTTAAATAAATAATTTATTTTCATAA
40377464 TATTTAAATAAAT
1 TATTTAAATAAAT
40377477 CTATTTTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
25 7 0.21
26 3 0.09
27 5 0.15
28 18 0.55
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (28 bp):
TATTTAAATAAATAATTTATTTTCATAA
Found at i:40377497 original size:25 final size:25
Alignment explanation
Indices: 40377445--40377499 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
40377435 TTATTTAAGT
* **
40377445 AAAT-AATTTATTTTTATAATATTT
1 AAATAAATCTATTTTTATAATATGC
*
40377469 AAATAAATCTATTTTTATAGTATGC
1 AAATAAATCTATTTTTATAATATGC
40377494 AAATAA
1 AAATAA
40377500 TTTTTGAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 4 0.15
25 22 0.85
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (25 bp):
AAATAAATCTATTTTTATAATATGC
Found at i:40380344 original size:21 final size:21
Alignment explanation
Indices: 40380321--40380362 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40380311 TTATCCCGAA
40380321 CCCATAATCATGAATCATAAAC
1 CCCA-AATCATGAATCATAAAC
* *
40380343 CCCAAATCTTGAATCGTAAA
1 CCCAAATCATGAATCATAAA
40380363 TCTTAAATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.43, C:0.26, G:0.07, T:0.24
Consensus pattern (21 bp):
CCCAAATCATGAATCATAAAC
Found at i:40383060 original size:14 final size:15
Alignment explanation
Indices: 40383041--40383073 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
40383031 ACGAGTTTAA
40383041 TATATTTTCTTCAT-
1 TATATTTTCTTCATC
40383055 TATATTTTCTTCATC
1 TATATTTTCTTCATC
40383070 TATA
1 TATA
40383074 AAATTTAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.61
Consensus pattern (15 bp):
TATATTTTCTTCATC
Found at i:40384594 original size:19 final size:20
Alignment explanation
Indices: 40384548--40384594 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
40384538 CTCAATGACT
*
40384548 ATAA-TTAGTGATCATATTGC
1 ATAATTTAGTGATCATA-TAC
*
40384568 AAAATTTAGTGATCATA-AC
1 ATAATTTAGTGATCATATAC
40384587 ATAATTTA
1 ATAATTTA
40384595 AATAATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 8 0.35
20 3 0.13
21 12 0.52
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.38
Consensus pattern (20 bp):
ATAATTTAGTGATCATATAC
Found at i:40384898 original size:17 final size:17
Alignment explanation
Indices: 40384868--40384901 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40384858 TCTCCTTCTC
**
40384868 TTTTATAATTTAGTTTT
1 TTTTATAAAATAGTTTT
40384885 TTTTATAAAATAGTTTT
1 TTTTATAAAATAGTTTT
40384902 GAACGTCATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTTATAAAATAGTTTT
Found at i:40390832 original size:100 final size:99
Alignment explanation
Indices: 40390679--40390875 Score: 243
Period size: 100 Copynumber: 2.0 Consensus size: 99
40390669 TCAATTCGTT
* * * *
40390679 TTCATTTCAAGTAACATTGGTCTGTACAACACAAGACAAGTTCAAAGTAATATTCTTATTAGGCA
1 TTCATTTCAAGAAACATTGGTATGTACAACACAAGACAAATTCAAAG-AATATTCTTACTAGGCA
* *
40390744 TATTAAAATAGAATCGATCTGCATTCATTTCAACA
65 TACTAAAATAGAATCGATCTACATTCATTTCAACA
* * * *
40390779 TTCATTTTAAGAAACATTGGTATGTACGATACAAGACAAATTC-AAGACGATATTTTTACTAGGC
1 TTCATTTCAAGAAACATTGGTATGTACAACACAAGACAAATTCAAAGA--ATATTCTTACTAGGC
* * *
40390843 ATACTGAAATAGGATCGTTCTACATTCATTTCA
64 ATACTAAAATAGAATCGATCTACATTCATTTCA
40390876 GGTAACATTG
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
98 1 0.01
99 3 0.04
100 78 0.95
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (99 bp):
TTCATTTCAAGAAACATTGGTATGTACAACACAAGACAAATTCAAAGAATATTCTTACTAGGCAT
ACTAAAATAGAATCGATCTACATTCATTTCAACA
Found at i:40391006 original size:87 final size:88
Alignment explanation
Indices: 40390776--40391033 Score: 349
Period size: 88 Copynumber: 2.9 Consensus size: 88
40390766 ATTCATTTCA
* * * * * * * *
40390776 ACATTCATTTTAAGAAACATTGGTATGTACGATACAAGACAAATTCAAGACGATATTTTTACTAG
1 ACATTCATTTCAGGTAACATTGGCATGCACAATACAAGACAAATTCAAGACAATATTTTTGCTAG
*
40390841 GCATACTGAAATAGGATCGTTCT
66 GCATACTGAAATAGAATCGTTCT
40390864 ACATTCATTTCAGGTAACATTGGCATGCACAATACAAGACAAATTCAAGACAATATTTTTGCTAG
1 ACATTCATTTCAGGTAACATTGGCATGCACAATACAAGACAAATTCAAGACAATATTTTTGCTAG
40390929 GCATACTGAAATAGAATCGTTCT
66 GCATACTGAAATAGAATCGTTCT
* * * * *
40390952 GCA-TCATTTCAGGTAACATTGGCATGCACAATGCAAGACAAATTTAGGGA-AATATTTTTGTTA
1 ACATTCATTTCAGGTAACATTGGCATGCACAATACAAGACAAATTCA-AGACAATATTTTTGCTA
* *
40391015 GGCATACCGAAAGAGAATC
65 GGCATACTGAAATAGAATC
40391034 AATATCCACA
Statistics
Matches: 153, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
87 70 0.46
88 83 0.54
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.29
Consensus pattern (88 bp):
ACATTCATTTCAGGTAACATTGGCATGCACAATACAAGACAAATTCAAGACAATATTTTTGCTAG
GCATACTGAAATAGAATCGTTCT
Found at i:40394489 original size:23 final size:23
Alignment explanation
Indices: 40394438--40394519 Score: 85
Period size: 23 Copynumber: 3.5 Consensus size: 23
40394428 AACATTATTC
*
40394438 GTGAACATGTTCAATTATATGTTT
1 GTGAACATGTTCGATTA-ATGTTT
* * *
40394462 ATGAATATGTTCGTTTAATGTTT
1 GTGAACATGTTCGATTAATGTTT
*
40394485 GTGAACATGTTCGATTAA-GTTAA
1 GTGAACATGTTCGATTAATGTT-T
*
40394508 ATGAACATGTTC
1 GTGAACATGTTC
40394520 ATGAACATTA
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
22 3 0.06
23 32 0.67
24 13 0.27
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (23 bp):
GTGAACATGTTCGATTAATGTTT
Found at i:40394530 original size:23 final size:23
Alignment explanation
Indices: 40394486--40394531 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
40394476 TTAATGTTTG
* *
40394486 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
40394509 TGAACATGTTC-ATGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
40394532 CAAATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:40395833 original size:16 final size:16
Alignment explanation
Indices: 40395794--40395825 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40395784 AATGTCGATG
*
40395794 CCAATCAAATTAAGAC
1 CCAATCAAACTAAGAC
40395810 CCAATCAAACTAAGAC
1 CCAATCAAACTAAGAC
40395826 TTAATCAACT
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:0.50, C:0.28, G:0.06, T:0.16
Consensus pattern (16 bp):
CCAATCAAACTAAGAC
Found at i:40395844 original size:15 final size:16
Alignment explanation
Indices: 40395796--40395837 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
40395786 TGTCGATGCC
* **
40395796 AATCAAATTAAGACCC
1 AATCAAACTAAGACTT
40395812 AATCAAACTAAGACTT
1 AATCAAACTAAGACTT
40395828 AATC-AACTAA
1 AATCAAACTAA
40395838 ACATTAAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.52, C:0.21, G:0.05, T:0.21
Consensus pattern (16 bp):
AATCAAACTAAGACTT
Found at i:40400464 original size:263 final size:261
Alignment explanation
Indices: 40399995--40400524 Score: 697
Period size: 263 Copynumber: 2.0 Consensus size: 261
40399985 TGGTAGAAAC
**
40399995 AAATCAATTGTCGTTGGTGAAACCTTATAGAAGAAAAAAACACCAACTAAAAAAAAAAAGCAAAT
1 AAATCAATTGTCACTGGTGAAACCTTATAGAAGAAAAAAACACCAACT--AAAAAAAAAGCAAAT
* * * * ** *
40400060 CCAGTGTGATAAATAGGAGTTTGAATTCATTAAAGCTTGCAATCCAAATAGCTGTCAGCAATACG
64 CCAGGGTGACAAATAAGAGTTTGAATTCATTAAAGCTTCCAATCCAAATAGCTGAAAGCAACACG
* *
40400125 ATCGGGCAATAAAGTGCCCTAAAAGTGCATCACTGGAGGAACATTGAGATCCAACTACACCTTTA
129 ATCGGGCAATAAAGTGCCCTAAAAGTGCATCACTGGAGGAACACTGAGATCCAACTACACCCTTA
* * * * *
40400190 GAGTAATTGGGTTCTTAAAGCAAATAATCGAATACTTTTGTATACCTATCAATTCTTACATAAAT
194 GAATAATTGGGTTCTCAAAGCAAATAATCGAATACTTGTGTATACATATCAATTCTCACATAAAT
40400255 TTG
259 TTG
* *
40400258 AAATCAATTGTCACTGGTGAAACCTTATAGAAGGAAAAAAGAACACCAACT-AAAAAAACGGAAA
1 AAATCAATTGTCACTGGTGAAACCTTATAGAA-G-AAAAA-AACACCAACTAAAAAAAAAGCAAA
* * *
40400322 TCTAGGGTGACAAATAAGAGTTTGACTTCATTAAAGCTTCCAATCCAAATAGGTAGAAAG-AACA
63 TCCAGGGTGACAAATAAGAGTTTGAATTCATTAAAGCTTCCAATCCAAATAGCT-GAAAGCAACA
* * * * *
40400386 CGATCGGGCAGTAAAGTGCCTTAAATGTGCATCACTGGAGGAATACTGA-AGTCCAATTACACCC
127 CGATCGGGCAATAAAGTGCCCTAAAAGTGCATCACTGGAGGAACACTGAGA-TCCAACTACACCC
* * * * *
40400450 TTAGAATTATTGGGTTCTCAAAGCTAATAATTGAGTACTTGTGTATACATGTCAATTCTCACATA
191 TTAGAATAATTGGGTTCTCAAAGCAAATAATCGAATACTTGTGTATACATATCAATTCTCACATA
40400515 AATTTG
256 AATTTG
40400521 AAAT
1 AAAT
40400525 TTGATTTGAT
Statistics
Matches: 231, Mismatches: 31, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
262 1 0.00
263 211 0.91
264 4 0.02
265 5 0.02
266 10 0.04
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (261 bp):
AAATCAATTGTCACTGGTGAAACCTTATAGAAGAAAAAAACACCAACTAAAAAAAAAGCAAATCC
AGGGTGACAAATAAGAGTTTGAATTCATTAAAGCTTCCAATCCAAATAGCTGAAAGCAACACGAT
CGGGCAATAAAGTGCCCTAAAAGTGCATCACTGGAGGAACACTGAGATCCAACTACACCCTTAGA
ATAATTGGGTTCTCAAAGCAAATAATCGAATACTTGTGTATACATATCAATTCTCACATAAATTT
G
Found at i:40403295 original size:8 final size:8
Alignment explanation
Indices: 40403282--40403311 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
40403272 TGGGTTAAGA
40403282 TTAAAATT
1 TTAAAATT
40403290 TTAAAATT
1 TTAAAATT
40403298 TTAAAATT
1 TTAAAATT
*
40403306 TGAAAA
1 TTAAAA
40403312 AGTATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (8 bp):
TTAAAATT
Found at i:40404247 original size:19 final size:18
Alignment explanation
Indices: 40404225--40404281 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 18
40404215 AATATTAAAA
*
40404225 AATATTTTTTTATATTTTT
1 AATA-TTTTTTAAATTTTT
* *
40404244 AATAGTTTTTAAATTTTAA
1 AATATTTTTTAAATTTT-T
40404263 AATAATTTTTTAAATTTTT
1 AAT-ATTTTTTAAATTTTT
40404282 TAATTTTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
18 11 0.35
19 7 0.23
20 13 0.42
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
AATATTTTTTAAATTTTT
Found at i:40404271 original size:28 final size:27
Alignment explanation
Indices: 40404238--40404297 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 27
40404228 ATTTTTTTAT
40404238 ATTTTTAATAGTTTTTAAATTTTAAAATA
1 ATTTTTAA-AGTTTTTAAATTTTAAAA-A
* *
40404267 ATTTTTTAAATTTTTTAATTTTTAAAAA
1 A-TTTTTAAAGTTTTTAAATTTTAAAAA
40404295 ATT
1 ATT
40404298 AATTGTTGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 2 0.07
28 2 0.07
29 17 0.61
30 7 0.25
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (27 bp):
ATTTTTAAAGTTTTTAAATTTTAAAAA
Found at i:40405061 original size:29 final size:29
Alignment explanation
Indices: 40405007--40405063 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
40404997 ATTCAATTCA
* *
40405007 ACTCTTTTTTAAATGTTATGGTCAAACTCG
1 ACTCTTTTTAAAATGTTA-GGACAAACTCG
40405037 ACTCTTTTTAAAATGTTCA-GACAAACT
1 ACTCTTTTTAAAATGTT-AGGACAAACT
40405064 AAAGCTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.29
30 16 0.67
31 1 0.04
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.40
Consensus pattern (29 bp):
ACTCTTTTTAAAATGTTAGGACAAACTCG
Found at i:40407131 original size:18 final size:17
Alignment explanation
Indices: 40407100--40407133 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40407090 TATGGAAAGA
*
40407100 TGAAAAATTGAAGATAT
1 TGAAAAATAGAAGATAT
40407117 TGAAAAATAGAAAGATA
1 TGAAAAATAG-AAGATA
40407134 GAAAATGCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.59, C:0.00, G:0.18, T:0.24
Consensus pattern (17 bp):
TGAAAAATAGAAGATAT
Found at i:40412216 original size:31 final size:30
Alignment explanation
Indices: 40412181--40412287 Score: 112
Period size: 31 Copynumber: 3.5 Consensus size: 30
40412171 TTAGGAAGCC
40412181 CTTATTTGAGCACTTTCGAAAAGGTTTGGTT
1 CTTATTTGAGCACTTT-GAAAAGGTTTGGTT
** * *
40412212 CTTATTTGAGCACTCTAAAAAAGTTTTGG-C
1 CTTATTTGAGCACT-TTGAAAAGGTTTGGTT
40412242 CTTTATTTGAGCACTTTG-AAAGGTTTGGTT
1 C-TTATTTGAGCACTTTGAAAAGGTTTGGTT
*
40412272 -TTCATTTGAACACTTT
1 CTT-ATTTGAGCACTTT
40412288 TGTAAATGTT
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
28 2 0.03
29 21 0.33
30 2 0.03
31 37 0.59
32 1 0.02
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.43
Consensus pattern (30 bp):
CTTATTTGAGCACTTTGAAAAGGTTTGGTT
Found at i:40413377 original size:17 final size:17
Alignment explanation
Indices: 40413346--40413387 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
40413336 GGAAAAAATA
*
40413346 GTTACAAGAATATGAAAG
1 GTTA-AAGAAGATGAAAG
40413364 GTTAAAGAAGATGAAAG
1 GTTAAAGAAGATGAAAG
40413381 GTTAAAG
1 GTTAAAG
40413388 GTTAATGAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.50, C:0.02, G:0.26, T:0.21
Consensus pattern (17 bp):
GTTAAAGAAGATGAAAG
Found at i:40413392 original size:24 final size:24
Alignment explanation
Indices: 40413360--40413407 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
40413350 CAAGAATATG
40413360 AAAGGTTAAAGAAGATGAAAGGTT
1 AAAGGTTAAAGAAGATGAAAGGTT
*
40413384 AAAGGTTAATGAAGATGAAAGGTT
1 AAAGGTTAAAGAAGATGAAAGGTT
40413408 GAACATTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.29, T:0.23
Consensus pattern (24 bp):
AAAGGTTAAAGAAGATGAAAGGTT
Found at i:40420526 original size:34 final size:34
Alignment explanation
Indices: 40420486--40420639 Score: 202
Period size: 34 Copynumber: 4.5 Consensus size: 34
40420476 TACTACTGAT
* *
40420486 TTGATTTGTTATAAGCATATTAATTGCTATCATA
1 TTGATCTGTTATAAGCATATTAATTACTATCATA
* * * *
40420520 TCGATTTGTTATAAGCATATTAATTACTACCGTA
1 TTGATCTGTTATAAGCATATTAATTACTATCATA
*
40420554 TTGATCTGTTATAAGCATATTAATTACTATCGTA
1 TTGATCTGTTATAAGCATATTAATTACTATCATA
* * *
40420588 TTGATCTATTATAAGCACATTAATTGCTA-CAGTA
1 TTGATCTGTTATAAGCATATTAATTACTATCA-TA
40420622 TTGATCTGTTATAAGCAT
1 TTGATCTGTTATAAGCAT
40420640 GCCACATTGC
Statistics
Matches: 106, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
33 1 0.01
34 105 0.99
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (34 bp):
TTGATCTGTTATAAGCATATTAATTACTATCATA
Found at i:40420571 original size:68 final size:68
Alignment explanation
Indices: 40420486--40420639 Score: 227
Period size: 68 Copynumber: 2.3 Consensus size: 68
40420476 TACTACTGAT
* * * * * *
40420486 TTGATTTGTTATAAGCATATTAATTGCTATCATATCGATTTGTTATAAGCATATTAATTACTACC
1 TTGATCTGTTATAAGCATATTAATTACTATCATATCGATCTATTATAAGCACATTAATTACTACA
40420551 GTA
66 GTA
* * *
40420554 TTGATCTGTTATAAGCATATTAATTACTATCGTATTGATCTATTATAAGCACATTAATTGCTACA
1 TTGATCTGTTATAAGCATATTAATTACTATCATATCGATCTATTATAAGCACATTAATTACTACA
40420619 GTA
66 GTA
40420622 TTGATCTGTTATAAGCAT
1 TTGATCTGTTATAAGCAT
40420640 GCCACATTGC
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 77 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (68 bp):
TTGATCTGTTATAAGCATATTAATTACTATCATATCGATCTATTATAAGCACATTAATTACTACA
GTA
Found at i:40422704 original size:27 final size:27
Alignment explanation
Indices: 40422669--40422721 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
40422659 ATTTTTTATT
* *
40422669 TTGAAATTCCTTCCAAAATAAAAATTA
1 TTGAAATTCATTACAAAATAAAAATTA
*
40422696 TTGAAATTCATTACTAAATAAAAATT
1 TTGAAATTCATTACAAAATAAAAATT
40422722 CTTTCATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (27 bp):
TTGAAATTCATTACAAAATAAAAATTA
Done.