Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 60 of 193
Found at i:18873874 original size:21 final size:21
Alignment explanation
Indices: 18873850--18873925 Score: 107
Period size: 21 Copynumber: 3.6 Consensus size: 21
18873840 GAAATTTAAA
18873850 ACAAACATAATGAGGAGAGTT
1 ACAAACATAATGAGGAGAGTT
* * *
18873871 ACAAAACATTACGAGAAGAGTT
1 AC-AAACATAATGAGGAGAGTT
*
18873893 ACAAACATTATGAGGAGAGTT
1 ACAAACATAATGAGGAGAGTT
18873914 ACAAACATAATG
1 ACAAACATAATG
18873926 TTTTGTAGGT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
21 30 0.62
22 18 0.38
ACGTcount: A:0.49, C:0.12, G:0.20, T:0.20
Consensus pattern (21 bp):
ACAAACATAATGAGGAGAGTT
Found at i:18888296 original size:15 final size:15
Alignment explanation
Indices: 18888276--18888312 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
18888266 TCGCACGAGT
* *
18888276 AGAAGAAGTAGAAGA
1 AGAAGAAGGAAAAGA
18888291 AGAAGAAGGAAAAGA
1 AGAAGAAGGAAAAGA
18888306 AGAAGAA
1 AGAAGAA
18888313 AGAGAGGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (15 bp):
AGAAGAAGGAAAAGA
Found at i:18888305 original size:12 final size:12
Alignment explanation
Indices: 18888276--18888331 Score: 51
Period size: 12 Copynumber: 4.4 Consensus size: 12
18888266 TCGCACGAGT
18888276 AGAAGAAGTAGAAGA
1 AGAAGAAG--GAA-A
18888291 AGAAGAAGGAAA
1 AGAAGAAGGAAA
18888303 AGAAGAA-GAAA
1 AGAAGAAGGAAA
*
18888314 GAGAGGAAGGAAA
1 -AGAAGAAGGAAA
*
18888327 TGAAG
1 AGAAG
18888332 TTGAGGCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
11 4 0.11
12 17 0.47
13 7 0.19
15 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.36, T:0.04
Consensus pattern (12 bp):
AGAAGAAGGAAA
Found at i:18888312 original size:24 final size:24
Alignment explanation
Indices: 18888276--18888331 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
18888266 TCGCACGAGT
18888276 AGAAGAAGTAGAAGAAGAAGAAGGAAA
1 AGAAGAAG-A-AAG-AGAAGAAGGAAA
*
18888303 AGAAGAAGAAAGAGAGGAAGGAAA
1 AGAAGAAGAAAGAGAAGAAGGAAA
*
18888327 TGAAG
1 AGAAG
18888332 TTGAGGCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 15 0.56
25 3 0.11
26 1 0.04
27 8 0.30
ACGTcount: A:0.61, C:0.00, G:0.36, T:0.04
Consensus pattern (24 bp):
AGAAGAAGAAAGAGAAGAAGGAAA
Found at i:18888322 original size:15 final size:15
Alignment explanation
Indices: 18888276--18888322 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
18888266 TCGCACGAGT
18888276 AGAAG-AAGTAGAAGA
1 AGAAGAAAG-AGAAGA
* *
18888291 AGAAGAAGGAAAAGA
1 AGAAGAAAGAGAAGA
*
18888306 AGAAGAAAGAGAGGA
1 AGAAGAAAGAGAAGA
18888321 AG
1 AG
18888323 GAAATGAAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 24 0.92
16 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02
Consensus pattern (15 bp):
AGAAGAAAGAGAAGA
Found at i:18888803 original size:34 final size:34
Alignment explanation
Indices: 18888740--18888809 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 34
18888730 GTAGCTATAA
*
18888740 TTTAACTGTCACCACATTTCCTTTATCATTGCAT
1 TTTAACTGTCACCACATTTCCATTATCATTGCAT
* * * * *
18888774 TTTAATTGTCACTACATTTGCATTGTCATTGTAT
1 TTTAACTGTCACCACATTTCCATTATCATTGCAT
18888808 TT
1 TT
18888810 CCATTCGTCG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.23, C:0.20, G:0.09, T:0.49
Consensus pattern (34 bp):
TTTAACTGTCACCACATTTCCATTATCATTGCAT
Found at i:18891282 original size:2 final size:2
Alignment explanation
Indices: 18891213--18891263 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
18891203 ATCTCCCTTC
* * * * *
18891213 CT CT CT CT TT AT CT CT CG CT CT CT CT CT CT CA CT CT TT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
18891255 CT CT CT CT C
1 CT CT CT CT C
18891264 CATCCCTCCC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.04, C:0.45, G:0.02, T:0.49
Consensus pattern (2 bp):
CT
Found at i:18896608 original size:40 final size:41
Alignment explanation
Indices: 18896553--18896636 Score: 152
Period size: 40 Copynumber: 2.1 Consensus size: 41
18896543 AGGGTTTTTA
18896553 GTCTTATTGTGTTACTGTTTTCCTTCACAGTATTA-ATTAG
1 GTCTTATTGTGTTACTGTTTTCCTTCACAGTATTACATTAG
*
18896593 GTCTTATTGTGTTACTGTTTTCCTTCACATTATTACATTAG
1 GTCTTATTGTGTTACTGTTTTCCTTCACAGTATTACATTAG
18896634 GTC
1 GTC
18896637 AATGAGTCAA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
40 34 0.81
41 8 0.19
ACGTcount: A:0.19, C:0.17, G:0.14, T:0.50
Consensus pattern (41 bp):
GTCTTATTGTGTTACTGTTTTCCTTCACAGTATTACATTAG
Found at i:18897689 original size:49 final size:48
Alignment explanation
Indices: 18897617--18897725 Score: 155
Period size: 49 Copynumber: 2.2 Consensus size: 48
18897607 AGTCTCCATT
** *
18897617 ATATATATTTTTCTAGTCATCATCTAATCTCTCACCCTCTCACTCTAC
1 ATATATATTAATCTAGTCATCATCTAATCTCACACCCTCTCACTCTAC
* * *
18897665 ATATATATTAATCGTAGTCTTCATCTAATCTCACACTCTCTCACTCTCC
1 ATATATATTAATC-TAGTCATCATCTAATCTCACACCCTCTCACTCTAC
18897714 ATATATATTAAT
1 ATATATATTAAT
18897726 TATTTGGATT
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
48 11 0.20
49 43 0.80
ACGTcount: A:0.28, C:0.28, G:0.03, T:0.41
Consensus pattern (48 bp):
ATATATATTAATCTAGTCATCATCTAATCTCACACCCTCTCACTCTAC
Found at i:18898978 original size:41 final size:41
Alignment explanation
Indices: 18898916--18898996 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 41
18898906 AAATCTCCAT
* * *
18898916 ATATATATTACTCATAATCTTCATCTACTCTCTTACTCTCC
1 ATATATATTAATCATAATCTTCATCTAATCTCTCACTCTCC
*
18898957 ATATATATTAATCATACTCTTCATCTAATCTCTCACTCTC
1 ATATATATTAATCATAATCTTCATCTAATCTCTCACTCTC
18898997 TCAATGTCTC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.43
Consensus pattern (41 bp):
ATATATATTAATCATAATCTTCATCTAATCTCTCACTCTCC
Found at i:18900445 original size:30 final size:30
Alignment explanation
Indices: 18900404--18900472 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
18900394 TGTCCACGAA
* *
18900404 TATTTTTGGTGAAAAGAATACCATAAGTGG
1 TATTCTTGGTGAAAAGAAGACCATAAGTGG
* *
18900434 TATTCTTGGTGACAAGAAGACCATAATTGG
1 TATTCTTGGTGAAAAGAAGACCATAAGTGG
18900464 TATTCTTGG
1 TATTCTTGG
18900473 ACTAGGAACA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (30 bp):
TATTCTTGGTGAAAAGAAGACCATAAGTGG
Found at i:18920625 original size:5 final size:5
Alignment explanation
Indices: 18920615--18920643 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
18920605 AACCCATTCT
18920615 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
18920644 TCGTCTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:18922724 original size:23 final size:23
Alignment explanation
Indices: 18922694--18922744 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
18922684 CGTGGCGTCT
* *
18922694 AGTCAACAGCTTCTAGAAGATCC
1 AGTCAACAACTTCCAGAAGATCC
* *
18922717 AGTCAACAACTTCCAGAAGGTCT
1 AGTCAACAACTTCCAGAAGATCC
18922740 AGTCA
1 AGTCA
18922745 GCAAGGATAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (23 bp):
AGTCAACAACTTCCAGAAGATCC
Found at i:18925756 original size:182 final size:183
Alignment explanation
Indices: 18925350--18925757 Score: 470
Period size: 186 Copynumber: 2.2 Consensus size: 183
18925340 CAAATAGGTG
* * * * *
18925350 AAGAATATAAAATAAAGCACGTGTAAGTCGATAAACTCGTTCCAAAGTATGTGAAAGTTAATATG
1 AAGAATATAAAATAGAGCACGTGTAAGTTGATAAACTCGTTCCAAAGAATGCGAAAGTGAATATG
* * * * * *
18925415 TACAACAATAAATGCAAAACAATTAAATTCAAAATGATATAATAGAACACGTGTAAGTCGATAAA
66 CACAACAATAAATACAAAAAAATTAAA-T-AAAATGATAAAACAGAACACCTGTAAGTCGATAAA
* * * *
18925480 CTGCTACAATTGAAATTATAAATCGTTACATTGAAATAGAAGGAAAGACTTAATTC
129 CTGCTACAACTGAAATTATAAATCCTTACAATGAAATAGAA-GAAACACTTAATTC
* * *
18925536 AAGAATATAAAATAGAGTACGTGTAAGTTGAAAAACTCGTTGCAAAGAATGCGATAAG-GAATAT
1 AAGAATATAAAATAGAGCACGTGTAAGTTGATAAACTCGTTCCAAAGAATGCGA-AAGTGAATAT
* *
18925600 GCACATCAATAAATACATAAAAAATTAAA-AAACAT-ATAAAACAGAACACCTGTATGTCGATAA
65 GCACAACAATAAATACA-AAAAAATTAAATAAA-ATGATAAAACAGAACACCTGTAAGTCGATAA
* * *
18925663 ACTGGTTACTACTGAAATTATAAATCCTTACAATGAAAATA-AA-AAACA-TTAATTT
128 ACT-GCTACAACTGAAATTATAAATCCTTACAATG-AAATAGAAGAAACACTTAATTC
*
18925718 AA-AAGTATAAAATAGAGCACTTGTAAGTTGATAAACTCGT
1 AAGAA-TATAAAATAGAGCACGTGTAAGTTGATAAACTCGT
18925758 GGTAAGTATG
Statistics
Matches: 190, Mismatches: 26, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
181 2 0.01
182 40 0.21
183 4 0.02
184 30 0.16
185 30 0.16
186 71 0.37
187 13 0.07
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (183 bp):
AAGAATATAAAATAGAGCACGTGTAAGTTGATAAACTCGTTCCAAAGAATGCGAAAGTGAATATG
CACAACAATAAATACAAAAAAATTAAATAAAATGATAAAACAGAACACCTGTAAGTCGATAAACT
GCTACAACTGAAATTATAAATCCTTACAATGAAATAGAAGAAACACTTAATTC
Found at i:18926357 original size:4 final size:4
Alignment explanation
Indices: 18926348--18926399 Score: 61
Period size: 4 Copynumber: 12.8 Consensus size: 4
18926338 TTCATCTAAT
* *
18926348 CTCC CTCC CTCC CTCTC CTCC CTCC CTCTC C-CT CTCC CTCC ATCC CTCC
1 CTCC CTCC CTCC CTC-C CTCC CTCC CTC-C CTCC CTCC CTCC CTCC CTCC
18926397 CTC
1 CTC
18926400 TCTCTCTCTC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 1 0.02
4 34 0.83
5 6 0.15
ACGTcount: A:0.02, C:0.69, G:0.00, T:0.29
Consensus pattern (4 bp):
CTCC
Found at i:18926369 original size:13 final size:13
Alignment explanation
Indices: 18926351--18926401 Score: 70
Period size: 12 Copynumber: 4.1 Consensus size: 13
18926341 ATCTAATCTC
18926351 CCTCCCTCCCTCT
1 CCTCCCTCCCTCT
18926364 CCTCCCTCCCTCT
1 CCTCCCTCCCTCT
*
18926377 CC-CTCTCCCTC-
1 CCTCCCTCCCTCT
*
18926388 CATCCCTCCCTCT
1 CCTCCCTCCCTCT
18926401 C
1 C
18926402 TCTCTCTCTC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
11 1 0.03
12 16 0.48
13 16 0.48
ACGTcount: A:0.02, C:0.69, G:0.00, T:0.29
Consensus pattern (13 bp):
CCTCCCTCCCTCT
Found at i:18926398 original size:24 final size:23
Alignment explanation
Indices: 18926352--18926413 Score: 81
Period size: 24 Copynumber: 2.7 Consensus size: 23
18926342 TCTAATCTCC
18926352 CTCCCTC-CCTCTCCTCCCTCCCT
1 CTCCCTCTCC-CTCCTCCCTCCCT
18926375 CTCCCTCTCCCTCCATCCCTCCCT
1 CTCCCTCTCCCTCC-TCCCTCCCT
* *
18926399 CTCTCTCTCTCTCCT
1 CTCCCTCTCCCTCCT
18926414 TCACTCTCAC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 12 0.34
24 23 0.66
ACGTcount: A:0.02, C:0.65, G:0.00, T:0.34
Consensus pattern (23 bp):
CTCCCTCTCCCTCCTCCCTCCCT
Found at i:18926745 original size:3 final size:3
Alignment explanation
Indices: 18926737--18926763 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
18926727 CTCTATCACA
18926737 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
18926764 TGAATAGCTA
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:18928043 original size:53 final size:50
Alignment explanation
Indices: 18927967--18928090 Score: 169
Period size: 53 Copynumber: 2.4 Consensus size: 50
18927957 ATACAATTTT
* *
18927967 TGAAC-AAACAATATAAATAAATATTTATATTTATATAAAAACACCATATC
1 TGAACAAAACAATTTAAATAAATATTTATATTTATAT-AAAACACCAGATC
* *
18928017 TGAACAAAAAACAATTTAAATAAATATTTATTTTTATATAAAACACTAGATC
1 TGAAC--AAAACAATTTAAATAAATATTTATATTTATATAAAACACCAGATC
*
18928069 TGAACAAAACAATTTAGATAAA
1 TGAACAAAACAATTTAAATAAA
18928091 CAAGTTCTAA
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
50 21 0.32
52 16 0.24
53 29 0.44
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.31
Consensus pattern (50 bp):
TGAACAAAACAATTTAAATAAATATTTATATTTATATAAAACACCAGATC
Found at i:18930898 original size:82 final size:82
Alignment explanation
Indices: 18930720--18931318 Score: 644
Period size: 82 Copynumber: 7.4 Consensus size: 82
18930710 TTAAACAATA
** * * * *
18930720 GGAATAAATCCTAAAACATAACTATTTAATTAATTCTTGTTTGGAAACAAAATCAAAATA-AATT
1 GGAATAAATCCCGAAACAGAATTATTCAATTAATTCTTGTTTGGAAACAAAATCAAAATAGAATA
* *
18930784 ATAT-TGAATG-ACA---
66 AAATCTG-TTGAACAGCG
* * * * *
18930797 GGAATAAATCTCAAAACAGAATTAATCAATTAATTCTTGTTTGGAAACAAAATCAGAATTGAATA
1 GGAATAAATCCCGAAACAGAATTATTCAATTAATTCTTGTTTGGAAACAAAATCAAAATAGAATA
18930862 AAATCTGTTGAACAGCG
66 AAATCTGTTGAACAGCG
* * *
18930879 GGAATAAATCCCGAAACAGAATTATTCTATTAATTCTTGTTTGGAAGCAAAATCATAATAGAATA
1 GGAATAAATCCCGAAACAGAATTATTCAATTAATTCTTGTTTGGAAACAAAATCAAAATAGAATA
* *
18930944 AAATCTGTTGTA-AGACA
66 AAATCTGTTGAACAG-CG
* * * *
18930961 GGAATAAATCCTGAAACAGAATTATTCAACTAA-TCGTTGTTTGGAAGCAAAATTAAAATAGAAT
1 GGAATAAATCCCGAAACAGAATTATTCAATTAATTC-TTGTTTGGAAACAAAATCAAAATAGAAT
** *
18931025 AAAATCTGTTGAATGGTG
65 AAAATCTGTTGAACAGCG
* * *
18931043 GGAATAAATCCCGAAACAGAATTATTCAATTAATCCTTGCTTGGAAATAAAATCAAAATAGAATA
1 GGAATAAATCCCGAAACAGAATTATTCAATTAATTCTTGTTTGGAAACAAAATCAAAATAGAATA
* * **
18931108 AAATTTGTCGAACAATG
66 AAATCTGTTGAACAGCG
** * *
18931125 GGAATAAATCTTGAAACAAAATTATTCAATTAA-TCATTGTTTGGAAACAAAATCAAAATATAAT
1 GGAATAAATCCCGAAACAGAATTATTCAATTAATTC-TTGTTTGGAAACAAAATCAAAATAGAAT
* * *
18931189 AAACTCTATTGAACTGCG
65 AAAATCTGTTGAACAGCG
** * * * *
18931207 GGAATAAATCTAGAGACAGATTTATTAAATTAATTCTT-TTTGGAAACAAAATCACAATAGAATA
1 GGAATAAATCCCGAAACAGAATTATTCAATTAATTCTTGTTTGGAAACAAAATCAAAATAGAATA
**
18931271 AAATAAGTTGAAC-GACG
66 AAATCTGTTGAACAG-CG
*
18931288 GGAATAAATCCCGAAACAGATTTATTCAATT
1 GGAATAAATCCCGAAACAGAATTATTCAATT
18931319 TTAACTTTTA
Statistics
Matches: 439, Mismatches: 70, Indels: 22
0.83 0.13 0.04
Matches are distributed among these distances:
77 52 0.12
78 8 0.02
79 5 0.01
80 1 0.00
81 67 0.15
82 302 0.69
83 4 0.01
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (82 bp):
GGAATAAATCCCGAAACAGAATTATTCAATTAATTCTTGTTTGGAAACAAAATCAAAATAGAATA
AAATCTGTTGAACAGCG
Found at i:18931841 original size:49 final size:50
Alignment explanation
Indices: 18931788--18931964 Score: 223
Period size: 49 Copynumber: 3.5 Consensus size: 50
18931778 CGTAAATACA
* * *
18931788 AGATCT-AAAAAAACAATATAAATAAATATTTCTATTTATGTAAAACACC
1 AGATCTGAAAAAAACAATTTAAATAAATATTTATATTTATATAAAACACC
* *
18931837 AGATCTGAACAAAA-AATTTAAATAAATATTTATATTTATATAAAACACT
1 AGATCTGAAAAAAACAATTTAAATAAATATTTATATTTATATAAAACACC
* * *
18931886 AGATCCGAACAAAAAATAATTTAAATAAATATTTATTTTTATATAAAACACC
1 AGATCTG-A-AAAAAACAATTTAAATAAATATTTATATTTATATAAAACACC
* * *
18931938 AAATCTGAACAAAACAATTTAGATAAA
1 AGATCTGAAAAAAACAATTTAAATAAA
18931965 CAAGTTCTAA
Statistics
Matches: 110, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
49 43 0.39
50 23 0.21
51 6 0.05
52 38 0.35
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.31
Consensus pattern (50 bp):
AGATCTGAAAAAAACAATTTAAATAAATATTTATATTTATATAAAACACC
Found at i:18931903 original size:43 final size:45
Alignment explanation
Indices: 18931799--18931951 Score: 135
Period size: 52 Copynumber: 3.2 Consensus size: 45
18931789 GATCTAAAAA
* * * *
18931799 AACAATATAAATAAATATTTCTATTTATGTAAAACACCAGATCTG
1 AACAAAATAAATAAATATTTATATTTATATAAAACACCAGATCCG
*
18931844 AACAAAAAATTTAAATAAATATTTATATTTATATAAAACACTAGATCCG
1 AAC--AAAA--TAAATAAATATTTATATTTATATAAAACACCAGATCCG
* * *
18931893 AACAAAAAATAATTTAAATAAATATTTATTTTTATATAAAACACCAAATCTG
1 AAC----AA-AA--TAAATAAATATTTATATTTATATAAAACACCAGATCCG
18931945 AACAAAA
1 AACAAAA
18931952 CAATTTAGAT
Statistics
Matches: 92, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
45 3 0.03
47 5 0.05
48 2 0.02
49 37 0.40
51 4 0.04
52 41 0.45
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.32
Consensus pattern (45 bp):
AACAAAATAAATAAATATTTATATTTATATAAAACACCAGATCCG
Found at i:18937905 original size:49 final size:49
Alignment explanation
Indices: 18937846--18938009 Score: 224
Period size: 49 Copynumber: 3.4 Consensus size: 49
18937836 ATGTTTTTAC
* * *
18937846 TAGT-TTCATCTAATCTCTCAGC-CACTCACTCTCCATATATACTAATCA
1 TAGTCTTCATCTAATCTCACA-CTCTCTCACTCTCCATATATATTAATCA
*
18937894 TAATCTTCATCTAATCTCACACTCTCTCACTCTCCATATATATTAATCA
1 TAGTCTTCATCTAATCTCACACTCTCTCACTCTCCATATATATTAATCA
* * *
18937943 TAGTTTTCATCTAAACTCACACTCTCTCACTCTCCGTATATATTAATCA
1 TAGTCTTCATCTAATCTCACACTCTCTCACTCTCCATATATATTAATCA
* *
18937992 TAGTCTTCTTTTAATCTC
1 TAGTCTTCATCTAATCTC
18938010 TCACCCTCCA
Statistics
Matches: 102, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
48 4 0.04
49 98 0.96
ACGTcount: A:0.28, C:0.29, G:0.03, T:0.40
Consensus pattern (49 bp):
TAGTCTTCATCTAATCTCACACTCTCTCACTCTCCATATATATTAATCA
Found at i:18939269 original size:49 final size:49
Alignment explanation
Indices: 18939216--18939408 Score: 159
Period size: 57 Copynumber: 3.9 Consensus size: 49
18939206 ATTGTTTGTC
* *
18939216 TAGTCTTCATCTAATCTTTCACTCTCTAACTCTCCATATATATTAGTCA
1 TAGTCTTCATCTAATCTCTCACTCTCTAACTCTCCATATATATTAATCA
*
18939265 TAGTCTTCATCT-A---CT--CTCTC--ACTCTTCATATATATTAATCA
1 TAGTCTTCATCTAATCTCTCACTCTCTAACTCTCCATATATATTAATCA
* * *
18939306 TAGTCTTAATCTAATCCCTCACTCTCTCATTGTCTCACTTTCCATATATATTAATCA
1 TAGTCTTCATCTAATCTCTCACTCTCT-A-------ACTCTCCATATATATTAATCA
* * * * *
18939363 TAGCCTTTATCTAATCTCTCACTCTTTCACTCTCAATATATATTAA
1 TAGTCTTCATCTAATCTCTCACTCTCTAACTCTCCATATATATTAA
18939409 CCCTTTGACT
Statistics
Matches: 115, Mismatches: 13, Indels: 32
0.72 0.08 0.20
Matches are distributed among these distances:
41 30 0.26
42 1 0.01
43 5 0.04
45 3 0.03
47 5 0.04
48 1 0.01
49 28 0.24
57 42 0.37
ACGTcount: A:0.27, C:0.27, G:0.03, T:0.43
Consensus pattern (49 bp):
TAGTCTTCATCTAATCTCTCACTCTCTAACTCTCCATATATATTAATCA
Found at i:18939327 original size:41 final size:41
Alignment explanation
Indices: 18939244--18939335 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 41
18939234 TCACTCTCTA
* * * * *
18939244 ACTCTCCATATATATTAGTCATAGTCTTCATCTACTCTCTC
1 ACTCTTCATATATATTAATCATAGTCTTAATCTAATCCCTC
18939285 ACTCTTCATATATATTAATCATAGTCTTAATCTAATCCCTC
1 ACTCTTCATATATATTAATCATAGTCTTAATCTAATCCCTC
18939326 ACTCTCTCAT
1 ACTCT-TCAT
18939336 TGTCTCACTT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 41 0.91
42 4 0.09
ACGTcount: A:0.27, C:0.28, G:0.03, T:0.41
Consensus pattern (41 bp):
ACTCTTCATATATATTAATCATAGTCTTAATCTAATCCCTC
Found at i:18942925 original size:24 final size:23
Alignment explanation
Indices: 18942865--18942928 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 23
18942855 GTTTGATTTA
18942865 AAAATATATAA-AAAATGAAATC
1 AAAATATATAATAAAATGAAATC
*
18942887 ATAAATATTTAAATAAAA-GAAACTAC
1 A-AAATATAT-AATAAAATGAAA-T-C
18942913 AAAATATATAATAAAA
1 AAAATATATAATAAAA
18942929 CACCTCTAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
22 1 0.03
23 7 0.20
24 13 0.37
25 12 0.34
26 2 0.06
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.25
Consensus pattern (23 bp):
AAAATATATAATAAAATGAAATC
Found at i:18945055 original size:22 final size:22
Alignment explanation
Indices: 18945028--18945077 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
18945018 TCCTTCTCTG
18945028 TCTCTCCATCCCTACCTCACTC
1 TCTCTCCATCCCTACCTCACTC
* * *
18945050 TCTCTCCCTCCCTTCCTCCCTC
1 TCTCTCCATCCCTACCTCACTC
*
18945072 TTTCTC
1 TCTCTC
18945078 TCTCCTTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.06, C:0.56, G:0.00, T:0.38
Consensus pattern (22 bp):
TCTCTCCATCCCTACCTCACTC
Found at i:18945953 original size:65 final size:65
Alignment explanation
Indices: 18945846--18945969 Score: 221
Period size: 65 Copynumber: 1.9 Consensus size: 65
18945836 GCCCATCCCA
*
18945846 TGCTCCCCCATATCTATTGCTACTCATCCTATTGCCTCCGCACAATAAGAACTACCTATAGTCGG
1 TGCTCCCCCATATCTATCGCTACTCATCCTATTGCCTCCGCACAATAAGAACTACCTATAGTCGG
* *
18945911 TGCTCCCCTATATCTATCGCTACTCATCCTATTGCCTTCGCACAATAAGAACTACCTAT
1 TGCTCCCCCATATCTATCGCTACTCATCCTATTGCCTCCGCACAATAAGAACTACCTAT
18945970 GGTCTGTACA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 56 1.00
ACGTcount: A:0.25, C:0.34, G:0.10, T:0.31
Consensus pattern (65 bp):
TGCTCCCCCATATCTATCGCTACTCATCCTATTGCCTCCGCACAATAAGAACTACCTATAGTCGG
Found at i:18951181 original size:18 final size:17
Alignment explanation
Indices: 18951154--18951188 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
18951144 CTTCATCTAA
18951154 TCTCCTCCCTCCCTCCC
1 TCTCCTCCCTCCCTCCC
18951171 TCTCTCTCCCTCCCTCCC
1 TCTC-CTCCCTCCCTCCC
18951189 CCACTTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.00, C:0.69, G:0.00, T:0.31
Consensus pattern (17 bp):
TCTCCTCCCTCCCTCCC
Found at i:18953846 original size:26 final size:26
Alignment explanation
Indices: 18953817--18953880 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
18953807 CATAAGCTAA
*
18953817 ATTTCTTTTAAAAGTG-TTAAAATTAT
1 ATTTCTTATAAAAGTGCTT-AAATTAT
* *
18953843 ATTT-ATATATAAGTGCTTAAATTAT
1 ATTTCTTATAAAAGTGCTTAAATTAT
18953868 ATTTCTATATAAA
1 ATTTCT-TATAAA
18953881 TTTGTGAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
25 19 0.63
26 6 0.20
27 5 0.17
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.48
Consensus pattern (26 bp):
ATTTCTTATAAAAGTGCTTAAATTAT
Found at i:18953856 original size:25 final size:25
Alignment explanation
Indices: 18953828--18953879 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
18953818 TTTCTTTTAA
18953828 AAGTG-TTAAAATTATATTTATATAT
1 AAGTGCTT-AAATTATATTTATATAT
*
18953853 AAGTGCTTAAATTATATTTCTATAT
1 AAGTGCTTAAATTATATTTATATAT
18953878 AA
1 AA
18953880 ATTTGTGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (25 bp):
AAGTGCTTAAATTATATTTATATAT
Found at i:18956734 original size:22 final size:22
Alignment explanation
Indices: 18956687--18956735 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
18956677 TTCATCTAAT
* *
18956687 CTCTCTCTCTCCATCCCTCCCC
1 CTCTCTCTCTCCATCACTCCCA
* *
18956709 CTCTCTCTCTCCTTCACTCTCA
1 CTCTCTCTCTCCATCACTCCCA
18956731 CTCTC
1 CTCTC
18956736 CATATATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.06, C:0.57, G:0.00, T:0.37
Consensus pattern (22 bp):
CTCTCTCTCTCCATCACTCCCA
Found at i:18959541 original size:25 final size:23
Alignment explanation
Indices: 18959513--18959558 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
18959503 GTTGGATCCA
18959513 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
18959538 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
18959559 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:18961522 original size:6 final size:6
Alignment explanation
Indices: 18961513--18961583 Score: 67
Period size: 6 Copynumber: 12.3 Consensus size: 6
18961503 AGTGAATAAT
* * *
18961513 AAAATA AAAA-A ATAA-A AAAATA AAACT- AAAATA AAAATA AAAATG
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
* * *
18961558 AAAATG AAAATG AAAATG AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AA
18961584 TGTACTAATT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
5 12 0.21
6 45 0.79
ACGTcount: A:0.77, C:0.01, G:0.06, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:18961524 original size:8 final size:8
Alignment explanation
Indices: 18961507--18961555 Score: 55
Period size: 8 Copynumber: 6.0 Consensus size: 8
18961497 AAAAATAGTG
*
18961507 AATAATAA
1 AATAAAAA
18961515 AATAAAAA
1 AATAAAAA
18961523 AATAAAAA
1 AATAAAAA
18961531 AATAAAACTA
1 AATAAAA--A
*
18961541 AA-ATAAA
1 AATAAAAA
18961548 AATAAAAA
1 AATAAAAA
18961556 TGAAAATGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
7 3 0.09
8 26 0.74
9 3 0.09
10 3 0.09
ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16
Consensus pattern (8 bp):
AATAAAAA
Found at i:18961555 original size:18 final size:18
Alignment explanation
Indices: 18961528--18961583 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 18
18961518 AAAAAAATAA
*
18961528 AAAAATAAAACT-AAAAT
1 AAAAATAAAAATGAAAAT
18961545 AAAAATAAAAATGAAAAT
1 AAAAATAAAAATGAAAAT
* *
18961563 GAAAATGAAAATGAAAAT
1 AAAAATAAAAATGAAAAT
18961581 AAA
1 AAA
18961584 TGTACTAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 11 0.32
18 23 0.68
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.16
Consensus pattern (18 bp):
AAAAATAAAAATGAAAAT
Found at i:18963753 original size:6 final size:6
Alignment explanation
Indices: 18963742--18963784 Score: 59
Period size: 6 Copynumber: 6.8 Consensus size: 6
18963732 TATAGCAATA
*
18963742 TTTCTT TTTCTT TTCTCTT TTTCTT TTTTTCT TTTCTT TTTCT
1 TTTCTT TTTCTT TT-TCTT TTTCTT TTTCT-T TTTCTT TTTCT
18963785 CGTTCAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 22 0.67
7 11 0.33
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTCTT
Found at i:18963762 original size:13 final size:12
Alignment explanation
Indices: 18963742--18963784 Score: 59
Period size: 13 Copynumber: 3.4 Consensus size: 12
18963732 TATAGCAATA
18963742 TTTCTTTTTCTT
1 TTTCTTTTTCTT
18963754 TTCTCTTTTTCTT
1 TT-TCTTTTTCTT
*
18963767 TTTTTCTTTTCTT
1 TTTCT-TTTTCTT
18963780 TTTCT
1 TTTCT
18963785 CGTTCAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 4 0.15
13 23 0.85
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTCTTTTTCTT
Found at i:18963766 original size:19 final size:19
Alignment explanation
Indices: 18963742--18963784 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
18963732 TATAGCAATA
18963742 TTTCTTTTTCTT-TTCTCTT
1 TTTCTTTTT-TTCTTCTCTT
*
18963761 TTTCTTTTTTTCTTTTCTT
1 TTTCTTTTTTTCTTCTCTT
18963780 TTTCT
1 TTTCT
18963785 CGTTCAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.09
19 20 0.91
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTCTTTTTTTCTTCTCTT
Found at i:18964368 original size:34 final size:34
Alignment explanation
Indices: 18964330--18964406 Score: 154
Period size: 34 Copynumber: 2.3 Consensus size: 34
18964320 AATAAGAATT
18964330 GAAATGCAACTACAATTCAACTAAATTAACAAAA
1 GAAATGCAACTACAATTCAACTAAATTAACAAAA
18964364 GAAATGCAACTACAATTCAACTAAATTAACAAAA
1 GAAATGCAACTACAATTCAACTAAATTAACAAAA
18964398 GAAATGCAA
1 GAAATGCAA
18964407 TGACAAAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.56, C:0.17, G:0.08, T:0.19
Consensus pattern (34 bp):
GAAATGCAACTACAATTCAACTAAATTAACAAAA
Found at i:18964427 original size:18 final size:17
Alignment explanation
Indices: 18964392--18964439 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
18964382 AACTAAATTA
* **
18964392 ACAAAAGAAATGCAATG
1 ACAAAAAAAATGTGATG
18964409 ACAAAATAAAATGTGATG
1 ACAAAA-AAAATGTGATG
*
18964427 ACAATAAAAATGT
1 ACAAAAAAAATGT
18964440 ATGCAATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.58, C:0.08, G:0.15, T:0.19
Consensus pattern (17 bp):
ACAAAAAAAATGTGATG
Found at i:18966523 original size:15 final size:15
Alignment explanation
Indices: 18966499--18966534 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
18966489 GCATAAAATT
* *
18966499 TAAAAATGAAACAAG
1 TAAAAGTGAAACAAA
18966514 TAAAAGTGAAACAAA
1 TAAAAGTGAAACAAA
18966529 TAAAAG
1 TAAAAG
18966535 AAAATGTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.67, C:0.06, G:0.14, T:0.14
Consensus pattern (15 bp):
TAAAAGTGAAACAAA
Found at i:18978179 original size:41 final size:41
Alignment explanation
Indices: 18978098--18978477 Score: 510
Period size: 41 Copynumber: 9.2 Consensus size: 41
18978088 TCGAGTCAAA
* * *
18978098 AGTCTTCCTTTAACCATATTCTCATTCTTATCTCGAGACATG
1 AGTCTTCC-TTAATCATAATCTCATTCTCATCTCGAGACATG
* * * * *
18978140 AGTCTTCCTTAATCAAAATCTCATTCTCATTTTGTGACATA
1 AGTCTTCCTTAATCATAATCTCATTCTCATCTCGAGACATG
*
18978181 AGTCTTCCTTAGTCATAATCTCATTCTCATCTCGAGACATG
1 AGTCTTCCTTAATCATAATCTCATTCTCATCTCGAGACATG
* *
18978222 AGTCTTCCTTATTCATAATCTCATTCTCATCTCAAGACATG
1 AGTCTTCCTTAATCATAATCTCATTCTCATCTCGAGACATG
* *
18978263 AGTCTTCCTTATTCATAATCTCATTCTCATGTCGAGACATG
1 AGTCTTCCTTAATCATAATCTCATTCTCATCTCGAGACATG
* * * * * *
18978304 AGTCTTCCATTTATACA-ATTTTTCATTCTCAACCCGGGACATG
1 AGTCTTCC-TTAAT-CATA-ATCTCATTCTCATCTCGAGACATG
*
18978347 AGTCTTCCTTAATCAAAATCTCATTCTCATCTCGAGACATG
1 AGTCTTCCTTAATCATAATCTCATTCTCATCTCGAGACATG
*
18978388 AGTCTTCCTTATTCATAATCTCATTCTCATCTCGAGACATG
1 AGTCTTCCTTAATCATAATCTCATTCTCATCTCGAGACATG
* *
18978429 AGTCTTACTTATTCATAATCTCATTCTCATCTCGAGACATG
1 AGTCTTCCTTAATCATAATCTCATTCTCATCTCGAGACATG
18978470 AGTCTTCC
1 AGTCTTCC
18978478 ATTTATACAA
Statistics
Matches: 298, Mismatches: 36, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
41 253 0.85
42 17 0.06
43 28 0.09
ACGTcount: A:0.26, C:0.26, G:0.10, T:0.38
Consensus pattern (41 bp):
AGTCTTCCTTAATCATAATCTCATTCTCATCTCGAGACATG
Found at i:18978371 original size:166 final size:166
Alignment explanation
Indices: 18978098--18978522 Score: 622
Period size: 166 Copynumber: 2.6 Consensus size: 166
18978088 TCGAGTCAAA
** * * * ** *
18978098 AGTCTTCCTTTAACCATATTCTCATTCTTATCTCGAGACATGAGTCTTCC-TTAAT-CAAAATCT
1 AGTCTTCC-TTATTCATAATCTCATTCTCATCTCGAGACATGAGTCTTCCATTTATACAATTTTT
**** * * * *
18978161 CATTCTCATTTTGTGACATAAGTCTTCCTTAGTCATAATCTCATTCTCATCTCGAGACATGAGTC
65 CATTCTCAACCCGGGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATCTCGAGACATGAGTC
18978226 TTCCTTATTCATAATCTCATTCTCATCTCAAGACATG
130 TTCCTTATTCATAATCTCATTCTCATCTCAAGACATG
*
18978263 AGTCTTCCTTATTCATAATCTCATTCTCATGTCGAGACATGAGTCTTCCATTTATACAATTTTTC
1 AGTCTTCCTTATTCATAATCTCATTCTCATCTCGAGACATGAGTCTTCCATTTATACAATTTTTC
18978328 ATTCTCAACCCGGGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATCTCGAGACATGAGTCT
66 ATTCTCAACCCGGGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATCTCGAGACATGAGTCT
*
18978393 TCCTTATTCATAATCTCATTCTCATCTCGAGACATG
131 TCCTTATTCATAATCTCATTCTCATCTCAAGACATG
*
18978429 AGTCTTACTTATTCATAATCTCATTCTCATCTCGAGACATGAGTCTTCCATTTATACAATTTTTC
1 AGTCTTCCTTATTCATAATCTCATTCTCATCTCGAGACATGAGTCTTCCATTTATACAATTTTTC
* *
18978494 ATGC-CAAACCCAGGACATGAGTCTTCCTT
66 ATTCTC-AACCCGGGACATGAGTCTTCCTT
18978523 TTTATACACC
Statistics
Matches: 235, Mismatches: 22, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
164 36 0.15
165 13 0.06
166 186 0.79
ACGTcount: A:0.26, C:0.26, G:0.10, T:0.38
Consensus pattern (166 bp):
AGTCTTCCTTATTCATAATCTCATTCTCATCTCGAGACATGAGTCTTCCATTTATACAATTTTTC
ATTCTCAACCCGGGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATCTCGAGACATGAGTCT
TCCTTATTCATAATCTCATTCTCATCTCAAGACATG
Found at i:18979367 original size:22 final size:21
Alignment explanation
Indices: 18979320--18979367 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
18979310 GACTTTCATA
*
18979320 ATTAACTTAATTAATCATCTT
1 ATTAACTTAATTAATCATATT
* * *
18979341 TTTAACCTTAATTTATCCTATT
1 ATTAA-CTTAATTAATCATATT
18979363 ATTAA
1 ATTAA
18979368 TCAATATTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTAACTTAATTAATCATATT
Found at i:18989317 original size:20 final size:17
Alignment explanation
Indices: 18989265--18989302 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
18989255 TGAAAAATAG
*
18989265 AAAT-ATTTTTA-GAAA
1 AAATAATTTTTAGGTAA
18989280 AAATAATTTTTAGGTAA
1 AAATAATTTTTAGGTAA
18989297 AAATAA
1 AAATAA
18989303 ATATTTTGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 7 0.35
17 9 0.45
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (17 bp):
AAATAATTTTTAGGTAA
Found at i:18999886 original size:20 final size:20
Alignment explanation
Indices: 18999858--18999900 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
18999848 CTTTTTTGTT
18999858 TTTACTCTTACTCTCT-CAAG
1 TTTACTCTT-CTCTCTGCAAG
* *
18999878 TTTATTCTTTTCTCTGCAAG
1 TTTACTCTTCTCTCTGCAAG
18999898 TTT
1 TTT
18999901 CTTTTAACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.16, C:0.23, G:0.07, T:0.53
Consensus pattern (20 bp):
TTTACTCTTCTCTCTGCAAG
Found at i:19005009 original size:12 final size:12
Alignment explanation
Indices: 19004988--19005017 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
19004978 CTGTGGAGAC
*
19004988 AGAAGCGGAAAA
1 AGAAGAGGAAAA
19005000 AGAAGAGGAAAA
1 AGAAGAGGAAAA
19005012 AGAAGA
1 AGAAGA
19005018 AAGAGAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.63, C:0.03, G:0.33, T:0.00
Consensus pattern (12 bp):
AGAAGAGGAAAA
Found at i:19021134 original size:17 final size:17
Alignment explanation
Indices: 19021118--19021149 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19021108 TTTTACTTGT
19021118 TAGTT-CATTTCCATTG
1 TAGTTGCATTTCCATTG
19021134 TAGTTGCATTTCCATT
1 TAGTTGCATTTCCATT
19021150 CTAATTTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.50
Consensus pattern (17 bp):
TAGTTGCATTTCCATTG
Found at i:19021753 original size:21 final size:21
Alignment explanation
Indices: 19021712--19021755 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
19021702 AATAGAGAAG
*
19021712 AAGAAGAAAAAGAAAGCAAAA
1 AAGAAGAAAAAGAAAGAAAAA
*
19021733 AAGAAGAGAAAAG-CAGAAAAA
1 AAGAAGA-AAAAGAAAGAAAAA
19021754 AA
1 AA
19021756 TATATATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.75, C:0.05, G:0.20, T:0.00
Consensus pattern (21 bp):
AAGAAGAAAAAGAAAGAAAAA
Found at i:19023800 original size:23 final size:23
Alignment explanation
Indices: 19023765--19023820 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
19023755 ATCTTAATTC
*
19023765 TTTAAGCACAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* *
19023788 TTTGAGCATAAATCATATTAATA
1 TTTAAGCATAAATCACATTAATA
19023811 TTTAAGCATA
1 TTTAAGCATA
19023821 GATATCTACG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (23 bp):
TTTAAGCATAAATCACATTAATA
Found at i:19027426 original size:27 final size:27
Alignment explanation
Indices: 19027388--19027492 Score: 102
Period size: 27 Copynumber: 3.9 Consensus size: 27
19027378 AAAAAATCTG
* * *
19027388 GCTCAAAAGAGCGACACTCTTTTTCTA
1 GCTCGAAAGAGCGATACTCTATTTCTA
*
19027415 GCTCGAAAGAGCGATACTCTATTTCTG
1 GCTCGAAAGAGCGATACTCTATTTCTA
* * * * *
19027442 GCTCGTAAGAGTGATACTCTGTTCCTG
1 GCTCGAAAGAGCGATACTCTATTTCTA
* * *
19027469 GCTTGAATGAGAGATACTCTATTT
1 GCTCGAAAGAGCGATACTCTATTT
19027493 TCGGCTCGAA
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (27 bp):
GCTCGAAAGAGCGATACTCTATTTCTA
Found at i:19037616 original size:142 final size:140
Alignment explanation
Indices: 19037409--19037785 Score: 456
Period size: 140 Copynumber: 2.7 Consensus size: 140
19037399 ATCAATATAT
* * * *
19037409 GCTTTGGCCAACT-TTTTATATAAGAGTTGAGATATGCATGCTTAAGACAACACTTAAATAAGAG
1 GCTTTTGCCAACTCTTTTATATAAGGGTTGGGATATGCATGCTTAAGGCAACACTTAAATAAGAG
* * * * * * * *
19037473 TTGCCTTTGTCCAACACTATGCTGACGCTTTTGGGGGCGACACTTTCCTAAGTGTTGGGATAGAT
66 TTG-CTTTGTCCAACATTATGCTAACACTTTT-GCGACGACACTATCCTAAGTGTTGGAATAGAC
*
19037538 TTGCTAGCATAC
129 TTGCTAGCAAAC
* * * *
19037550 GCTTTTGCCAACTCTTTTCTATAAGGGTTGGGATATACATGCTTAAGGTAACGCTTAAATAAGAG
1 GCTTTTGCCAACTCTTTTATATAAGGGTTGGGATATGCATGCTTAAGGCAACACTTAAATAAGAG
*
19037615 TTGGCTTTGTCCAACATTATGATAACACTTTTGCGACGACACTATCCTAAGTGTTGGAATAGACT
66 TT-GCTTTGTCCAACATTATGCTAACACTTTTGCGACGACACTATCCTAAGTGTTGGAATAGACT
*
19037680 TGCTGGCAAAC
130 TGCTAGCAAAC
* * * * *
19037691 G-TTTTGACCAACTC-TTTGTATAAGGGCTGGAATATGCATGCCTAAAGCAACACTTAAATAAGA
1 GCTTTTG-CCAACTCTTTTATATAAGGGTTGGGATATGCATGCTTAAGGCAACACTTAAATAAGA
*
19037754 GTTAGCTTTGTCCAACATTATGCCAAC-CTTTT
65 GTT-GCTTTGTCCAACATTATGCTAACACTTTT
19037786 TAAGGTTGTC
Statistics
Matches: 203, Mismatches: 30, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
139 5 0.02
140 70 0.34
141 57 0.28
142 70 0.34
143 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (140 bp):
GCTTTTGCCAACTCTTTTATATAAGGGTTGGGATATGCATGCTTAAGGCAACACTTAAATAAGAG
TTGCTTTGTCCAACATTATGCTAACACTTTTGCGACGACACTATCCTAAGTGTTGGAATAGACTT
GCTAGCAAAC
Found at i:19037873 original size:37 final size:35
Alignment explanation
Indices: 19037776--19037897 Score: 165
Period size: 36 Copynumber: 3.4 Consensus size: 35
19037766 CAACATTATG
*
19037776 CCAACCTTTTTAAGGTTGTCTTAGACAAGGTCTATC
1 CCAACCTTTTTAAGGTTGCCTTAGACAA-GTCTATC
19037812 CCAACCTTTTTAAGGTTGCCTTAGACAAGTCTATC
1 CCAACCTTTTTAAGGTTGCCTTAGACAAGTCTATC
* *
19037847 CCAACCTTTTTTAAAGGTTACCTTAGACAAGACT-TAC
1 CCAACC-TTTTT-AAGGTTGCCTTAGACAAGTCTAT-C
19037884 CTCAACCTTTTTAA
1 C-CAACCTTTTTAA
19037898 AGTTTTTTTT
Statistics
Matches: 79, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
35 13 0.16
36 35 0.44
37 26 0.33
38 5 0.06
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (35 bp):
CCAACCTTTTTAAGGTTGCCTTAGACAAGTCTATC
Found at i:19039162 original size:13 final size:14
Alignment explanation
Indices: 19039117--19039163 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
19039107 AAACCTTGAG
*
19039117 AGGTTCGAGATTTA
1 AGGTTCGAGATTCA
**
19039131 AGGTTTAAGATTCA
1 AGGTTCGAGATTCA
*
19039145 GGGTTCGAG-TTCA
1 AGGTTCGAGATTCA
19039158 AGGTTC
1 AGGTTC
19039164 TAGGATGTAG
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.26, C:0.11, G:0.30, T:0.34
Consensus pattern (14 bp):
AGGTTCGAGATTCA
Found at i:19039876 original size:5 final size:5
Alignment explanation
Indices: 19039860--19039889 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
19039850 GAATGATATA
19039860 GAATT CGAATT GAATT GAATT GAATT GAAT
1 GAATT -GAATT GAATT GAATT GAATT GAAT
19039890 ATATTTGTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.37
Consensus pattern (5 bp):
GAATT
Found at i:19040113 original size:19 final size:19
Alignment explanation
Indices: 19040074--19040109 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19040064 AAATAAGCAA
*
19040074 AAGTTCAAGTAAACAACAT
1 AAGTCCAAGTAAACAACAT
19040093 AAGTCCAAGT-AACAACA
1 AAGTCCAAGTAAACAACA
19040110 ATAATACAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.53, C:0.19, G:0.11, T:0.17
Consensus pattern (19 bp):
AAGTCCAAGTAAACAACAT
Found at i:19043921 original size:57 final size:58
Alignment explanation
Indices: 19043838--19043957 Score: 170
Period size: 57 Copynumber: 2.1 Consensus size: 58
19043828 TGGGGTTATG
* * ** * *
19043838 TTTATGAGTGTTTTTTAAGACTAAAATTATATTTGGGTTTAAAAGTATTTAGGTTTAA
1 TTTATGAGTGTTTTTTAAAAATAAAATTATATTTGAATTTAAAAATATTTAGGGTTAA
*
19043896 TTTATGAGT-TTTTTTAAAAATAAAATTATATTTGAATTTAAAAATATTTAGGGTTAG
1 TTTATGAGTGTTTTTTAAAAATAAAATTATATTTGAATTTAAAAATATTTAGGGTTAA
19043953 TTTAT
1 TTTAT
19043958 TGATGAGTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
57 46 0.84
58 9 0.16
ACGTcount: A:0.36, C:0.01, G:0.14, T:0.49
Consensus pattern (58 bp):
TTTATGAGTGTTTTTTAAAAATAAAATTATATTTGAATTTAAAAATATTTAGGGTTAA
Found at i:19046222 original size:38 final size:37
Alignment explanation
Indices: 19046118--19046574 Score: 260
Period size: 38 Copynumber: 12.3 Consensus size: 37
19046108 ATTCCAATCT
** * *
19046118 TTTTTAAAGGTTGTTTTAGACAAAGTGTAT-TCCAACC
1 TTTTTAAAGGTTGCCTTAGACAAGGTTTATCT-CAACC
*** *
19046155 TTTTTTAAAGGTTATGTTAGACAAAGTTTATCTCAACC
1 -TTTTTAAAGGTTGCCTTAGACAAGGTTTATCTCAACC
* *
19046193 TTTTTAAAAGGTTACCTTAGACAAGGTTTATC-CTAA-T
1 TTTTT-AAAGGTTGCCTTAGACAAGGTTTATCTC-AACC
* *
19046230 TTATTTAAAAGGTTGCCTTAAATAAGGTTTATC-CTAA-C
1 TT-TTT-AAAGGTTGCCTTAGACAAGGTTTATCTC-AACC
* * * * * *
19046268 TTTTTTAAGGTTACTTTAG--ATGGCTTTATATCAACTT
1 TTTTTAAAGGTTGCCTTAGACAAGG-TTTATCTCAAC-C
* * **
19046305 TTTTTAAAAGTTGCCTTAGATAAAATTTATC-CTAACC
1 TTTTTAAAGGTTGCCTTAGACAAGGTTTATCTC-AACC
*
19046342 -TTTTAAAGGTTGCATTAGACATA--TTTATCTCAACC
1 TTTTTAAAGGTTGCCTTAGACA-AGGTTTATCTCAACC
* * * * * *
19046377 TTTTTTAAAGATTGCCCTAAATAAGGTATATCCCAA-C
1 -TTTTTAAAGGTTGCCTTAGACAAGGTTTATCTCAACC
* * *
19046414 TTTTTTAAGGTTGCTTTAGACAAGGCTTATCTCAACC
1 TTTTTAAAGGTTGCCTTAGACAAGGTTTATCTCAACC
* * * *
19046451 TATTTTAAAGGTTGCTTTAGGCAGGGTTTATCCCAACC
1 T-TTTTAAAGGTTGCCTTAGACAAGGTTTATCTCAACC
* * * *
19046489 TTTTT-AAGGTTTCTTTAGAC-TGGTTTATC-CTAACTT
1 TTTTTAAAGGTTGCCTTAGACAAGGTTTATCTC-AAC-C
* ** *
19046525 TTTTTAAAAGGTTGCCCTAGACAAGACTTGTCTCAACC
1 TTTTT-AAAGGTTGCCTTAGACAAGGTTTATCTCAACC
19046563 TTTTTTAAAGGT
1 -TTTTTAAAGGT
19046575 CAGTATTGAC
Statistics
Matches: 330, Mismatches: 63, Indels: 52
0.74 0.14 0.12
Matches are distributed among these distances:
34 4 0.01
35 28 0.08
36 75 0.23
37 51 0.15
38 156 0.47
39 15 0.05
40 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (37 bp):
TTTTTAAAGGTTGCCTTAGACAAGGTTTATCTCAACC
Found at i:19046562 original size:74 final size:74
Alignment explanation
Indices: 19046181--19046567 Score: 299
Period size: 73 Copynumber: 5.2 Consensus size: 74
19046171 TTAGACAAAG
* * *
19046181 TTTATCTCAACCTTTTTAAAAGGTTACCTTAGACAAGGTTTATC-CTAA-TTTATTTAAAAGGTT
1 TTTATC-CAACCTTTTT--AAGGTTACTTTAGACATGGTTTATCTC-AACTTTTTTTAAAAGGTT
* *
19046244 GCCTTAAATAAGG
62 GCCTTAGATAAGA
* *
19046257 TTTATCCTAACTTTTTTAAGGTTACTTTAG--ATGGCTTTATATCAACTTTTTTTAAAA-GTTGC
1 TTTATCC-AACCTTTTTAAGGTTACTTTAGACATGG-TTTATCTCAACTTTTTTTAAAAGGTTGC
*
19046319 CTTAGATAAAA
64 CTTAGATAAGA
* * * * * *
19046330 TTTATCCTAACCTTTTAAAGGTTGCATTAGACAT-ATTTATCTCAACCTTTTTT-AAAGATTGCC
1 TTTATCC-AACCTTTTTAAGGTTACTTTAGACATGGTTTATCTCAACTTTTTTTAAAAGGTTGCC
* * *
19046393 CTAAATAAGG
65 TTAGATAAGA
* * * * * * * *
19046403 TATATCCCAACTTTTTTAAGGTTGCTTTAGACAAGGCTTATCTCAACCTATTTT-AAAGGTTGCT
1 TTTAT-CCAACCTTTTTAAGGTTACTTTAGACATGGTTTATCTCAACTTTTTTTAAAAGGTTGCC
** * *
19046467 TTAGGCAGGG
65 TTAGATAAGA
*
19046477 TTTATCCCAACCTTTTTAAGGTTTCTTTAGAC-TGGTTTATC-CTAACTTTTTTTAAAAGGTTGC
1 TTTAT-CCAACCTTTTTAAGGTTACTTTAGACATGGTTTATCTC-AACTTTTTTTAAAAGGTTGC
* *
19046540 CCTAGACAAGA
64 CTTAGATAAGA
* *
19046551 CTTGTCTCAACCTTTTT
1 TTTATC-CAACCTTTTT
19046568 TAAAGGTCAG
Statistics
Matches: 250, Mismatches: 49, Indels: 26
0.77 0.15 0.08
Matches are distributed among these distances:
72 7 0.03
73 115 0.46
74 111 0.44
75 3 0.01
76 14 0.06
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (74 bp):
TTTATCCAACCTTTTTAAGGTTACTTTAGACATGGTTTATCTCAACTTTTTTTAAAAGGTTGCCT
TAGATAAGA
Found at i:19051916 original size:21 final size:21
Alignment explanation
Indices: 19051878--19051917 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
19051868 GATTGACTCC
*
19051878 AAGGACAAGAAAAGAAAGAGG
1 AAGGACAAGAAAAAAAAGAGG
19051899 AAGGACAA-AAAGAAAAAGA
1 AAGGACAAGAAA-AAAAAGA
19051918 AGCATAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.68, C:0.05, G:0.28, T:0.00
Consensus pattern (21 bp):
AAGGACAAGAAAAAAAAGAGG
Found at i:19055776 original size:16 final size:19
Alignment explanation
Indices: 19055742--19055782 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
19055732 ACTATAATGT
19055742 AAATGT-GAGAACAAGT-A
1 AAATGTAGAGAACAAGTAA
19055759 AAATGTAGAG-ACAA-TAA
1 AAATGTAGAGAACAAGTAA
19055776 AAATGTA
1 AAATGTA
19055783 ATTACAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 1 0.05
17 18 0.82
18 3 0.14
ACGTcount: A:0.56, C:0.05, G:0.20, T:0.20
Consensus pattern (19 bp):
AAATGTAGAGAACAAGTAA
Found at i:19066796 original size:13 final size:14
Alignment explanation
Indices: 19066778--19066807 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
19066768 ATCAACACAA
19066778 TCAGA-GCTAAATG
1 TCAGAGGCTAAATG
19066791 TCAGAGGCTAAATG
1 TCAGAGGCTAAATG
19066805 TCA
1 TCA
19066808 ATGTATTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (14 bp):
TCAGAGGCTAAATG
Found at i:19076247 original size:22 final size:19
Alignment explanation
Indices: 19076222--19076261 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 19
19076212 ATAATAAAAT
19076222 ATATATAATTATATTTATTATA
1 ATATAT-ATTA-A-TTATTATA
19076244 ATATATATTAATTATTAT
1 ATATATATTAATTATTAT
19076262 CAAATTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 1 0.06
21 4 0.22
22 6 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATATATTAATTATTATA
Found at i:19076252 original size:16 final size:15
Alignment explanation
Indices: 19076225--19076258 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
19076215 ATAAAATATA
*
19076225 TATAATTATATTTAT
1 TATAATTATATTAAT
19076240 TATAATATATATTAAT
1 TATAAT-TATATTAAT
19076256 TAT
1 TAT
19076259 TATCAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATAATTATATTAAT
Found at i:19078746 original size:15 final size:15
Alignment explanation
Indices: 19078726--19078756 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
19078716 TAAAGTTCAA
*
19078726 TTATCTTAATGATTG
1 TTATCTCAATGATTG
19078741 TTATCTCAATGATTG
1 TTATCTCAATGATTG
19078756 T
1 T
19078757 GATGTTAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.52
Consensus pattern (15 bp):
TTATCTCAATGATTG
Found at i:19079221 original size:21 final size:23
Alignment explanation
Indices: 19079195--19079248 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 23
19079185 TAAGATGCTC
*
19079195 AAGAAAA-AAAAG-AGAAAAAAG
1 AAGAAAAGAAAAGAAAAAAAAAG
*
19079216 AAGAAAATGAAATGAAAAAAAAAG
1 AAGAAAA-GAAAAGAAAAAAAAAG
19079240 AAGAAAAGA
1 AAGAAAAGA
19079249 GCATGTGTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 7 0.25
23 6 0.21
24 15 0.54
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.04
Consensus pattern (23 bp):
AAGAAAAGAAAAGAAAAAAAAAG
Found at i:19086280 original size:41 final size:41
Alignment explanation
Indices: 19086222--19086311 Score: 162
Period size: 41 Copynumber: 2.2 Consensus size: 41
19086212 TGTTCGTAGT
19086222 GAATTCTTGTCAAGGTGGAGATTGTTAGAATTGGGTGACTA
1 GAATTCTTGTCAAGGTGGAGATTGTTAGAATTGGGTGACTA
* *
19086263 GAATTCTTGTTATGGTGGAGATTGTTAGAATTGGGTGACTA
1 GAATTCTTGTCAAGGTGGAGATTGTTAGAATTGGGTGACTA
19086304 GAATTCTT
1 GAATTCTT
19086312 ATTAAAATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.26, C:0.07, G:0.30, T:0.38
Consensus pattern (41 bp):
GAATTCTTGTCAAGGTGGAGATTGTTAGAATTGGGTGACTA
Found at i:19089442 original size:18 final size:16
Alignment explanation
Indices: 19089410--19089453 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
19089400 ATGGAATGAG
19089410 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
19089426 AATAAA--TTTAATTA
1 AATAAATTTTTAATTA
*
19089440 ATTAAAATTTTTAA
1 AAT-AAATTTTTAA
19089454 ACCCTAAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 6 0.25
17 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:19089823 original size:14 final size:14
Alignment explanation
Indices: 19089806--19089836 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
19089796 AGGGTTTAAA
19089806 AAATTTAATTAATT
1 AAATTTAATTAATT
*
19089820 AAATTTATTTAATT
1 AAATTTAATTAATT
19089834 AAA
1 AAA
19089837 GATTTATTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATTTAATTAATT
Found at i:19094481 original size:12 final size:12
Alignment explanation
Indices: 19094463--19094492 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
19094453 TAAAAAATAC
19094463 AAAAAGATAAAA
1 AAAAAGATAAAA
*
19094475 GAAAAGATAAAA
1 AAAAAGATAAAA
19094487 AAAAAG
1 AAAAAG
19094493 TCCATGGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (12 bp):
AAAAAGATAAAA
Found at i:19098053 original size:25 final size:23
Alignment explanation
Indices: 19098025--19098070 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
19098015 GTTGGATCCA
19098025 AATTAAATTCTAAAAAGATAATTAT
1 AATTAAA-TCTAAAAA-ATAATTAT
*
19098050 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
19098071 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAT
Found at i:19099142 original size:21 final size:21
Alignment explanation
Indices: 19099118--19099157 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
19099108 TTTTGTTCTC
*
19099118 TTTTTCTC-AATTTTCTTTTT
1 TTTTTTTCAAATTTTCTTTTT
19099138 TTTTTTTCAAATTTTCTTTT
1 TTTTTTTCAAATTTTCTTTT
19099158 CGACTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTTTTCAAATTTTCTTTTT
Found at i:19100122 original size:12 final size:12
Alignment explanation
Indices: 19100107--19100137 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
19100097 AAATAAAATT
19100107 AAATAAAAATGA
1 AAATAAAAATGA
*
19100119 AAATGAAAATGA
1 AAATAAAAATGA
19100131 AAATAAA
1 AAATAAA
19100138 TATACTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (12 bp):
AAATAAAAATGA
Found at i:19100168 original size:10 final size:9
Alignment explanation
Indices: 19100143--19100201 Score: 66
Period size: 9 Copynumber: 6.3 Consensus size: 9
19100133 ATAAATATAC
19100143 TAATTTTTT
1 TAATTTTTT
19100152 TAATTTTTT
1 TAATTTTTT
*
19100161 GAATTTTTT
1 TAATTTTTT
19100170 TCAATTTTTT
1 T-AATTTTTT
19100180 T-ATTTGTTT
1 TAATTT-TTT
*
19100189 TCCATTTTTT
1 T-AATTTTTT
19100199 TAA
1 TAA
19100202 AAACATGAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
8 4 0.09
9 22 0.51
10 13 0.30
11 4 0.09
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.71
Consensus pattern (9 bp):
TAATTTTTT
Found at i:19100189 original size:19 final size:18
Alignment explanation
Indices: 19100145--19100200 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 18
19100135 AAATATACTA
*
19100145 ATTTTTTT-AATTTTTTGA
1 ATTTTTTTCAATTTTTT-T
19100163 ATTTTTTTCAATTTTTTT
1 ATTTTTTTCAATTTTTTT
*
19100181 ATTTGTTTTCCATTTTTTT
1 ATTT-TTTTCAATTTTTTT
19100200 A
1 A
19100201 AAAACATGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 12 0.35
19 22 0.65
ACGTcount: A:0.18, C:0.05, G:0.04, T:0.73
Consensus pattern (18 bp):
ATTTTTTTCAATTTTTTT
Found at i:19105188 original size:19 final size:21
Alignment explanation
Indices: 19105146--19105192 Score: 64
Period size: 19 Copynumber: 2.3 Consensus size: 21
19105136 AACACCTAAG
19105146 ACCCAA-CACCTAAATCATCTA
1 ACCCAATCACCTAAATCA-CTA
19105167 ACCCAATCACCTAAA-C-CTA
1 ACCCAATCACCTAAATCACTA
19105186 ACCCAAT
1 ACCCAAT
19105193 TACCCACCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.40
21 7 0.28
22 8 0.32
ACGTcount: A:0.43, C:0.40, G:0.00, T:0.17
Consensus pattern (21 bp):
ACCCAATCACCTAAATCACTA
Found at i:19106428 original size:294 final size:297
Alignment explanation
Indices: 19105897--19106486 Score: 983
Period size: 294 Copynumber: 2.0 Consensus size: 297
19105887 CGACGGTCGT
* *
19105897 CGGTGTCGATGATCGACAGACGAAGATCGAGACCTGGGGCCGGATGGAGGAGGGGTTAAAGAAAA
1 CGGTGTCGATGATCGACAAACGAAGATCGAGACCTGGGGCCGGACGGAGGAGGGGTTAAAGAAAA
** * *
19105962 AAAAAGGGAATGAAAAGCTTTTTCTAAATTTAAAGTAGAAATGAAGATTTTGCAAAAAAAAAGAT
66 AAAAAGGGAATGAAAAGCTTTTTCTAAATGAAAAGAAGAAATGAAGATTTTGCAAAAAAAAAGAA
19106027 TTATATAGTGACCCCGTACAGCGTCGTTTTGAGGTGTGAGTTTTGAATTCAAAACGGCGCCGTTT
131 TTATATAGTGACCCCGTACAGCGTCGTTTTGAGGTGTGAGTTTTGAATTCAAAACGGCGCCGTTT
* * * *
19106092 CATGCAACCTGATCAGACCCGCTTCGGACCCATCAAGGGTCCGCTTGTTTTCAAT-GTGGGAAAT
196 CATGCAACCTGATCAAACCCGCTCCGAACCCATCAAGGGTCCGCTTGTTTTCAATAGGGGGAAAT
19106156 TATCTCCGTGGTTCTCCCTTGTTTTAAAGGTTTTCAC
261 TATCTCCGTGGTTCTCCCTTGTTTTAAAGGTTTTCAC
19106193 CGGTGTCGATGATCGACAAAC-AGAGATCGAGACCTGGGGCCGGACGGAGGAGGGGTTAAAG-AA
1 CGGTGTCGATGATCGACAAACGA-AGATCGAGACCTGGGGCCGGACGGAGGAGGGGTTAAAGAAA
*
19106256 AAAAAAGGGAATGAAAAGCTTTTTTTAAATGAAAAGAAGAAATGAAGATTTTGCAAAAAAAAA-A
65 AAAAAAGGGAATGAAAAGCTTTTTCTAAATGAAAAGAAGAAATGAAGATTTTGCAAAAAAAAAGA
* * *
19106320 ATTATATAGTGACCCCGTACGGCGTCGTTTT-ATGGTGTGAGTTTTGAATTCAAAATGGTGCCGT
130 ATTATATAGTGACCCCGTACAGCGTCGTTTTGA-GGTGTGAGTTTTGAATTCAAAACGGCGCCGT
*
19106384 TTCATGCAACCTGATCAAACCTGCTCCGAACCCATCAAGGGTCCGCTTGTTTTCAATAGGGGGAA
194 TTCATGCAACCTGATCAAACCCGCTCCGAACCCATCAAGGGTCCGCTTGTTTTCAATAGGGGGAA
*
19106449 ATTATCTCCGTGGTTCTCCCTTGTTTTAAGGGTTTTCA
259 ATTATCTCCGTGGTTCTCCCTTGTTTTAAAGGTTTTCA
19106487 ATTTAATCCT
Statistics
Matches: 275, Mismatches: 16, Indels: 7
0.92 0.05 0.02
Matches are distributed among these distances:
293 1 0.00
294 112 0.41
295 105 0.38
296 57 0.21
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (297 bp):
CGGTGTCGATGATCGACAAACGAAGATCGAGACCTGGGGCCGGACGGAGGAGGGGTTAAAGAAAA
AAAAAGGGAATGAAAAGCTTTTTCTAAATGAAAAGAAGAAATGAAGATTTTGCAAAAAAAAAGAA
TTATATAGTGACCCCGTACAGCGTCGTTTTGAGGTGTGAGTTTTGAATTCAAAACGGCGCCGTTT
CATGCAACCTGATCAAACCCGCTCCGAACCCATCAAGGGTCCGCTTGTTTTCAATAGGGGGAAAT
TATCTCCGTGGTTCTCCCTTGTTTTAAAGGTTTTCAC
Found at i:19108473 original size:50 final size:48
Alignment explanation
Indices: 19108398--19108630 Score: 149
Period size: 50 Copynumber: 4.8 Consensus size: 48
19108388 TAAAGATCTG
** * *
19108398 TTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAAGTTATGAT
1 TTTTTTAACTATTTGAAA-AAAAAGTTTAAATTTTTAACAAA-TTATAAT
* * *
19108448 TTTTTTAACTATTTCGAAACAAAAGTTTAAATTTTTAAGCAAAATAGTGAT
1 TTTTTTAACTATTT-GAAAAAAAAGTTTAAATTTTTAA-CAAATTA-TAAT
* * * * *
19108499 TTCTTTAA--A----AAAGAGAAAGTTTAGATTTTTAA-AAATAAAAAT
1 TTTTTTAACTATTTGAAA-AAAAAGTTTAAATTTTTAACAAATTATAAT
** *
19108541 CTGTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAAGTT-TAAAT
1 -T-TTTTTAACTATTTGAAA-AAAAAGTTTAAATTTTTAACAAA-TTAT-AAT
* *
19108593 TTTTTTAACTATTTTGAAATAAAAGTTTAGATTTTTAA
1 TTTTTTAACTA-TTTGAAAAAAAAGTTTAAATTTTTAA
19108631 GTTAAATAGT
Statistics
Matches: 143, Mismatches: 24, Indels: 32
0.72 0.12 0.16
Matches are distributed among these distances:
42 2 0.01
43 5 0.03
44 8 0.06
45 16 0.11
46 1 0.01
49 1 0.01
50 78 0.55
51 28 0.20
52 4 0.03
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (48 bp):
TTTTTTAACTATTTGAAAAAAAAGTTTAAATTTTTAACAAATTATAAT
Found at i:19108595 original size:145 final size:146
Alignment explanation
Indices: 19108184--19108940 Score: 1062
Period size: 145 Copynumber: 5.2 Consensus size: 146
19108174 CTTTGATTTT
*
19108184 TTTTTAAGTAAAATAGTGATTTTCTTTAAAAAA-ATGAAAGTTTAGATTTTTAAAAATAAAAATA
1 TTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAGA-GAAAGTTTAGATTTTTAAAAATAAAAATC
* ** * *
19108248 TGTTTTTTAGTTGTTTTAAAGAAAATTTTTAAATTTTTAACAAAATTTTGATTTTTTTTAACTAT
65 TG-TTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAAGTTTAGA-TTTTTTTAACTAT
* *
19108313 TTCAAAATAAAAGTTTCGA
128 TTCGAAATAAAAGTTTAGA
* * * * *
19108332 TTTTTAGGTAAAATAGTGATTTTATTTAAAAAGGAGAAAGTTTATATTTTTAAAAATAAAGATCT
1 TTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATCT
19108397 GTTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAAG-TTATGATTTTTTTAACTATT
66 G-TTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAAGTTTA-GATTTTTTTAACTATT
* *
19108461 TCGAAACAAAAGTTTAAA
129 TCGAAATAAAAGTTTAGA
*
19108479 TTTTTAAGCAAAATAGTGA-TTTCTTTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATCT
1 TTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATCT
* *
19108543 GTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAAGTTTAAATTTTTTTAACTATTTT
66 GTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAAGTTTAGATTTTTTTAACTATTTC
19108608 GAAATAAAAGTTTAGA
131 GAAATAAAAGTTTAGA
*
19108624 TTTTTAAGTTAAATAGTGATTTTCTTTAAAAACTA-AG-AAGTTT--ATTTTT-AAAATAAAAAT
1 TTTTTAAGTAAAATAGTGATTTTCTTTAAAAA--AGAGAAAGTTTAGATTTTTAAAAATAAAAAT
* * * * *
19108684 ATATTTTTTAGTTATTTTAAAGAAAAAATTTAAATTTTTAACAAAGTTTTGATTTTTTCTAACAA
64 CT-GTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAAGTTTAGATTTTTT-TAACTA
* *
19108749 TTTCGAAATAAAAATTTGGA
127 TTTCGAAATAAAAGTTTAGA
*
19108769 TTTTTAAGTAAAATAATGATTTTCTTTAAAAAAAGAGAAAGTTTAGATTTTTAAAAATATAAAAA
1 TTTTTAAGTAAAATAGTGATTTTCTTT-AAAAAAGAGAAAGTTTAGATTTTT-AAAA-ATAAAAA
* * *
19108834 TCTATTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAACTTTTGATTTTTTTAACTAT
63 TCTGTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAAGTTTAGATTTTTTTAACTAT
19108899 TTCGAAATAAAAGTTTAGA
128 TTCGAAATAAAAGTTTAGA
* *
19108918 TTTTTAAGTAAAGTAGTAATTTT
1 TTTTTAAGTAAAATAGTGATTTT
19108941 TGTTTAATCA
Statistics
Matches: 545, Mismatches: 48, Indels: 31
0.87 0.08 0.05
Matches are distributed among these distances:
143 12 0.02
144 58 0.11
145 138 0.25
146 74 0.14
147 49 0.09
148 106 0.19
149 44 0.08
150 55 0.10
151 9 0.02
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.45
Consensus pattern (146 bp):
TTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATCT
GTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAAGTTTAGATTTTTTTAACTATTTC
GAAATAAAAGTTTAGA
Found at i:19108912 original size:294 final size:295
Alignment explanation
Indices: 19108184--19108940 Score: 1104
Period size: 294 Copynumber: 2.6 Consensus size: 295
19108174 CTTTGATTTT
*
19108184 TTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAA-TGAAAGTTTAGATTTTTAAAAATA-AAAAT
1 TTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAAGAGAAAGTTTAGATTTTTAAAAATATAAAA-
* * **
19108247 ATGTTTTTTAGTTGTTTTAAAGAAAATTTTTAAATTTTTAACAAAATTTTGATTTTTTTTAACTA
65 ATCTTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAAATTTTGA-TTTTTTTAACTA
* * * * *
19108312 TTTCAAAATAAAAGTTTCGATTTTTAGGTAAAATAGTGATTTTATTTAAAAAGGAGAAAGTTTAT
129 TTTCGAAATAAAAGTTTAGATTTTTAAGTTAAATAGTGATTTTATTTAAAAAGAAGAAAGTTTAT
* * * *
19108377 ATTTTTAAAAATAAAGATCTGTTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAAGT
194 ATTTTTAAAAATAAAAATATATTTTTTAGTTATTTTAAAGAAAAAATTTAAATTTTTAACAAAGT
* *
19108442 TATGATTTTTTTAACTATTTCGAAACAAAAGTTTAAA
259 TATGATTTTTTTAACAATTTCGAAACAAAAATTTAAA
*
19108479 TTTTTAAGCAAAATAGTGA-TTTCTTT-AAAAAAGAGAAAGTTTAGATTTTT-AAAA-ATAAAAA
1 TTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAAGAGAAAGTTTAGATTTTTAAAAATATAAAAA
* **
19108540 TCTGTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAAGTTTAAATTTTTTTAACTAT
66 TCT-TTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAAATTTTGATTTTTTTAACTAT
* * *
19108605 TTTGAAATAAAAGTTTAGATTTTTAAGTTAAATAGTGATTTTCTTTAAAAACTAAG-AAG-TT-T
130 TTCGAAATAAAAGTTTAGATTTTTAAGTTAAATAGTGATTTTATTTAAAAA-GAAGAAAGTTTAT
19108667 ATTTTT-AAAATAAAAATATATTTTTTAGTTATTTTAAAGAAAAAATTTAAATTTTTAACAAAGT
194 ATTTTTAAAAATAAAAATATATTTTTTAGTTATTTTAAAGAAAAAATTTAAATTTTTAACAAAGT
* * **
19108731 TTTGATTTTTTCTAACAATTTCGAAATAAAAATTTGGA
259 TATGATTTTTT-TAACAATTTCGAAACAAAAATTTAAA
*
19108769 TTTTTAAGTAAAATAATGATTTTCTTTAAAAAAAGAGAAAGTTTAGATTTTTAAAAATATAAAAA
1 TTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAAGAGAAAGTTTAGATTTTTAAAAATATAAAAA
*
19108834 TCTATTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAACTTTTGATTTTTTTAACTAT
66 TCT-TTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAAATTTTGATTTTTTTAACTAT
*
19108899 TTCGAAATAAAAGTTTAGATTTTTAAG-TAAAGTAGTAATTTT
130 TTCGAAATAAAAGTTTAGATTTTTAAGTTAAA-TAGTGATTTT
19108941 TGTTTAATCA
Statistics
Matches: 417, Mismatches: 35, Indels: 21
0.88 0.07 0.04
Matches are distributed among these distances:
289 64 0.15
290 45 0.11
291 9 0.02
292 89 0.21
293 66 0.16
294 126 0.30
295 18 0.04
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.45
Consensus pattern (295 bp):
TTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAAGAGAAAGTTTAGATTTTTAAAAATATAAAAA
TCTTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAAATTTTGATTTTTTTAACTATT
TCGAAATAAAAGTTTAGATTTTTAAGTTAAATAGTGATTTTATTTAAAAAGAAGAAAGTTTATAT
TTTTAAAAATAAAAATATATTTTTTAGTTATTTTAAAGAAAAAATTTAAATTTTTAACAAAGTTA
TGATTTTTTTAACAATTTCGAAACAAAAATTTAAA
Found at i:19119910 original size:16 final size:16
Alignment explanation
Indices: 19119881--19119928 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
19119871 TTAAATCAAG
* *
19119881 AAAAAAATACAAAAAA
1 AAAAAAAGAGAAAAAA
*
19119897 AATAAAAGAGAAAAAA
1 AAAAAAAGAGAAAAAA
*
19119913 AAAAAAATAGAAAAAA
1 AAAAAAAGAGAAAAAA
19119929 TAGAAAGAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.85, C:0.02, G:0.06, T:0.06
Consensus pattern (16 bp):
AAAAAAAGAGAAAAAA
Found at i:19119912 original size:15 final size:15
Alignment explanation
Indices: 19119892--19119938 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
19119882 AAAAAATACA
19119892 AAAAAAATAAAAGAG
1 AAAAAAATAAAAGAG
* *
19119907 AAAAAAA-AAAAAAT
1 AAAAAAATAAAAGAG
19119921 AGAAAAAATAGAAAGAG
1 A-AAAAAATA-AAAGAG
19119938 A
1 A
19119939 GAGCAGATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 6 0.24
15 13 0.52
16 1 0.04
17 5 0.20
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (15 bp):
AAAAAAATAAAAGAG
Found at i:19119931 original size:9 final size:9
Alignment explanation
Indices: 19119882--19119934 Score: 51
Period size: 9 Copynumber: 6.3 Consensus size: 9
19119872 TAAATCAAGA
*
19119882 AAAAAATAC
1 AAAAAATAG
19119891 AAAAAA-A-
1 AAAAAATAG
* *
19119898 ATAAAAGAG
1 AAAAAATAG
19119907 AAAAAA-A-
1 AAAAAATAG
19119914 AAAAAATAG
1 AAAAAATAG
19119923 AAAAAATAG
1 AAAAAATAG
19119932 AAA
1 AAA
19119935 GAGAGAGCAG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 11 0.29
8 4 0.11
9 23 0.61
ACGTcount: A:0.83, C:0.02, G:0.08, T:0.08
Consensus pattern (9 bp):
AAAAAATAG
Found at i:19120874 original size:42 final size:42
Alignment explanation
Indices: 19120332--19120854 Score: 758
Period size: 42 Copynumber: 12.5 Consensus size: 42
19120322 AAAGAAAGCA
* *
19120332 TTCATTGCATTTAGAGGCCTAGGTGTAGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
19120374 TCCATTGAATTTAGAGGCCCAGGTGTGGAGGTCCATTTATTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
19120416 TTCATTGCATTCAAAGGCTCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
19120458 TTCATTGCATTTAAAGGCCCAGGTGTAGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
19120500 TTCATCGCATTTAGAGGCCTAGGTGTGGAGGTTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
19120542 TTCATTTCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
19120584 TTCATTGCATTTAGAGGCCCAAGAGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
** *
19120626 TTCATTGCATTTAGAGGCCCAGGTGTAAAGGTCGATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
** *
19120668 TTCATTGCATTTAGAGGCCCAGGTGTAAAGGTCGATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
19120710 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
19120752 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
** *
19120794 TTCATTGCATTCGGAGGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
19120836 TTCATTGCAATTAGAGGCC
1 TTCATTGCATTTAGAGGCC
19120855 TAAGCAAAGA
Statistics
Matches: 435, Mismatches: 46, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 435 1.00
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.36
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Found at i:19121833 original size:145 final size:147
Alignment explanation
Indices: 19121627--19122383 Score: 1168
Period size: 145 Copynumber: 5.2 Consensus size: 147
19121617 TTGATTATTT
* *
19121627 TTTTTAAGCAAAATAGTGATTTTCTTTAAAAAAGAGAAAGTTTAAATTTTTAAAAATAAAAATCT
1 TTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATCT
* * *
19121692 -ATTTTTAGTTATTGTAAAGAAAAATTTTAAATTTTTAACAAAGTTTTGATTTTTTTAACTATTT
66 GTTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAAGTTTTGATTTTTTTAACTATTT
19121756 CGAAATAAAAGTTTGGA
131 CGAAATAAAAGTTTGGA
* * * *
19121773 TTTCTAGGTAAAATAGTGATTTTATTT-AAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATCT
1 TTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATCT
* * *
19121837 ATTTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTGAACAAAGTTTTAATTTTTTTAACTATT
66 -GTTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAAGTTTTGATTTTTTTAACTATT
*
19121902 TCGAAATAAAAGTTTGTA
130 TCGAAATAAAAGTTTGGA
* * *
19121920 TTGTTAAGCAAAATAGTGATTTTCTTTAAAAAAGAGAAAGTTTAGA-TTTTAAAAATAAAAATTT
1 TTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATCT
*
19121984 GTTTTTTAGTTAATTTAAAGAAAAA-TTTAAATTTTTAACAAAGTTTTGATTTTTTTTAACTATT
66 GTTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAAGTTTTGA-TTTTTTTAACTATT
*
19122048 TCGAAATAAAAGTTTAGA
130 TCGAAATAAAAGTTTGGA
* *
19122066 TTTTTAAGTAAAATAGTAATTTT-TTT--AAAAGAGAAAGTTTATATTTTTAAAAATAAAAATCT
1 TTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATCT
* *
19122128 GTTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAAGTTTTGATTGTTTCTAACAATT
66 GTTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAAGTTTTGATT-TTTTTAACTATT
19122193 TCGAAATAAAAGTTTGGA
130 TCGAAATAAAAGTTTGGA
19122211 TTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAAGAGAAAGTTTAGATTTTTAAAAAAATAAAAA
1 TTTTTAAGTAAAATAGTGATTTTCTTT-AAAAAAGAGAAAGTTTAGATTTTT--AAAAATAAAAA
* *
19122276 TCTGTTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAAATTTTTATTTTTTTAACTA
63 TCTGTTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAAGTTTTGATTTTTTTAACTA
* *
19122341 TTTCGAAATAAAAATTTAGA
128 TTTCGAAATAAAAGTTTGGA
*
19122361 TTTTTAAGTAAAGTAGTGATTTT
1 TTTTTAAGTAAAATAGTGATTTT
19122384 TGTTTAATCA
Statistics
Matches: 556, Mismatches: 42, Indels: 22
0.90 0.07 0.04
Matches are distributed among these distances:
143 16 0.03
144 43 0.08
145 134 0.24
146 99 0.18
147 114 0.21
148 17 0.03
149 21 0.04
150 48 0.09
151 64 0.12
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.44
Consensus pattern (147 bp):
TTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATCT
GTTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAAGTTTTGATTTTTTTAACTATTT
CGAAATAAAAGTTTGGA
Found at i:19121843 original size:22 final size:23
Alignment explanation
Indices: 19121791--19121845 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
19121781 TAAAATAGTG
* *
19121791 ATTTTATTTAAAAAGAGAAAGTTT
1 ATTTT-TTTAAAAAGAGAAAATCT
* *
19121815 ATATTTTTAAAAATA-AAAATCT
1 ATTTTTTTAAAAAGAGAAAATCT
19121837 ATTTTTTTA
1 ATTTTTTTA
19121846 GTTATTTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 13 0.50
23 9 0.35
24 4 0.15
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.47
Consensus pattern (23 bp):
ATTTTTTTAAAAAGAGAAAATCT
Found at i:19122089 original size:51 final size:49
Alignment explanation
Indices: 19121887--19122384 Score: 135
Period size: 51 Copynumber: 10.1 Consensus size: 49
19121877 CAAAGTTTTA
* *
19121887 ATTTTTTTAACTATTTCGAAATAAAAGTTT-GTATTGTTAAGCAAAATAGTG
1 ATTTTTTTAACTATTT-GAAATAAAAGTTTAG-ATTTTTAA-TAAAATAGTG
* *
19121938 ATTTTCTTTAA--A----AAAGAGAAAGTTTAGATTTTAAAAATAAAA-A-T-
1 ATTTT-TTTAACTATTTGAAATA-AAAGTTTAGATTTT--TAATAAAATAGTG
* ** * * * * * **
19121982 TTGTTTTTTAGTTAATTT-AAAGAAAAATTTAAATTTTTAACAAAGTTTTG
1 AT-TTTTTTAACT-ATTTGAAATAAAAGTTTAGATTTTTAATAAAATAGTG
*
19122032 ATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAATAGTA
1 A-TTTTTTTAACTATTT-GAAATAAAAGTTTAGATTTTTAA-TAAAATAGTG
* * * * * *
19122084 ATTTTTTTAA--A----AGA-GAAAGTTTATATTTTTAAAAATAAAAAT-
1 ATTTTTTTAACTATTTGAAATAAAAGTTTAGATTTTTAATAA-AATAGTG
* ** * * * * * **
19122126 CTGTTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAAGTTTTG
1 AT-TTTTTTAACTATTTGAAA-TAAAAGTTTAGATTTTTAATAAAATAGTG
* * *
19122177 ATTGTTTCTAACAATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTG
1 ATT-TTTTTAACTATTT-GAAATAAAAGTTTAGATTTTTAA-TAAAATAGTG
* * * ***
19122229 ATTTTCTTTAA--A---AAAAGAGAAAGTTTAGATTTTTAAAAAAATAAAA
1 ATTTT-TTTAACTATTTGAAATA-AAAGTTTAGATTTTTAATAAAATAGTG
** * * * * ** *
19122275 ATCTGTTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAACAAAATTTTT
1 A--T-TTTTTTAACTATTTGAAA-TAAAAGTTTAGATTTTTAATAAAATAGTG
* *
19122328 ATTTTTTTAACTATTTCGAAATAAAAATTTAGATTTTTAAGTAAAGTAGTG
1 ATTTTTTTAACTATTT-GAAATAAAAGTTTAGATTTTTAA-TAAAATAGTG
19122379 ATTTTT
1 ATTTTT
19122385 GTTTAATCAA
Statistics
Matches: 321, Mismatches: 80, Indels: 92
0.65 0.16 0.19
Matches are distributed among these distances:
42 3 0.01
43 27 0.08
44 7 0.02
45 9 0.03
46 23 0.07
47 27 0.08
48 7 0.02
49 23 0.07
50 47 0.15
51 95 0.30
52 27 0.08
53 25 0.08
54 1 0.00
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (49 bp):
ATTTTTTTAACTATTTGAAATAAAAGTTTAGATTTTTAATAAAATAGTG
Found at i:19127930 original size:24 final size:24
Alignment explanation
Indices: 19127895--19127963 Score: 102
Period size: 24 Copynumber: 2.9 Consensus size: 24
19127885 AATCTTTTAG
*
19127895 TTAAACTCTGTTTGTTTGTTTCAA
1 TTAAACTCTGTTTATTTGTTTCAA
*
19127919 TTAAACTTTGTTTATTTGTTTCAA
1 TTAAACTCTGTTTATTTGTTTCAA
* *
19127943 TTAAACCCTATTTATTTGTTT
1 TTAAACTCTGTTTATTTGTTT
19127964 AAGTCAAACT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.23, C:0.12, G:0.09, T:0.57
Consensus pattern (24 bp):
TTAAACTCTGTTTATTTGTTTCAA
Found at i:19137657 original size:40 final size:40
Alignment explanation
Indices: 19137551--19137914 Score: 202
Period size: 40 Copynumber: 9.3 Consensus size: 40
19137541 AACGGATCCG
* * * * *
19137551 ATCTCTTACCCCAACCAAGGGGCAAATTGAAGACACCATT-T
1 ATCTTTTACCCTAACCATGAGGCAGATTGAAGAC-CC-TTCT
* * *
19137592 GATCTCTTACCCCAACCATGGGGCAGATTGAAGACCCTTCT
1 -ATCTTTTACCCTAACCATGAGGCAGATTGAAGACCCTTCT
* * * *
19137633 ATCTTTTACCCTAACCATGAGGCAGGTTGAAGACCGTCCA
1 ATCTTTTACCCTAACCATGAGGCAGATTGAAGACCCTTCT
* * * * * * * *
19137673 ATCTCTTACCCTAGCTA-GAGGGCAGATTAAAGATCATCCG
1 ATCTTTTACCCTAACCATGA-GGCAGATTGAAGACCCTTCT
* * * *
19137713 ATCTCTTACCCTAACCA-GAGGGTAGATTGAAGACCATTCG
1 ATCTTTTACCCTAACCATGA-GGCAGATTGAAGACCCTTCT
* * * *
19137753 ATCTTTTACCCCAACCATGAGACAGATTGAAGA-CCGTCG
1 ATCTTTTACCCTAACCATGAGGCAGATTGAAGACCCTTCT
* * * *
19137792 ATC---T---CTTACCATGAGGTAGATTG-AGAACCATCCT
1 ATCTTTTACCCTAACCATGAGGCAGATTGAAG-ACCCTTCT
* * *
19137826 ATCTTTTACCATAACCA-AAGGGCAGATTGAAGA-CCATCT
1 ATCTTTTACCCTAACCATGA-GGCAGATTGAAGACCCTTCT
* *
19137865 GATCTTTTACCCTAACCAT-AGGTAGATTGAAG--CCATCT
1 -ATCTTTTACCCTAACCATGAGGCAGATTGAAGACCCTTCT
19137903 AGTCTTTTACCC
1 A-TCTTTTACCC
19137915 CATCTAGAGG
Statistics
Matches: 260, Mismatches: 46, Indels: 36
0.76 0.13 0.11
Matches are distributed among these distances:
32 2 0.01
33 16 0.06
34 5 0.02
36 1 0.00
37 2 0.01
38 16 0.06
39 24 0.09
40 155 0.60
41 7 0.03
42 32 0.12
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (40 bp):
ATCTTTTACCCTAACCATGAGGCAGATTGAAGACCCTTCT
Found at i:19137762 original size:80 final size:79
Alignment explanation
Indices: 19137546--19137935 Score: 289
Period size: 80 Copynumber: 5.0 Consensus size: 79
19137536 ACAGTAACGG
* * * * * *
19137546 ATCCGATCTCTTACCCCAACCAAGGGGCAAATTGAAGACACCATTTGATCTCTTACCCCAACCAT
1 ATCCGATCTCTTACCCTAACC-AGAGGTAGATTGAAG--ACCATTCGATCTTTTACCCCAACCA-
19137611 G-GGGCAGATTGAAGACC
62 GAGGGCAGATTGAAGACC
* * * * * * * * * * * * *
19137628 CTTCTATCTTTTACCCTAACCATGAGGCAGGTTGAAGACCGTCCAATCTCTTACCCTAGCTAGAG
1 ATCCGATCTCTTACCCTAACCA-GAGGTAGATTGAAGACCATTCGATCTTTTACCCCAACCAGAG
* *
19137693 GGCAGATTAAAGATC
65 GGCAGATTGAAGACC
19137708 ATCCGATCTCTTACCCTAACCAGAGGGTAGATTGAAGACCATTCGATCTTTTACCCCAACCATGA
1 ATCCGATCTCTTACCCTAACCAGA-GGTAGATTGAAGACCATTCGATCTTTTACCCCAACCA-GA
*
19137773 -GACAGATTGAAGACC
64 GGGCAGATTGAAGACC
* * * * ** *
19137788 GT-CGATCTCTTA-CC--A--TGAGGTAGATTG-AGAACCATCCTATCTTTTACCATAACCAAAG
1 ATCCGATCTCTTACCCTAACCAGAGGTAGATTGAAG-ACCATTCGATCTTTTACCCCAACCAGAG
19137846 GGCAGATTGAAGACC
65 GGCAGATTGAAGACC
* * * * * *
19137861 ATCTGATCTTTTACCCTAACCATAGGTAGATTGAAG-CCA-TCTAGTCTTTTACCCCATCTAGAG
1 ATCCGATCTCTTACCCTAACCAGAGGTAGATTGAAGACCATTCGA-TCTTTTACCCCAACCAGAG
* *
19137924 GGTAGACTGAAG
65 GGCAGATTGAAG
19137936 TATGAAAGTG
Statistics
Matches: 240, Mismatches: 54, Indels: 32
0.74 0.17 0.10
Matches are distributed among these distances:
72 3 0.01
73 45 0.19
74 10 0.04
75 2 0.01
76 1 0.00
77 4 0.02
78 29 0.12
79 23 0.10
80 93 0.39
81 3 0.01
82 27 0.11
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (79 bp):
ATCCGATCTCTTACCCTAACCAGAGGTAGATTGAAGACCATTCGATCTTTTACCCCAACCAGAGG
GCAGATTGAAGACC
Found at i:19137769 original size:120 final size:113
Alignment explanation
Indices: 19137592--19137896 Score: 348
Period size: 120 Copynumber: 2.6 Consensus size: 113
19137582 GACACCATTT
* * *
19137592 GATCTCTTACCCCAACCATG-GGGCAGATTGAAGACCCTTCTATCTTTTACCCTAACCATGAGGC
1 GATCTCTTACCCTAACCA-GAGGGCAGATTGAAGACCATTCGATCTTTTACCCTAACCATGAGGC
* *
19137656 AGGTTGAAGACCGTCCAATCTCTTACCCTAGCTAGAGGGCAGATTAA-AGATCATCC
65 AGATTGAAGACCGT-CAATCTCTTA-CC-A--T-GA-GGCAGATTAAGA-ACCATCC
* * *
19137712 GATCTCTTACCCTAACCAGAGGGTAGATTGAAGACCATTCGATCTTTTACCCCAACCATGAGACA
1 GATCTCTTACCCTAACCAGAGGGCAGATTGAAGACCATTCGATCTTTTACCCTAACCATGAGGCA
* * *
19137777 GATTGAAGACCGTCGATCTCTTACCATGAGGTAGATTGAGAACCATCC
66 GATTGAAGACCGTCAATCTCTTACCATGAGGCAGATTAAGAACCATCC
* * * * *
19137825 TATCTTTTACCATAACCAAAGGGCAGATTGAAGACCA-TCTGATCTTTTACCCTAACCAT-AGGT
1 GATCTCTTACCCTAACCAGAGGGCAGATTGAAGACCATTC-GATCTTTTACCCTAACCATGAGGC
19137888 AGATTGAAG
65 AGATTGAAG
19137897 CCATCTAGTC
Statistics
Matches: 163, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
112 13 0.08
113 64 0.39
114 3 0.02
115 1 0.01
117 1 0.01
118 2 0.01
119 10 0.06
120 69 0.42
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (113 bp):
GATCTCTTACCCTAACCAGAGGGCAGATTGAAGACCATTCGATCTTTTACCCTAACCATGAGGCA
GATTGAAGACCGTCAATCTCTTACCATGAGGCAGATTAAGAACCATCC
Found at i:19137842 original size:73 final size:74
Alignment explanation
Indices: 19137733--19137875 Score: 175
Period size: 73 Copynumber: 1.9 Consensus size: 74
19137723 CTAACCAGAG
* * * *
19137733 GGTAGATTGAAGACCATTCGATCTTTTACCCCAACC-ATGAGACAGATTGAAGACCGTC-GATCT
1 GGTAGATTGAAGACCATCCGATCTTTTACCACAACCAAAG-GACAGATTGAAGACCATCTGATCT
19137796 CTTACCATGA
65 CTTACCATGA
* * *
19137806 GGTAGATTG-AGAACCATCCTATCTTTTACCATAACCAAAGGGCAGATTGAAGACCATCTGATCT
1 GGTAGATTGAAG-ACCATCCGATCTTTTACCACAACCAAAGGACAGATTGAAGACCATCTGATCT
*
19137870 TTTACC
65 CTTACC
19137876 CTAACCATAG
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
72 2 0.03
73 45 0.76
74 12 0.20
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (74 bp):
GGTAGATTGAAGACCATCCGATCTTTTACCACAACCAAAGGACAGATTGAAGACCATCTGATCTC
TTACCATGA
Found at i:19137869 original size:113 final size:119
Alignment explanation
Indices: 19137592--19137896 Score: 342
Period size: 113 Copynumber: 2.6 Consensus size: 119
19137582 GACACCATTT
** ** *
19137592 GATCTCTTACCCCAACCATGGGGCAGATTGAAGACCCTTCT-ATCTTTTACCCTAACCATGAGGC
1 GATCTCTTACCATAACCAAAGGGCAGATTGAAGA-CCATCTGATCTTTTACCCTAACCATGAGGC
* *
19137656 AGGTTGAAGACCGTCCAATCTCTTACCCTAGCTAGAGGGCAGATTAAAGATCATCC
65 AGATTGAAGACCGTCCAATCTCTTACCCTA-CTAGAGGGCAGATTAAAGACCATCC
* * * * *
19137712 GATCTCTTACCCTAACCAGAGGGTAGATTGAAGACCAT-TCGATCTTTTACCCCAACCATGAGAC
1 GATCTCTTACCATAACCAAAGGGCAGATTGAAGACCATCT-GATCTTTTACCCTAACCATGAGGC
* * *
19137776 AGATTGAAGACCGT-CGATCTCTTA-CC-A-T-GA-GGTAGATT-GAGAACCATCC
65 AGATTGAAGACCGTCCAATCTCTTACCCTACTAGAGGGCAGATTAAAG-ACCATCC
* * *
19137825 TATCTTTTACCATAACCAAAGGGCAGATTGAAGACCATCTGATCTTTTACCCTAACCAT-AGGTA
1 GATCTCTTACCATAACCAAAGGGCAGATTGAAGACCATCTGATCTTTTACCCTAACCATGAGGCA
19137889 GATTGAAG
66 GATTGAAG
19137897 CCATCTAGTC
Statistics
Matches: 161, Mismatches: 20, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
112 13 0.08
113 64 0.40
114 3 0.02
115 1 0.01
117 1 0.01
118 3 0.02
119 12 0.07
120 64 0.40
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (119 bp):
GATCTCTTACCATAACCAAAGGGCAGATTGAAGACCATCTGATCTTTTACCCTAACCATGAGGCA
GATTGAAGACCGTCCAATCTCTTACCCTACTAGAGGGCAGATTAAAGACCATCC
Found at i:19137928 original size:39 final size:40
Alignment explanation
Indices: 19137806--19137935 Score: 117
Period size: 40 Copynumber: 3.3 Consensus size: 40
19137796 CTTACCATGA
** *
19137806 GGTAGATTG-AGAACCATCCT-ATCTTTTACCATAACCAAAG
1 GGTAGATTGAAG-ACCAT-CTGATCTTTTACCCCAACCAGAG
* * *
19137846 GGCAGATTGAAGACCATCTGATCTTTTACCCTAACCATA-
1 GGTAGATTGAAGACCATCTGATCTTTTACCCCAACCAGAG
* *
19137885 GGTAGATTGAAG-CCATCT-AGTCTTTTACCCCATCTAGAG
1 GGTAGATTGAAGACCATCTGA-TCTTTTACCCCAACCAGAG
*
19137924 GGTAGACTGAAG
1 GGTAGATTGAAG
19137936 TATGAAAGTG
Statistics
Matches: 77, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
37 1 0.01
38 20 0.26
39 24 0.31
40 30 0.39
41 2 0.03
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (40 bp):
GGTAGATTGAAGACCATCTGATCTTTTACCCCAACCAGAG
Found at i:19138325 original size:17 final size:17
Alignment explanation
Indices: 19138305--19138337 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
19138295 ACCCACCTAA
19138305 CCCAAAC-ACCCTAAGAG
1 CCCAAACGACCC-AAGAG
19138322 CCCAAACGACCCAAGA
1 CCCAAACGACCCAAGA
19138338 CCTTAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.42, G:0.12, T:0.03
Consensus pattern (17 bp):
CCCAAACGACCCAAGAG
Found at i:19139294 original size:30 final size:30
Alignment explanation
Indices: 19139254--19139455 Score: 187
Period size: 30 Copynumber: 6.8 Consensus size: 30
19139244 TTCGAAGAAT
19139254 TTTG-GGGTTAAAATGTAATTTTAGAAAAG
1 TTTGAGGGTTAAAATGTAATTTTAGAAAAG
*
19139283 TTTGAGGGTTAAAAATGCAATTTTAG-AAA-
1 TTTGAGGGTT-AAAATGTAATTTTAGAAAAG
* * *
19139312 TTTTAGGGGTTAAAATGCAATTTTGGAAAAG
1 TTTGA-GGGTTAAAATGTAATTTTAGAAAAG
* * *
19139343 TTT-AGTGGTTAGAATGTAGTTTTGGAAAAG
1 TTTGAG-GGTTAAAATGTAATTTTAGAAAAG
* *
19139373 TTTAAGGGTTAAAATGTAATTTTGGAAAAG
1 TTTGAGGGTTAAAATGTAATTTTAGAAAAG
* * ** *
19139403 TTCGAGGGTCAAAATACAATTTTAGAGAAG
1 TTTGAGGGTTAAAATGTAATTTTAGAAAAG
* * * *
19139433 TTCGAGAGTCAAAATATAATTTT
1 TTTGAGGGTTAAAATGTAATTTT
19139456 TAAATAAAAT
Statistics
Matches: 149, Mismatches: 17, Indels: 13
0.83 0.09 0.07
Matches are distributed among these distances:
29 23 0.15
30 107 0.72
31 19 0.13
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (30 bp):
TTTGAGGGTTAAAATGTAATTTTAGAAAAG
Found at i:19139326 original size:60 final size:59
Alignment explanation
Indices: 19139251--19139428 Score: 216
Period size: 60 Copynumber: 3.0 Consensus size: 59
19139241 CGTTTCGAAG
*
19139251 AATTTT-GGGGTTAAAATGTAATTTTAGAAAAGTTTGAGGGTTAAAAATGCAATTTTAGA
1 AATTTTAGGGGTTAAAATGTAATTTTGGAAAAGTTTGAGGGTT-AAAATGCAATTTTAGA
* * * * *
19139310 AATTTTAGGGGTTAAAATGCAATTTTGGAAAAGTTT-AGTGGTTAGAATGTAGTTTTGGAA
1 AATTTTAGGGGTTAAAATGTAATTTTGGAAAAGTTTGAG-GGTTAAAATGCAATTTTAG-A
* * * * *
19139370 AAGTTTAAGGGTTAAAATGTAATTTTGGAAAAGTTCGAGGGTCAAAATACAATTTTAGA
1 AATTTTAGGGGTTAAAATGTAATTTTGGAAAAGTTTGAGGGTTAAAATGCAATTTTAGA
19139429 GAAGTTCGAG
Statistics
Matches: 99, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
59 20 0.20
60 77 0.78
61 2 0.02
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.36
Consensus pattern (59 bp):
AATTTTAGGGGTTAAAATGTAATTTTGGAAAAGTTTGAGGGTTAAAATGCAATTTTAGA
Found at i:19139417 original size:90 final size:90
Alignment explanation
Indices: 19139259--19139434 Score: 219
Period size: 90 Copynumber: 2.0 Consensus size: 90
19139249 AGAATTTTGG
* ** *
19139259 GGTTAAAATGTAATTTTAGAAAAGTTTGAGGGTTAAAAATGCAATTTTAGAAATTTTAGGGGTTA
1 GGTTAAAATGTAATTTTAGAAAAGTTTAAGGGTTAAAAATGCAATTTTAGAAAAGTTAGGGGTCA
* *
19139324 AAATGCAATTTTGGAAAAGTTTAGT
66 AAATACAATTTTAGAAAAGTTTAGT
* * * * * *
19139349 GGTTAGAATGTAGTTTTGGAAAAGTTTAAGGGTT-AAAATGTAATTTTGGAAAAGTTCGAGGGTC
1 GGTTAAAATGTAATTTTAGAAAAGTTTAAGGGTTAAAAATGCAATTTTAGAAAAGTTAG-GGGTC
*
19139413 AAAATACAATTTTAGAGAAGTT
65 AAAATACAATTTTAGAAAAGTT
19139435 CGAGAGTCAA
Statistics
Matches: 72, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
89 19 0.26
90 53 0.74
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (90 bp):
GGTTAAAATGTAATTTTAGAAAAGTTTAAGGGTTAAAAATGCAATTTTAGAAAAGTTAGGGGTCA
AAATACAATTTTAGAAAAGTTTAGT
Found at i:19141567 original size:85 final size:85
Alignment explanation
Indices: 19141411--19141567 Score: 199
Period size: 85 Copynumber: 1.8 Consensus size: 85
19141401 ACTTCTCTAT
* * * * * * * *
19141411 ATCTCATTATGAAGATGATCGCTTCATTGTTTTAATCCACTTCTCTCTATCTCATCAAGAAGACG
1 ATCTCATCAGGAAGATGAACACTTCATTGCTTTAACCCACTTCTCTATATCTCATCAAGAAGAAG
19141476 GATTTGGTTCACTTCTTTGC
66 GATTTGGTTCACTTCTTTGC
* *
19141496 ATCTCATCAGGAAGATGAACACTTTATTGCTTTAACCCAC-TCTCTATATCTCATCAGGAAGATA
1 ATCTCATCAGGAAGATGAACACTTCATTGCTTTAACCCACTTCTCTATATCTCATCAAGAAGA-A
*
19141560 GGGTTTGG
65 GGATTTGG
19141568 AAGTTTCACT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
84 20 0.33
85 40 0.67
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (85 bp):
ATCTCATCAGGAAGATGAACACTTCATTGCTTTAACCCACTTCTCTATATCTCATCAAGAAGAAG
GATTTGGTTCACTTCTTTGC
Found at i:19142055 original size:209 final size:209
Alignment explanation
Indices: 19141394--19142221 Score: 1185
Period size: 208 Copynumber: 4.0 Consensus size: 209
19141384 GCTTCATCTC
* * * *
19141394 TTGGTCTACTTCTCTATATCTCATTATGAAGATGA-TCGCTTCATTGTTTTAATCCACTTCTCTC
1 TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACT-GCTTCATTGTTTTAATCCACTTCTCTG
* *
19141458 TATCTCATCAAGAAGACGGATTTGGTTCACTTCTTTGCATCTCATCAGGAAGATGAACACTTTAT
65 TATCTCATCAAGAAGACAGATTTGGTTCACTTCTCTGCATCTCATCAGGAAGATGAACACTTTAT
* * * * *
19141523 TGCTTTAACCCAC-TCTCTATATCTCATCAGGAAGATAGGGTTTGGAAGTTTCACTCACTTTGAG
130 TGCTTCAACCCACTTCTCTATATCTCATCAAGAAGATGGGGTTTGGAAGTTTCACTCACATTAAG
*
19141587 CTTCACTTCGTTGAA
195 CTTCGCTTCGTTGAA
* * * *
19141602 TTGGTCTACTTTTTTGTATCTCATCAGGAAGATGACCGCTTCATTGTTTTAATCCACTTCTCTAT
1 TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACTGCTTCATTGTTTTAATCCACTTCTCTGT
* * * *
19141667 ATCTCATCAAAAAGACAGATTTGGTTCATTTCTCTACATCTCTTCAGGAAGATGAACACTTTATT
66 ATCTCATCAAGAAGACAGATTTGGTTCACTTCTCTGCATCTCATCAGGAAGATGAACACTTTATT
* * * * * *
19141732 GCTTCGACCCACTTCTCTGTATCTCAT-AGGAATATGGGGTTTGGAACTTTCACTCAAATTAAGC
131 GCTTCAACCCACTTCTCTATATCTCATCAAGAAGATGGGGTTTGGAAGTTTCACTCACATTAAGC
*
19141796 TTCGCTTAGTTGAA
196 TTCGCTTCGTTGAA
* *
19141810 TTGGTCTACTTATCTGTATCTCATCGGGAAGATGACTGCTTCATTGTTTTAATCCACTTCTCTGT
1 TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACTGCTTCATTGTTTTAATCCACTTCTCTGT
* * * * * * *
19141875 ATCTTATTAGGAAGACGGATTTGGTTCACTTCTCTGCATCTCGTCAGGAAGTTGACCACTTTATT
66 ATCTCATCAAGAAGACAGATTTGGTTCACTTCTCTGCATCTCATCAGGAAGATGAACACTTTATT
* *
19141940 GCTTCGACCCACTTCGCTATATCTCATCAAGAAGATGGGGTTTGGAAGTTTCACTCACATTAAGC
131 GCTTCAACCCACTTCTCTATATCTCATCAAGAAGATGGGGTTTGGAAGTTTCACTCACATTAAGC
19142005 TTCGCTTCGTTGAA
196 TTCGCTTCGTTGAA
* *
19142019 TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACTGCTTCATTGTTTTAATCCACTTTTTTGT
1 TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACTGCTTCATTGTTTTAATCCACTTCTCTGT
* * * *
19142084 ATCTCATCAGGAAGACAGATGTGGTTCACTTCTCTGCATCTCATCAAGAAGATGACCACTTTATT
66 ATCTCATCAAGAAGACAGATTTGGTTCACTTCTCTGCATCTCATCAGGAAGATGAACACTTTATT
* * * * *
19142149 ACTTCAACCCACTTTTCTATATCTCATCAAGAAGATGGGGTTTAGAAATTTCACTCACATTGAGC
131 GCTTCAACCCACTTCTCTATATCTCATCAAGAAGATGGGGTTTGGAAGTTTCACTCACATTAAGC
19142214 TTCGCTTC
196 TTCGCTTC
19142222 ATTTGATGGT
Statistics
Matches: 553, Mismatches: 64, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
208 309 0.56
209 244 0.44
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.37
Consensus pattern (209 bp):
TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACTGCTTCATTGTTTTAATCCACTTCTCTGT
ATCTCATCAAGAAGACAGATTTGGTTCACTTCTCTGCATCTCATCAGGAAGATGAACACTTTATT
GCTTCAACCCACTTCTCTATATCTCATCAAGAAGATGGGGTTTGGAAGTTTCACTCACATTAAGC
TTCGCTTCGTTGAA
Found at i:19142172 original size:85 final size:85
Alignment explanation
Indices: 19142026--19142183 Score: 208
Period size: 85 Copynumber: 1.9 Consensus size: 85
19142016 GAATTGGTCT
* * ** ** * * * *
19142026 ACTTCTCTGTATCTCATCAGGAAGATGACTGCTTCATTGTTTTAATCCACTTTTTTGTATCTCAT
1 ACTTCTCTGCATCTCATCAAGAAGATGACCACTTCATTACTTCAACCCACTTTTCTATATCTCAT
*
19142091 CAGGAAGACAGATGTGGTTC
66 CAAGAAGACAGATGTGGTTC
*
19142111 ACTTCTCTGCATCTCATCAAGAAGATGACCACTTTATTACTTCAACCCACTTTTCTATATCTCAT
1 ACTTCTCTGCATCTCATCAAGAAGATGACCACTTCATTACTTCAACCCACTTTTCTATATCTCAT
19142176 CAAGAAGA
66 CAAGAAGA
19142184 TGGGGTTTAG
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
85 61 1.00
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.36
Consensus pattern (85 bp):
ACTTCTCTGCATCTCATCAAGAAGATGACCACTTCATTACTTCAACCCACTTTTCTATATCTCAT
CAAGAAGACAGATGTGGTTC
Found at i:19144101 original size:46 final size:44
Alignment explanation
Indices: 19143922--19144093 Score: 202
Period size: 46 Copynumber: 3.8 Consensus size: 44
19143912 GATCAGAATG
** *
19143922 TGGCTTCAATCTACCCCTCTTGATTTAGGGGTAAAAGATTGGATGA
1 TGGCTTCAAT-TTGCCCTCTTGACTTAGGGGT-AAAGATTGGATGA
**
19143968 TGGCTTCAACCTGACCCTCTTGACTTAGGGGTGAAAGATTGGAATG-
1 TGGCTTCAATTTG-CCCTCTTGACTTAGGGGT-AAAGATTGG-ATGA
*
19144014 TGGCTTCAATTTGCCTCTCTTGATTTAGGGGTAAATGATTGGATGA
1 TGGCTTCAATTTGCC-CTCTTGACTTAGGGGTAAA-GATTGGATGA
*
19144060 TGGCTTTAATTTGTCCCTCTTGACTTAGGGGTAA
1 TGGCTTCAATTTG-CCCTCTTGACTTAGGGGTAA
19144094 GATATTGGTG
Statistics
Matches: 109, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
45 8 0.07
46 96 0.88
47 5 0.05
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.35
Consensus pattern (44 bp):
TGGCTTCAATTTGCCCTCTTGACTTAGGGGTAAAGATTGGATGA
Found at i:19144101 original size:92 final size:92
Alignment explanation
Indices: 19143917--19144091 Score: 278
Period size: 92 Copynumber: 1.9 Consensus size: 92
19143907 TAAAAGATCA
19143917 GAATGTGGCTTCAATCTACCCCTCTTGATTTAGGGGTAAAAGATTGGATGATGGCTTCAACCTGA
1 GAATGTGGCTTCAATCTACCCCTCTTGATTTAGGGGTAAAAGATTGGATGATGGCTTCAACCTGA
19143982 CCCTCTTGACTTAGGGGTGAAAGATTG
66 CCCTCTTGACTTAGGGGTGAAAGATTG
* * * * * ** *
19144009 GAATGTGGCTTCAATTTGCCTCTCTTGATTTAGGGGTAAATGATTGGATGATGGCTTTAATTTGT
1 GAATGTGGCTTCAATCTACCCCTCTTGATTTAGGGGTAAAAGATTGGATGATGGCTTCAACCTGA
19144074 CCCTCTTGACTTAGGGGT
66 CCCTCTTGACTTAGGGGT
19144092 AAGATATTGG
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
92 75 1.00
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (92 bp):
GAATGTGGCTTCAATCTACCCCTCTTGATTTAGGGGTAAAAGATTGGATGATGGCTTCAACCTGA
CCCTCTTGACTTAGGGGTGAAAGATTG
Found at i:19155925 original size:30 final size:29
Alignment explanation
Indices: 19155884--19156051 Score: 149
Period size: 30 Copynumber: 5.6 Consensus size: 29
19155874 GAGAATTTGG
*
19155884 GGGTTAAAATGTAATTTTAGAAAAGTTTA
1 GGGTCAAAATGTAATTTTAGAAAAGTTTA
* *
19155913 GAGTCAAAAATGTAATTTTGGAAAAGTTTAA
1 GGGTC-AAAATGTAATTTTAGAAAAGTTT-A
* *
19155944 GGGTCAAAATGCAATTTTGGAAAAGTTTA
1 GGGTCAAAATGTAATTTTAGAAAAGTTTA
* * **
19155973 GGGGTTAAAATATAATTTTAGAGAAA-TTCG
1 -GGGTCAAAATGTAATTTTAGA-AAAGTTTA
* * *
19156003 GTGGTTAAAATGTAATTTTAGAGAAGTTCGA
1 G-GGTCAAAATGTAATTTTAGAAAAGTT-TA
* *
19156034 GAGTCAAAATGAAATTTT
1 GGGTCAAAATGTAATTTT
19156052 TAAATAAAAC
Statistics
Matches: 114, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
29 7 0.06
30 98 0.86
31 9 0.08
ACGTcount: A:0.40, C:0.04, G:0.22, T:0.34
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTAGAAAAGTTTA
Found at i:19155953 original size:60 final size:58
Alignment explanation
Indices: 19155884--19156051 Score: 167
Period size: 60 Copynumber: 2.8 Consensus size: 58
19155874 GAGAATTTGG
*
19155884 GGGTTAAAATGTAATTTTAGAAAAGTTTAGAGTCAAAAATGTAATTTTGGA-AAAGTTTAA
1 GGGTTAAAATGTAATTTTAGAAAAGTTTAGAGTC-AAAATGTAATTTTAGAGAAA--TTAA
* * * * * * **
19155944 GGGTCAAAATGCAATTTTGGAAAAGTTTAGGGGTTAAAATATAATTTTAGAGAAATTCG
1 GGGTTAAAATGTAATTTTAGAAAAGTTTA-GAGTCAAAATGTAATTTTAGAGAAATTAA
* * *
19156003 GTGGTTAAAATGTAATTTTAGAGAAGTTCGAGAGTCAAAATGAAATTTT
1 G-GGTTAAAATGTAATTTTAGAAAAGTT-TAGAGTCAAAATGTAATTTT
19156052 TAAATAAAAC
Statistics
Matches: 86, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
59 3 0.03
60 76 0.88
61 7 0.08
ACGTcount: A:0.40, C:0.04, G:0.22, T:0.34
Consensus pattern (58 bp):
GGGTTAAAATGTAATTTTAGAAAAGTTTAGAGTCAAAATGTAATTTTAGAGAAATTAA
Found at i:19157766 original size:21 final size:20
Alignment explanation
Indices: 19157726--19157768 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 20
19157716 CCTACACCAA
19157726 AGAAGAAAATAGAAGCAAAAC
1 AGAAGAAAATAGAA-CAAAAC
19157747 AGAAGACAAATAGGAA-AAAAC
1 AGAAGA-AAATA-GAACAAAAC
19157768 A
1 A
19157769 AAAAAACAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 12 0.60
22 5 0.25
23 3 0.15
ACGTcount: A:0.67, C:0.09, G:0.19, T:0.05
Consensus pattern (20 bp):
AGAAGAAAATAGAACAAAAC
Found at i:19158443 original size:21 final size:21
Alignment explanation
Indices: 19158414--19158453 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
19158404 TATTAAAATA
19158414 TATAATAATATATT-CATTTTT
1 TATAATAATAT-TTCCATTTTT
*
19158435 TATATTAATATTTCCATTT
1 TATAATAATATTTCCATTT
19158454 ATTGATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.57
Consensus pattern (21 bp):
TATAATAATATTTCCATTTTT
Found at i:19159503 original size:30 final size:30
Alignment explanation
Indices: 19159463--19159848 Score: 400
Period size: 30 Copynumber: 13.1 Consensus size: 30
19159453 TGCTAAGAGG
* *
19159463 CCCTCGAACTTCCCAAAAATCACATTTTAA
1 CCCTCAAACTTTCCAAAAATCACATTTTAA
19159493 CCCTCAAACTTTCCAAAAATCACATTTTAA
1 CCCTCAAACTTTCCAAAAATCACATTTTAA
*
19159523 CCCTCAAACTTTCCAAAAATTACATTTTAA
1 CCCTCAAACTTTCCAAAAATCACATTTTAA
* * **
19159553 CCCTCGAACTTTTCAAAAATCACATTTTGG
1 CCCTCAAACTTTCCAAAAATCACATTTTAA
* * * *
19159583 CCCTCAAACTTTTCAAAATTCATATTTTGA
1 CCCTCAAACTTTCCAAAAATCACATTTTAA
* *
19159613 CCCTTAAACTTTCCAAAAATCACATTTTGA
1 CCCTCAAACTTTCCAAAAATCACATTTTAA
19159643 CCCT-AAACTTTCC-AAAATCACATTTTAA
1 CCCTCAAACTTTCCAAAAATCACATTTTAA
* *
19159671 CCC-CTAAACTTT-CAAAAATTACA-TTTGA
1 CCCTC-AAACTTTCCAAAAATCACATTTTAA
* * *
19159699 CCCTTC-AA-TTTCCATAAATTACATTTTGA
1 CCC-TCAAACTTTCCAAAAATCACATTTTAA
*
19159728 CCC-CTAAACTTTCCAAAAATCATATTTTAA
1 CCCTC-AAACTTTCCAAAAATCACATTTTAA
* * *
19159758 CCCCCAAACTTTTCAAAAATCACATTTTGA
1 CCCTCAAACTTTCCAAAAATCACATTTTAA
* * * *
19159788 CCC-AAAAATTT-CTAAAACCACATTTTAA
1 CCCTCAAACTTTCCAAAAATCACATTTTAA
* *
19159816 TCCC-GAAACTTTCC-AATATCACATTTTAA
1 -CCCTCAAACTTTCCAAAAATCACATTTTAA
19159845 CCCT
1 CCCT
19159849 AAATTCTCTT
Statistics
Matches: 306, Mismatches: 36, Indels: 29
0.82 0.10 0.08
Matches are distributed among these distances:
27 4 0.01
28 54 0.18
29 62 0.20
30 185 0.60
31 1 0.00
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.33
Consensus pattern (30 bp):
CCCTCAAACTTTCCAAAAATCACATTTTAA
Found at i:19161721 original size:22 final size:22
Alignment explanation
Indices: 19161695--19161736 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
19161685 AAATTAATCC
*
19161695 TTTTAGTTTTAT-CTTTTTTATT
1 TTTTA-TTTTATACTGTTTTATT
19161717 TTTTATTTTATACTGTTTTA
1 TTTTATTTTATACTGTTTTA
19161737 AAAAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.74
Consensus pattern (22 bp):
TTTTATTTTATACTGTTTTATT
Found at i:19164259 original size:52 final size:52
Alignment explanation
Indices: 19164177--19164626 Score: 693
Period size: 52 Copynumber: 8.7 Consensus size: 52
19164167 ATTCCATTTA
* * * * * * *
19164177 ATACTTACGATGACACATAGTCATCAGACCTCTTAATCCGTGAGGGAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
*
19164229 ATACTCACGATGACACATAGTCATCGGACCTCTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
*
19164281 ATACTCACGATGACACATGGTCATCGGACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
* * * *
19164333 ATACCCACAATGACACATGGTCATCGGACCTTTTAATTCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
* * *
19164385 ATACTCACGATGACACATGGTCATCGGACCTTTTAATCTATAAAGGATTCAC
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
* *
19164437 ATACTCATGATGACACATAGTCATCGGACCTTTTAATCCATTAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
* *
19164489 ATACTCAGGATGACACATAGTCATCAGACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
* *
19164541 ATCCTCACGATGACACATAGTCATCAGACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
*
19164593 ATATTCACGATGACACATAGTCATCGGACCTTTT
1 ATACTCACGATGACACATAGTCATCGGACCTTTT
19164627 CTTTATTTAC
Statistics
Matches: 369, Mismatches: 29, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 369 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
Found at i:19166851 original size:12 final size:12
Alignment explanation
Indices: 19166834--19166858 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19166824 GAGGAGTAAA
19166834 TTGTAAAAGGGG
1 TTGTAAAAGGGG
19166846 TTGTAAAAGGGG
1 TTGTAAAAGGGG
19166858 T
1 T
19166859 AAAAGTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.40, T:0.28
Consensus pattern (12 bp):
TTGTAAAAGGGG
Found at i:19170176 original size:58 final size:58
Alignment explanation
Indices: 19170087--19170201 Score: 169
Period size: 58 Copynumber: 2.0 Consensus size: 58
19170077 AAAGGAGTTG
* * *
19170087 TTTATGAGTGTTATTTAGGAATAAAATTATATTTGAGTTTAAAAATATTTGGGTTTAA
1 TTTATAAGTGTTATTTAAGAATAAAACTATATTTGAGTTTAAAAATATTTGGGTTTAA
* *
19170145 TTTATAAGTGTT-TTTGAAGAATTAAACTATATTTGGGTTTAAAAATATTTGGGTTTA
1 TTTATAAGTGTTATTT-AAGAATAAAACTATATTTGAGTTTAAAAATATTTGGGTTTA
19170202 GTTTGTTGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 3 0.06
58 48 0.94
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.47
Consensus pattern (58 bp):
TTTATAAGTGTTATTTAAGAATAAAACTATATTTGAGTTTAAAAATATTTGGGTTTAA
Found at i:19171201 original size:52 final size:52
Alignment explanation
Indices: 19171119--19171776 Score: 1100
Period size: 52 Copynumber: 12.7 Consensus size: 52
19171109 TTCCAATTTA
* ** * *
19171119 ATACTCACGATGACACATAGTCATCGGACCTCTTAATCTGTGAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
* *
19171171 ATACTCAGGATGACACATAGTCATCAGACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
* * *
19171223 ATACTCACGATGGCATATGGTCATCGGACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
* * * *
19171275 ATACTCACGATGACAAATAATTATCGGACCTTTTATTCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
* *
19171327 ATGCTCACGATGACACATGGTCATCGGACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
19171379 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
**
19171431 ATACTCACGATGACACATAGTCATCAAACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
*
19171483 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
*
19171535 ATACTCACGATGACACATAGTCATCGAACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
*
19171587 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAGAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
19171639 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
* *
19171691 ATCCTCACGATGACACATAGTCATCAGACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
*
19171743 ATATTCACGATGACACATAGTCATCGGACCTTTT
1 ATACTCACGATGACACATAGTCATCGGACCTTTT
19171777 CTTTATTTAC
Statistics
Matches: 565, Mismatches: 41, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 565 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
Found at i:19177458 original size:19 final size:20
Alignment explanation
Indices: 19177434--19177471 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
19177424 TAAATATACT
*
19177434 AATTTTTTT-TTAATTTTTG
1 AATTTTTTTAATAATTTTTG
19177453 AATTTTTTTAATAATTTTT
1 AATTTTTTTAATAATTTTT
19177472 TTCCATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (20 bp):
AATTTTTTTAATAATTTTTG
Found at i:19180617 original size:25 final size:23
Alignment explanation
Indices: 19180589--19180634 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
19180579 GTAGGATCCA
19180589 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
19180614 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
19180635 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:19190041 original size:20 final size:21
Alignment explanation
Indices: 19189998--19190081 Score: 82
Period size: 22 Copynumber: 4.0 Consensus size: 21
19189988 CAGCAAATGA
* * *
19189998 TTTTAAAATTATTAAAGTTTT
1 TTTTAAAAATATTAAAATTAT
19190019 TTTTAAAAATA-TAAAATTA-
1 TTTTAAAAATATTAAAATTAT
*
19190038 TTTTAAAATTATTAAAATTATT
1 TTTTAAAAATATTAAAATTA-T
** *
19190060 TTTTTGAAATAATAAAATTAT
1 TTTTAAAAATATTAAAATTAT
19190081 T
1 T
19190082 AAATAATTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
19 10 0.19
20 14 0.27
21 12 0.23
22 16 0.31
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
TTTTAAAAATATTAAAATTAT
Found at i:19190041 original size:22 final size:22
Alignment explanation
Indices: 19189998--19190081 Score: 70
Period size: 21 Copynumber: 4.0 Consensus size: 22
19189988 CAGCAAATGA
* * *
19189998 TTTTAAAATTATTAAAGT-TTT
1 TTTTAAAAATATAAAATTATTT
19190019 TTTTAAAAATATAAAATTA---
1 TTTTAAAAATATAAAATTATTT
*
19190038 TTTTAAAATTATTAAAATTATTT
1 TTTTAAAAATA-TAAAATTATTT
*
19190061 TTTT-GAAATAATAAAATTATT
1 TTTTAAAAAT-ATAAAATTATT
19190082 AAATAATTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
19 10 0.20
20 8 0.16
21 15 0.29
22 13 0.25
23 5 0.10
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TTTTAAAAATATAAAATTATTT
Found at i:19190043 original size:19 final size:20
Alignment explanation
Indices: 19189992--19190061 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
19189982 TCATGTCAGC
* *
19189992 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAAATATTA
* *
19190012 AAGTTTTTTTTAAAAATA-TA
1 AA-ATTATTTTAAAAATATTA
*
19190032 AAATTATTTTAAAATTATTA
1 AAATTATTTTAAAAATATTA
19190052 AAATTATTTT
1 AAATTATTTT
19190062 TTTGAAATAA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
19 12 0.29
20 18 0.44
21 11 0.27
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
AAATTATTTTAAAAATATTA
Found at i:19190046 original size:11 final size:11
Alignment explanation
Indices: 19190030--19190061 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
19190020 TTTAAAAATA
19190030 TAAAATTATTT
1 TAAAATTATTT
19190041 TAAAATTA--T
1 TAAAATTATTT
19190050 TAAAATTATTT
1 TAAAATTATTT
19190061 T
1 T
19190062 TTTGAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.47
11 10 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TAAAATTATTT
Done.