Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007807.1 Hibiscus syriacus cultivar Beakdansim tig00110126_pilon, whole genome shotgun sequence
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: 2195110
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
File 3 of 9
Found at i:353834 original size:32 final size:32
Alignment explanation
Indices: 353795--354793 Score: 458
Period size: 32 Copynumber: 33.7 Consensus size: 32
353785 CAATCTATAT
353795 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
353827 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
353859 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
353881 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
353913 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
* *
353945 TTTAAAATAAATCAATCCATACAACTACA--A
1 TTTAAAATAAATCAATCCATACAAATAAATTA
353975 --T--AATAAATCAATCCAT----AT------
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
353993 TTTAAAATAAATCAATTCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
354025 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
354057 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
354079 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
* * *
354111 TTTAAAATAAATCAATTCATACAACTACA--A
1 TTTAAAATAAATCAATCCATACAAATAAATTA
354141 --T--AATAAATCAATCCAT----AT------
1 TTTAAAATAAATCAATCCATACAAATAAATTA
354159 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
* *
354191 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
354223 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACAAATAAATTA
* *
354245 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
* **
354277 TTTAAAATAAATCAATCCATACAACT--ACGA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
* * *
354307 --T--AATAAATCAATACATATTTGAAAATAAATCA
1 TTTAAAATAAATCAATCCATA----CAAATAAATTA
* ** * * * * ** *
354339 ATCCATACAAATAAAT-TATTTAAAGTAAATCAA
1 TTTAAAATAAATCAATCCATACAAA-TAAAT-TA
* * * ** * * *
354372 TCTATACTAATAAATTATTTAAAATAAATCAATCCATA
1 T-T-TA-AAATAAATCAATCCATACAAATAAAT---TA
*
354410 TTTTAAAATAAATCAATCCATACTAATAAATTA
1 -TTTAAAATAAATCAATCCATACAAATAAATTA
354443 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
354465 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
* *
354497 TTTAAAATAAATCAATCTATA-AAACTACA--A
1 TTTAAAATAAATCAATCCATACAAA-TAAATTA
*** *
354527 --T--AATAAATCAATCCATA-TTTTAAAATA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
**
354554 AAT-AAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
354585 TTTAAAATAAATCAATCCATACAACTACAA-TA
1 TTTAAAATAAATCAATCCATACAAATA-AATTA
* * ** *
354617 -AT-AAATCAATCTATAT-TTTA-AAATAAATAAA
1 TTTAAAATAAATC-A-ATCCATACAAATAAAT-TA
* * * ** * * *
354648 TCCATACAAATAAATTATTTAAAATAAATCAATCTATA
1 T--TTA-AAATAAATCAATCCATACAAAT-AA-AT-TA
*
354686 TTTTAAAATAAATCAATCCATACTAATAAATTA
1 -TTTAAAATAAATCAATCCATACAAATAAATTA
354719 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACAAATAAATTA
* *
354741 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
354773 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
354794 TTTTATAATA
Statistics
Matches: 749, Mismatches: 98, Indels: 240
0.69 0.09 0.22
Matches are distributed among these distances:
20 2 0.00
22 111 0.15
23 8 0.01
24 5 0.01
25 3 0.00
26 78 0.10
27 1 0.00
28 19 0.03
29 3 0.00
30 41 0.05
31 27 0.04
32 353 0.47
33 7 0.01
34 5 0.01
35 6 0.01
36 62 0.08
37 11 0.01
38 5 0.01
39 2 0.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACAAATAAATTA
Found at i:353885 original size:22 final size:22
Alignment explanation
Indices: 353859--353901 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
353849 TAATAAATTA
353859 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
353881 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
353902 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:353910 original size:22 final size:22
Alignment explanation
Indices: 353861--353909 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
353851 ATAAATTATT
**
353861 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
353883 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
353906 TAAA
1 TAAA
353910 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:353999 original size:166 final size:166
Alignment explanation
Indices: 353827--354793 Score: 1069
Period size: 166 Copynumber: 5.8 Consensus size: 166
353817 AAATAAATTA
* ** * *
353827 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAA
1 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTAT
* * ** **
353891 AT-CAATCCATACTAATAAAT-TATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATA
66 TTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATA
353954 AATCAATCCATACAACTACAATAATAAATCAATCCATAT
128 AATCAATCCATACAACTACAATAATAAATCAATCCATAT
*
353993 TTTAAAATAAATCAATTCATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTAT
1 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTAT
354058 TTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
66 TTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
*
354123 CAATTCATACAACTACAATAATAAATCAATCCATAT
131 CAATCCATACAACTACAATAATAAATCAATCCATAT
*
354159 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATTCATACTAATAAATTAT
1 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTAT
*
354224 TTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAAT
66 TTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
* *
354289 CAATCCATACAACTACGATAATAAATCAATACATAT
131 CAATCCATACAACTACAATAATAAATCAATCCATAT
* * *
354325 TTGAAAATAAATCAATCCATACAAATAAATTATTTAAAGTAAATCAATCTATACTAATAAATTAT
1 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTAT
354390 TTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
66 TTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
*** * * * *
354455 CAATCCATA-TTTTAAAATAAATCAATCCATACTAATAAATT
131 CAATCCATACAACTACAAT-AATAAATCAAT-C-CAT--A-T
* * ** *
354496 ATTTAAAATAAATCAATCTATA-AAACTACA--A--T--AATAAATCAATCCATA-TTTTAAAAT
1 -TTTAAAATAAATCAATCCATACAAA-TAAATTATTTAAAATAAATCAATCCATACTAATAAATT
** *
354553 AAAT-AAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATAC-AACTACA--
64 ATTTAAAATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATCAATCCATACTAA-TAAATT
* *** * * *
354614 A--T--AATAAATCAATCTATA-TTTTAAAATAAATAAATCCATACAAATAAATT
118 ATTTAAAATAAATCAATCCATACAACTACAAT-AATAAATCAAT-C-CAT--A-T
354664 ATTTAAAATAAATCAAT-C-T----AT--A-T-TTTAAAATAAATCAATCCATACTAATAAATTA
1 -TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTA
*
354719 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAA
65 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA
354784 TCAATCCATA
130 TCAATCCATA
354794 TTTTATAATA
Statistics
Matches: 709, Mismatches: 56, Indels: 76
0.84 0.07 0.09
Matches are distributed among these distances:
156 24 0.03
157 3 0.00
158 2 0.00
160 4 0.01
162 18 0.03
163 1 0.00
164 28 0.04
165 22 0.03
166 465 0.66
167 10 0.01
168 71 0.10
170 5 0.01
171 4 0.01
172 24 0.03
173 3 0.00
174 25 0.04
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (166 bp):
TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTAT
TTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
CAATCCATACAACTACAATAATAAATCAATCCATAT
Found at i:354083 original size:22 final size:22
Alignment explanation
Indices: 354057--354099 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
354047 TAATAAATTA
354057 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
354079 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
354100 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:354108 original size:22 final size:22
Alignment explanation
Indices: 354059--354107 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
354049 ATAAATTATT
**
354059 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
354081 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
354104 TAAA
1 TAAA
354108 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:354198 original size:14 final size:14
Alignment explanation
Indices: 354181--354234 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
354171 CAATCCATAC
354181 AAATAAATTATTTA
1 AAATAAATTATTTA
*
354195 AAATAAATCAATTCATA
1 AAATAAAT-TATT--TA
*
354212 CTAATAAATTATTTA
1 -AAATAAATTATTTA
354227 AAATAAAT
1 AAATAAAT
354235 CAATCCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.47
15 5 0.16
17 5 0.16
18 7 0.22
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:354274 original size:22 final size:22
Alignment explanation
Indices: 354225--354273 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
354215 ATAAATTATT
**
354225 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
354247 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
354270 TAAA
1 TAAA
354274 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:354415 original size:22 final size:22
Alignment explanation
Indices: 354389--354431 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
354379 TAATAAATTA
354389 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
354411 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
354432 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:354440 original size:22 final size:22
Alignment explanation
Indices: 354391--354439 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
354381 ATAAATTATT
**
354391 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
354413 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
354436 TAAA
1 TAAA
354440 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:354469 original size:22 final size:22
Alignment explanation
Indices: 354443--354485 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
354433 TAATAAATTA
354443 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
354465 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
354486 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:354494 original size:22 final size:22
Alignment explanation
Indices: 354445--354493 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
354435 ATAAATTATT
**
354445 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
354467 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
354490 TAAA
1 TAAA
354494 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:354531 original size:26 final size:26
Alignment explanation
Indices: 354501--354649 Score: 88
Period size: 26 Copynumber: 5.3 Consensus size: 26
354491 AAATTATTTA
354501 AAATAAATCAATCTATAAAACTACAAT
1 AAATAAATCAATCTATAAAA-TACAAT
354528 -AATAAATCAATCCATATTTTAAAATA-AAT
1 AAATAAATCAAT-C-TA---TAAAATACAAT
* *
354557 AAATAAATCAATCCATACAAATAAATTATTT
1 AAATAAATCAATCTATA-AAATACA--A--T
* *
354588 AAAATAAATCAATCCATACAACTACAAT
1 -AAATAAATCAATCTATA-AAATACAAT
*** *
354616 -AATAAATCAATCTATATTTTAAAAT
1 AAATAAATCAATCTATAAAATACAAT
354641 AAATAAATC
1 AAATAAATC
354650 CATACAAATA
Statistics
Matches: 100, Mismatches: 8, Indels: 29
0.73 0.06 0.21
Matches are distributed among these distances:
25 7 0.07
26 39 0.39
27 2 0.02
28 4 0.04
29 5 0.05
30 14 0.14
31 6 0.06
32 23 0.23
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.30
Consensus pattern (26 bp):
AAATAAATCAATCTATAAAATACAAT
Found at i:354545 original size:80 final size:80
Alignment explanation
Indices: 354448--354685 Score: 359
Period size: 88 Copynumber: 2.9 Consensus size: 80
354438 AATTATTTAA
*
354448 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
354513 CTATAAAACTACAAT
66 CTATAAAACTACAAT
354528 AATAAATCAATCCATATTTTAAAATAAATAAATAAATCAATCCATACAAATAAATTATTTAAAAT
1 AATAAATCAATCCATA-TTT----T--A-AAATAAATCAATCCATACAAATAAATTATTTAAAAT
* *
354593 AAATCAATCCATACAACTACAAT
58 AAATCAATCTATAAAACTACAAT
* *
354616 AATAAATCAATCTATATTTTAAAATAAATAAATCCATACAAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
354681 CTATA
66 CTATA
354686 TTTTAAAATA
Statistics
Matches: 144, Mismatches: 6, Indels: 16
0.87 0.04 0.10
Matches are distributed among these distances:
80 63 0.44
81 4 0.03
83 1 0.01
85 1 0.01
87 4 0.03
88 71 0.49
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
CTATAAAACTACAAT
Found at i:354580 original size:18 final size:18
Alignment explanation
Indices: 354557--354608 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
354547 TAAAATAAAT
354557 AAATAAATCAATCCATAC
1 AAATAAATCAATCCATAC
* *
354575 AAATAAAT-TAT--TTA-
1 AAATAAATCAATCCATAC
354589 AAATAAATCAATCCATAC
1 AAATAAATCAATCCATAC
354607 AA
1 AA
354609 CTACAATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
14 8 0.31
15 4 0.15
17 4 0.15
18 10 0.38
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (18 bp):
AAATAAATCAATCCATAC
Found at i:354716 original size:22 final size:22
Alignment explanation
Indices: 354667--354715 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
354657 ATAAATTATT
* **
354667 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCCATATAA
354689 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
354712 TAAA
1 TAAA
354716 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:354770 original size:22 final size:22
Alignment explanation
Indices: 354721--354769 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
354711 ATAAATTATT
**
354721 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
354743 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
354766 TAAA
1 TAAA
354770 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:354812 original size:15 final size:15
Alignment explanation
Indices: 354792--354896 Score: 165
Period size: 15 Copynumber: 7.0 Consensus size: 15
354782 AATCAATCCA
* *
354792 TATTTTATAATAATT
1 TATTTTAAAATAAAT
354807 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
*
354822 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
*
354837 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
354852 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
*
354867 TATTTTAAAACAAAT
1 TATTTTAAAATAAAT
354882 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
354897 AACCTTATTA
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 84 1.00
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTTTAAAATAAAT
Found at i:354846 original size:12 final size:15
Alignment explanation
Indices: 354792--354948 Score: 157
Period size: 15 Copynumber: 10.7 Consensus size: 15
354782 AATCAATCCA
*
354792 TATTTTATAATAATT
1 TATTTTATAATAAAT
*
354807 TATTTTAAAATAAAT
1 TATTTTATAATAAAT
354822 TATTTTATAATAAAT
1 TATTTTATAATAAAT
354837 TATTTTATAATAAAT
1 TATTTTATAATAAAT
*
354852 TATTTTAAAATAAAT
1 TATTTTATAATAAAT
* *
354867 TATTTTAAAACAAAT
1 TATTTTATAATAAAT
*
354882 TATTTTAAAATAAAT
1 TATTTTATAATAAAT
* **
354897 AACCTTAT--TAAAT
1 TATTTTATAATAAAT
354910 TA--TT-T-A-AAAT
1 TATTTTATAATAAAT
354920 TATTTTAATAAATAAAT
1 TATTTT-AT-AATAAAT
354937 ATATTTTATAAT
1 -TATTTTATAAT
354949 TATTCTTGAA
Statistics
Matches: 122, Mismatches: 11, Indels: 17
0.81 0.07 0.11
Matches are distributed among these distances:
10 7 0.06
11 2 0.02
12 2 0.02
13 6 0.05
14 1 0.01
15 88 0.72
16 4 0.03
17 6 0.05
18 6 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
TATTTTATAATAAAT
Found at i:357620 original size:25 final size:25
Alignment explanation
Indices: 357591--357644 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
357581 GATCAACGTT
357591 AAACTACAGAAACACATCAATGACC
1 AAACTACAGAAACACATCAATGACC
357616 AAACTACAGAAACACATCAATGACC
1 AAACTACAGAAACACATCAATGACC
357641 AAAC
1 AAAC
357645 CCAACTGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.54, C:0.28, G:0.07, T:0.11
Consensus pattern (25 bp):
AAACTACAGAAACACATCAATGACC
Found at i:361678 original size:220 final size:220
Alignment explanation
Indices: 361413--362373 Score: 1156
Period size: 220 Copynumber: 4.4 Consensus size: 220
361403 AGATCCAAAT
* * * * *
361413 AATCTGGAGATAATTTAGACACAATACGGTTCATTCGCATTGAGGAAGTCTGATTGTCTGAGGAT
1 AATCTGGAGATAATTCAGAGACAACACGGTTCCTTCGCTTTGAGGAAGTCTGATTGTCTGAGGAT
* * * * *
361478 GACAATGCTCATTCGCGTTGAGGAGATCAGGTCAATCTGGAGATAATTTGATGTTGAAGACAACA
66 GACACTGCTCCTTCGTGTTGAGGAGATCAGGTCAATATGGAGATAATTTGATGTTGAAGATAACA
* * * *
361543 CTGCTCATCCGTGTTGAAGAGATCTGGTTGTTTTCAGGTAAATTGTTTACTGGAGATGACGCTGT
131 CTGCTCATCCGTGTTGAAGAGATCTAGTCGTTTTCAGGTAAATTGTTTGCTGGAGATGACGTTGT
* * *
361608 TCATTCTCGTTGAGCAAATCGGGTC
196 TCCTTCTCGTTGAGGAAATCGAGTC
*
361633 AATCTGGAGATAATTCAGAGATAACACGGTTCCTTCGCTTTGAGGAAGTCTGATTGTCTGAGGAT
1 AATCTGGAGATAATTCAGAGACAACACGGTTCCTTCGCTTTGAGGAAGTCTGATTGTCTGAGGAT
* *
361698 GACTCTGCTCCTTCGTGTTGAGGAGATCAGGTCAATATGGAGATAATTTGATGTTGAAGATGACA
66 GACACTGCTCCTTCGTGTTGAGGAGATCAGGTCAATATGGAGATAATTTGATGTTGAAGATAACA
* * * * * * * *
361763 TTGCTCATCCGTGTTGAAGAGATTTGGTTGTTTTCAGGTAAATTGTTCGCTGGAAATGATGTTAT
131 CTGCTCATCCGTGTTGAAGAGATCTAGTCGTTTTCAGGTAAATTGTTTGCTGGAGATGACGTTGT
361828 TCCTTCTCGTTGAGGAAATCGAGTC
196 TCCTTCTCGTTGAGGAAATCGAGTC
* ** * * *
361853 AATCTAGAGATAATTTGGAGACAACACAGTTCCTTCGCGTTGAGGGAGTCTGATTGTCTGAGGAT
1 AATCTGGAGATAATTCAGAGACAACACGGTTCCTTCGCTTTGAGGAAGTCTGATTGTCTGAGGAT
* ** * ** * * ** *
361918 GACACTGATAATTTGTGTTGAGGAGATTGGGTTAATCTATAGATAATTTGATGTTAAAGATAACA
66 GACACTGCTCCTTCGTGTTGAGGAGATCAGGTCAATATGGAGATAATTTGATGTTGAAGATAACA
* * * * * * *
361983 CTGATCATCTGTGTTGAAGAGATATAGTCATTTTCAGGTAAATTATTTGTTGGAGATGACATTGT
131 CTGCTCATCCGTGTTGAAGAGATCTAGTCGTTTTCAGGTAAATTGTTTGCTGGAGATGACGTTGT
* *
362048 TCCTTCTCATTGAGGAAATCGAGTT
196 TCCTTCTCGTTGAGGAAATCGAGTC
* * * *
362073 AATCTGGAG---A--C--A-AC-ATA--GTTTCTTTGCTTTGAGGAAGTTTGATTGTCTGAGGAT
1 AATCTGGAGATAATTCAGAGACAACACGGTTCCTTCGCTTTGAGGAAGTCTGATTGTCTGAGGAT
* * ** * * * *
362127 GACACCGATCCTTCACGTTGAGGAAATCAGGTTAATATGGAGATAATTTGATGTTGAATATGACA
66 GACACTGCTCCTTCGTGTTGAGGAGATCAGGTCAATATGGAGATAATTTGATGTTGAAGATAACA
* *
362192 TTGCTCATCCGTGTTGAAGAGATCTAGTCGTTTTCAGGTAAATTGTTTGTTGGAGATGACGTTGT
131 CTGCTCATCCGTGTTGAAGAGATCTAGTCGTTTTCAGGTAAATTGTTTGCTGGAGATGACGTTGT
* * *
362257 TCCTTATTGTTGAGGAAATCGGGTC
196 TCCTTCTCGTTGAGGAAATCGAGTC
* *
362282 AATCTGGAGATAATGT-GGAGACAACACGGTTCCTTCACTTT-AGGAAGTCTGATTGTCTGAGGA
1 AATCTGGAGATAAT-TCAGAGACAACACGGTTCCTTCGCTTTGAGGAAGTCTGATTGTCTGAGGA
*
362345 TGACACTCCTCCTTCGTGTTGAGGAGATC
65 TGACACTGCTCCTTCGTGTTGAGGAGATC
362374 GAGTCAAAAC
Statistics
Matches: 623, Mismatches: 106, Indels: 25
0.83 0.14 0.03
Matches are distributed among these distances:
209 169 0.27
211 2 0.00
212 3 0.00
213 1 0.00
216 1 0.00
217 3 0.00
218 2 0.00
219 44 0.07
220 398 0.64
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.34
Consensus pattern (220 bp):
AATCTGGAGATAATTCAGAGACAACACGGTTCCTTCGCTTTGAGGAAGTCTGATTGTCTGAGGAT
GACACTGCTCCTTCGTGTTGAGGAGATCAGGTCAATATGGAGATAATTTGATGTTGAAGATAACA
CTGCTCATCCGTGTTGAAGAGATCTAGTCGTTTTCAGGTAAATTGTTTGCTGGAGATGACGTTGT
TCCTTCTCGTTGAGGAAATCGAGTC
Found at i:362233 original size:429 final size:433
Alignment explanation
Indices: 361413--362351 Score: 1222
Period size: 429 Copynumber: 2.2 Consensus size: 433
361403 AGATCCAAAT
* * * *
361413 AATCTGGAGATAATTTAGACACAATACGGTTCATTCGCATTGAGGAAGTCTGATTGTCTGAGGAT
1 AATCTGGAGATAATTTGGAGACAACACGGTTCCTTCGC-TTGAGGAAGTCTGATTGTCTGAGGAT
* * * * *
361478 GACAATGCTCATTCGCGTTGAGGAGATCAGGTCAATCTGGAGATAATTTGATGTTGAAGACAACA
65 GACACTGATAATTCGCGTTGAGGAGATCAGGTCAATCTAGAGATAATTTGATGTTAAAGACAACA
* * * ** * *
361543 CTGCTCATCCGTGTTGAAGAGATCTGGTTGTTTTCAGGTAAATTGTTTACTGGAGATGACGCTGT
130 CTGATCATCCGTGTTGAAGAGATATAGTCATTTTCAGGTAAATTATTTACTGGAGATGACACTGT
* * *
361608 TCATTCTCGTTGAGCAAATCGGGTCAATCTGGAGATAATTCAGAGATAACACGGTTCCTTCGCTT
195 TCATTCTCATTGAGCAAATCGAGTCAATCTGGAG--AA-TCAGACAT-A-AC-GTTCCTTCGCTT
* * * ** *
361673 TGAGGAAGTCTGATTGTCTGAGGATGACTCTGCTCCTTCGTGTTGAGGAGATCAGGTCAATATGG
254 TGAGGAAGTCTGATTGTCTGAGGATGACACCGATCCTTCACGTTGAGGAAATCAGGTCAATATGG
* * *
361738 AGATAATTTGATGTTGAAGATGACATTGCTCATCCGTGTTGAAGAGATTTGGTTGTTTTCAGGTA
319 AGATAATTTGATGTTGAAGATGACATTGCTCATCCGTGTTGAAGAGATCTAGTCGTTTTCAGGTA
* *
361803 AATTGTTCGCTGGAAATGATGTTATTCCTTCTCGTTGAGGAAATCGAGTC
384 AATTGTTCGCTGGAAATGACGTTATTCCTTATCGTTGAGGAAATCGAGTC
* * *
361853 AATCTAGAGATAATTTGGAGACAACACAGTTCCTTCGCGTTGAGGGAGTCTGATTGTCTGAGGAT
1 AATCTGGAGATAATTTGGAGACAACACGGTTCCTTCGC-TTGAGGAAGTCTGATTGTCTGAGGAT
* * ** * * *
361918 GACACTGATAATTTGTGTTGAGGAGATTGGGTTAATCTATAGATAATTTGATGTTAAAGATAACA
65 GACACTGATAATTCGCGTTGAGGAGATCAGGTCAATCTAGAGATAATTTGATGTTAAAGACAACA
* ** *
361983 CTGATCATCTGTGTTGAAGAGATATAGTCATTTTCAGGTAAATTATTTGTTGGAGATGACATTGT
130 CTGATCATCCGTGTTGAAGAGATATAGTCATTTTCAGGTAAATTATTTACTGGAGATGACACTGT
* * * * *
362048 TCCTTCTCATTGAGGAAATCGAGTTAATCTGGAG-A-CA-ACAT-A-GTTTCTTTGCTTTGAGGA
195 TCATTCTCATTGAGCAAATCGAGTCAATCTGGAGAATCAGACATAACGTTCCTTCGCTTTGAGGA
* *
362108 AGTTTGATTGTCTGAGGATGACACCGATCCTTCACGTTGAGGAAATCAGGTTAATATGGAGATAA
260 AGTCTGATTGTCTGAGGATGACACCGATCCTTCACGTTGAGGAAATCAGGTCAATATGGAGATAA
*
362173 TTTGATGTTGAATATGACATTGCTCATCCGTGTTGAAGAGATCTAGTCGTTTTCAGGTAAATTGT
325 TTTGATGTTGAAGATGACATTGCTCATCCGTGTTGAAGAGATCTAGTCGTTTTCAGGTAAATTGT
* * * * * *
362238 TTGTTGGAGATGACGTTGTTCCTTATTGTTGAGGAAATCGGGTC
390 TCGCTGGAAATGACGTTATTCCTTATCGTTGAGGAAATCGAGTC
* * *
362282 AATCTGGAGATAATGTGGAGACAACACGGTTCCTTCACTTTAGGAAGTCTGATTGTCTGAGGATG
1 AATCTGGAGATAATTTGGAGACAACACGGTTCCTTCGCTTGAGGAAGTCTGATTGTCTGAGGATG
362347 ACACT
66 ACACT
362352 CCTCCTTCGT
Statistics
Matches: 434, Mismatches: 65, Indels: 12
0.85 0.13 0.02
Matches are distributed among these distances:
428 30 0.07
429 204 0.47
431 1 0.00
434 3 0.01
435 2 0.00
437 1 0.00
440 193 0.44
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.34
Consensus pattern (433 bp):
AATCTGGAGATAATTTGGAGACAACACGGTTCCTTCGCTTGAGGAAGTCTGATTGTCTGAGGATG
ACACTGATAATTCGCGTTGAGGAGATCAGGTCAATCTAGAGATAATTTGATGTTAAAGACAACAC
TGATCATCCGTGTTGAAGAGATATAGTCATTTTCAGGTAAATTATTTACTGGAGATGACACTGTT
CATTCTCATTGAGCAAATCGAGTCAATCTGGAGAATCAGACATAACGTTCCTTCGCTTTGAGGAA
GTCTGATTGTCTGAGGATGACACCGATCCTTCACGTTGAGGAAATCAGGTCAATATGGAGATAAT
TTGATGTTGAAGATGACATTGCTCATCCGTGTTGAAGAGATCTAGTCGTTTTCAGGTAAATTGTT
CGCTGGAAATGACGTTATTCCTTATCGTTGAGGAAATCGAGTC
Found at i:363331 original size:25 final size:24
Alignment explanation
Indices: 363303--363381 Score: 81
Period size: 25 Copynumber: 3.2 Consensus size: 24
363293 ATCTTGACCA
363303 TTTTTCTTTTATTTTTTTATCTTTC
1 TTTTTCTTTTATTTTTTTAT-TTTC
*
363328 TTTTTCTTTTCTTTTTCTT-TTTTC
1 TTTTTCTTTTATTTTT-TTATTTTC
*
363352 GTTTTTC-TTCATTTTGTTTCATTTTC
1 -TTTTTCTTTTATTTT-TTT-ATTTTC
363378 TTTT
1 TTTT
363382 CATTTTCTTC
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
24 12 0.26
25 27 0.59
26 7 0.15
ACGTcount: A:0.05, C:0.14, G:0.03, T:0.78
Consensus pattern (24 bp):
TTTTTCTTTTATTTTTTTATTTTC
Found at i:363356 original size:8 final size:7
Alignment explanation
Indices: 363303--363360 Score: 50
Period size: 7 Copynumber: 8.1 Consensus size: 7
363293 ATCTTGACCA
363303 TTTTTCT
1 TTTTTCT
363310 TTTATT-T
1 TTT-TTCT
363317 TTTTATCT
1 TTTT-TCT
363325 TTCTTT-T
1 TT-TTTCT
363332 TCTTTTC-
1 T-TTTTCT
363339 TTTTTCT
1 TTTTTCT
*
363346 TTTTTCG
1 TTTTTCT
363353 TTTTTCT
1 TTTTTCT
363360 T
1 T
363361 CATTTTGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
6 6 0.14
7 27 0.64
8 7 0.17
9 2 0.05
ACGTcount: A:0.03, C:0.14, G:0.02, T:0.81
Consensus pattern (7 bp):
TTTTTCT
Found at i:363384 original size:11 final size:11
Alignment explanation
Indices: 363324--363390 Score: 57
Period size: 11 Copynumber: 6.1 Consensus size: 11
363314 TTTTTTTATC
*
363324 TTTCTTTTTCT
1 TTTCATTTTCT
*
363335 TTTCTTTTTCTTT
1 TTTCATTTTC--T
*
363348 TTTCGTTTT-T
1 TTTCATTTTCT
* *
363358 CTTCATTTT-G
1 TTTCATTTTCT
363368 TTTCATTTTCT
1 TTTCATTTTCT
363379 TTTCATTTTCT
1 TTTCATTTTCT
363390 T
1 T
363391 CTCTTCAGGT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
10 16 0.34
11 22 0.47
13 9 0.19
ACGTcount: A:0.04, C:0.16, G:0.03, T:0.76
Consensus pattern (11 bp):
TTTCATTTTCT
Found at i:369488 original size:22 final size:24
Alignment explanation
Indices: 369460--369509 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 24
369450 TTAGGGATTT
369460 TTTATTTAA-AATT-AATTAAATA
1 TTTATTTAATAATTGAATTAAATA
369482 TTTATTTAATTAATTGGAATTAAATA
1 TTTATTTAA-TAATT-GAATTAAATA
369508 TT
1 TT
369510 CGAGATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 9 0.38
24 4 0.17
26 11 0.46
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (24 bp):
TTTATTTAATAATTGAATTAAATA
Found at i:400163 original size:46 final size:46
Alignment explanation
Indices: 400091--400484 Score: 662
Period size: 46 Copynumber: 8.6 Consensus size: 46
400081 AAAACGAATT
*
400091 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAAGATGC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* *
400137 CATAACTAAAATGCATGAAAGTATGCAATAAGGCATGAAAGGATGC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
*
400183 CATAACTAAAATGCATGAAAGGATGCATTAAGACATGAAAGGATGC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * *
400229 CATAACTAAAATGCATTAAAGGATGCATTAAGACATGAAAGGATAC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* *
400275 CATAACTAAAATGCATGAAAGGAAGCATTAAGGCATGGAAGGATGC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* *
400321 CATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAAGATGC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
*
400367 CAAAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
*
400413 CATAACTAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
*
400459 CATAACTAAAATGCATGAAATGATGC
1 CATAACTAAAATGCATGAAAGGATGC
400485 CATAACTAAA
Statistics
Matches: 324, Mismatches: 24, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 324 1.00
ACGTcount: A:0.45, C:0.13, G:0.22, T:0.20
Consensus pattern (46 bp):
CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
Found at i:400491 original size:164 final size:164
Alignment explanation
Indices: 400307--400647 Score: 583
Period size: 164 Copynumber: 2.1 Consensus size: 164
400297 AAGCATTAAG
* * *
400307 GCATGGAAGGATGCCATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAAGATGCCAAAA
1 GCATGAAAGGATGCCATAACTAAAATGCATAAAAGGATGCATTAAGGCATGAAAAGATGCCAAAA
* *
400372 CTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAACGGAT
66 CTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATAAAAGGAT
400437 GCATTAAGGCATGAAAGGATGCCATAACTAAAAT
131 GCATTAAGGCATGAAAGGATGCCATAACTAAAAT
* * * * *
400471 GCATGAAATGATGCCATAACTAAAATTCATAAAAGGATGCTTTAAGGCATGAAAGGATGCCATAA
1 GCATGAAAGGATGCCATAACTAAAATGCATAAAAGGATGCATTAAGGCATGAAAAGATGCCAAAA
400536 CTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATAAAAGGAT
66 CTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATAAAAGGAT
*
400601 GCATTAAGGCATGAAAGGATTCCATAACTAAAAT
131 GCATTAAGGCATGAAAGGATGCCATAACTAAAAT
400635 GCATGAAAGGATG
1 GCATGAAAGGATG
400648 AATTAAGACT
Statistics
Matches: 165, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
164 165 1.00
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.21
Consensus pattern (164 bp):
GCATGAAAGGATGCCATAACTAAAATGCATAAAAGGATGCATTAAGGCATGAAAAGATGCCAAAA
CTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATAAAAGGAT
GCATTAAGGCATGAAAGGATGCCATAACTAAAAT
Found at i:400493 original size:210 final size:210
Alignment explanation
Indices: 400262--400680 Score: 685
Period size: 210 Copynumber: 2.0 Consensus size: 210
400252 TGCATTAAGA
* *
400262 CATGAAAGGATACCATAACTAAAATGCATGAAAGGAAGCATTAAGGCATGGAAGGATGCCATAAC
1 CATGAAAGGATACCATAACTAAAATGCATAAAAGGAAGCATTAAGGCATGAAAGGATGCCATAAC
* *
400327 TAAAATGCATGAAATGATGCATTAAGGCATGAAAAGATGCCAAAACTAAAATGCATGAAAGGATG
66 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAAGATGCCAAAACTAAAATGCATAAAAGGATG
* * * *
400392 CATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAGGCATGAAAGGAT
131 CATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGAATTAAGACATGAAAGGAC
400457 GCCATAACTAAAATG
196 GCCATAACTAAAATG
* * * * *
400472 CATGAAATGATGCCATAACTAAAATTCATAAAAGGATGCTTTAAGGCATGAAAGGATGCCATAAC
1 CATGAAAGGATACCATAACTAAAATGCATAAAAGGAAGCATTAAGGCATGAAAGGATGCCATAAC
* *
400537 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATAAAAGGATG
66 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAAGATGCCAAAACTAAAATGCATAAAAGGATG
* *
400602 CATTAAGGCATGAAAGGATTCCATAACTAAAATGCATGAAAGGATGAATTAAGACTTGAAAGGAC
131 CATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGAATTAAGACATGAAAGGAC
400667 GCCATAACTAAAAT
196 GCCATAACTAAAAT
400681 TTACACATAA
Statistics
Matches: 192, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
210 192 1.00
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.20
Consensus pattern (210 bp):
CATGAAAGGATACCATAACTAAAATGCATAAAAGGAAGCATTAAGGCATGAAAGGATGCCATAAC
TAAAATGCATGAAAGGATGCATTAAGGCATGAAAAGATGCCAAAACTAAAATGCATAAAAGGATG
CATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGAATTAAGACATGAAAGGAC
GCCATAACTAAAATG
Found at i:400521 original size:46 final size:46
Alignment explanation
Indices: 400471--400680 Score: 330
Period size: 46 Copynumber: 4.6 Consensus size: 46
400461 TAACTAAAAT
* * *
400471 GCATGAAATGATGCCATAACTAAAATTCATAAAAGGATGCTTTAAG
1 GCATGAAAGGATGCCATAACTAAAATGCATAAAAGGATGCATTAAG
*
400517 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAATGCATAAAAGGATGCATTAAG
400563 GCATGAAAGGATGCCATAACTAAAATGCATAAAAGGATGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAATGCATAAAAGGATGCATTAAG
* * *
400609 GCATGAAAGGATTCCATAACTAAAATGCATGAAAGGATGAATTAAG
1 GCATGAAAGGATGCCATAACTAAAATGCATAAAAGGATGCATTAAG
* * *
400655 ACTTGAAAGGACGCCATAACTAAAAT
1 GCATGAAAGGATGCCATAACTAAAAT
400681 TTACACATAA
Statistics
Matches: 152, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 152 1.00
ACGTcount: A:0.45, C:0.13, G:0.20, T:0.21
Consensus pattern (46 bp):
GCATGAAAGGATGCCATAACTAAAATGCATAAAAGGATGCATTAAG
Found at i:400521 original size:138 final size:133
Alignment explanation
Indices: 400099--400530 Score: 535
Period size: 138 Copynumber: 3.1 Consensus size: 133
400089 TTCATAACTA
* *
400099 AAATGCATGAAAGGATGCATTAAGGCATGAAAAGATGCCATAACTAAAATGCATGAAAGTATGCA
1 AAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCA
* * * *
400164 ATAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGACATGAAAGGATGC
66 TTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAATGATGCATTAAAACATAAAAGGATG-
*
400229 CATAACTA
130 ----ACTT
* * * *
400237 AAATGCATTAAAGGATGCATTAAGACATGAAAGGATACCATAACTAAAATGCATGAAAGGAAGCA
1 AAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCA
* **
400302 TTAAGGCATGGAAGGATGCCATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAA-GATG
66 TTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAATGATGCATTAAAACAT-AAAAGGATG
*
400366 CCAAAACTA
130 -----ACTT
*
400375 AAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAACGGATGCA
1 AAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCA
400440 TTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAATGATGCCATAACTAAAATTCATAAAA
66 TTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAATGATG-CAT---TAAAA--CATAAAA
400505 GGATG-CTT
125 GGATGACTT
* *
400513 TAAGGCATGAAAGGATGC
1 AAATGCATGAAAGGATGC
400531 CATAACTAAA
Statistics
Matches: 263, Mismatches: 23, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
138 243 0.92
139 6 0.02
142 3 0.01
143 4 0.02
144 7 0.03
ACGTcount: A:0.45, C:0.13, G:0.22, T:0.20
Consensus pattern (133 bp):
AAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCA
TTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAATGATGCATTAAAACATAAAAGGATGA
CTT
Found at i:400717 original size:15 final size:15
Alignment explanation
Indices: 400697--400725 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
400687 ATAATTACTA
400697 AAGAAAAAAATGTAC
1 AAGAAAAAAATGTAC
400712 AAGAAAAAAATGTA
1 AAGAAAAAAATGTA
400726 TGTTGGACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.03, G:0.14, T:0.14
Consensus pattern (15 bp):
AAGAAAAAAATGTAC
Found at i:404245 original size:24 final size:25
Alignment explanation
Indices: 404201--404250 Score: 59
Period size: 24 Copynumber: 2.0 Consensus size: 25
404191 TATAAACATA
* *
404201 ATTTTTATTTTTCATACACATGTTC
1 ATTTTTATTGTTCATACACATATTC
404226 ATTTTTA-TGTTCATGA-ACATATTC
1 ATTTTTATTGTTCAT-ACACATATTC
404250 A
1 A
404251 CAAACATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.28, C:0.14, G:0.06, T:0.52
Consensus pattern (25 bp):
ATTTTTATTGTTCATACACATATTC
Found at i:405644 original size:2 final size:2
Alignment explanation
Indices: 405639--405665 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
405629 AACAAGTGTG
405639 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
405666 TATTTTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:405796 original size:22 final size:22
Alignment explanation
Indices: 405771--405842 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 22
405761 TTTTGAAAAC
405771 ATATAATATTTAAAATAAATAT
1 ATATAATATTTAAAATAAATAT
* *
405793 ATATTATATTT----TGAA-AT
1 ATATAATATTTAAAATAAATAT
405810 ATATAATATTTAAAATAAATAT
1 ATATAATATTTAAAATAAATAT
*
405832 ATATTATATTT
1 ATATAATATTT
405843 TGAAATATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
17 12 0.30
18 3 0.08
21 3 0.08
22 22 0.55
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (22 bp):
ATATAATATTTAAAATAAATAT
Found at i:405811 original size:17 final size:17
Alignment explanation
Indices: 405791--405852 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 17
405781 TAAAATAAAT
405791 ATATATTATATTTTGAA
1 ATATATTATATTTTGAA
* *
405808 ATATATAATATTTAAAATAAA
1 ATATATTATATTT----TGAA
405829 TATATATTATATTTTGAA
1 -ATATATTATATTTTGAA
405847 ATATAT
1 ATATAT
405853 ATAGTTTTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
17 18 0.50
18 3 0.08
21 3 0.08
22 12 0.33
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
ATATATTATATTTTGAA
Found at i:405811 original size:19 final size:19
Alignment explanation
Indices: 405787--405854 Score: 79
Period size: 19 Copynumber: 3.5 Consensus size: 19
405777 TATTTAAAAT
405787 AAATATATATTATATTTTG
1 AAATATATATTATATTTTG
405806 AAATATATA--ATATTTAAAAT-
1 AAATATATATTATATTT----TG
405826 AAATATATATTATATTTTG
1 AAATATATATTATATTTTG
405845 AAATATATAT
1 AAATATATAT
405855 AGTTTTCAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
17 6 0.14
18 1 0.02
19 19 0.45
20 9 0.21
21 1 0.02
22 6 0.14
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
AAATATATATTATATTTTG
Found at i:405825 original size:39 final size:39
Alignment explanation
Indices: 405741--405853 Score: 190
Period size: 39 Copynumber: 2.8 Consensus size: 39
405731 ATTTTAAAAT
*
405741 AAATAAATATATATTATATTTTTTGAAAACATATAATATTTA
1 AAATAAATATATATTATA--TTTTG-AAATATATAATATTTA
405783 AAATAAATATATATTATATTTTGAAATATATAATATTTA
1 AAATAAATATATATTATATTTTGAAATATATAATATTTA
405822 AAATAAATATATATTATATTTTGAAATATATA
1 AAATAAATATATATTATATTTTGAAATATATA
405854 TAGTTTTCAA
Statistics
Matches: 70, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
39 47 0.67
40 5 0.07
42 18 0.26
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (39 bp):
AAATAAATATATATTATATTTTGAAATATATAATATTTA
Found at i:405873 original size:39 final size:39
Alignment explanation
Indices: 405749--405873 Score: 144
Period size: 39 Copynumber: 3.1 Consensus size: 39
405739 ATAAATAAAT
* * *
405749 ATATATTATATTTTTTGAAAACATATAATATTTAAAATAAAT
1 ATATATTATA--TTTTG-AAATATATAATATTTAAAAGAAAA
* *
405791 ATATATTATATTTTGAAATATATAATATTTAAAATAAAT
1 ATATATTATATTTTGAAATATATAATATTTAAAAGAAAA
**
405830 ATATATTATATTTTGAAATATAT-ATAGTTTTCAAGAAAA
1 ATATATTATATTTTGAAATATATAATA-TTTAAAAGAAAA
405869 ATATA
1 ATATA
405874 CGTATAATTA
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
38 3 0.04
39 59 0.77
40 5 0.06
42 10 0.13
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.45
Consensus pattern (39 bp):
ATATATTATATTTTGAAATATATAATATTTAAAAGAAAA
Found at i:405889 original size:2 final size:2
Alignment explanation
Indices: 405882--405906 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
405872 TACGTATAAT
405882 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
405907 TATTTTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:405993 original size:2 final size:2
Alignment explanation
Indices: 405986--406027 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
405976 AAATAAATAA
405986 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
406028 TTTGAAAACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:406051 original size:227 final size:235
Alignment explanation
Indices: 405641--406136 Score: 744
Period size: 227 Copynumber: 2.1 Consensus size: 235
405631 CAAGTGTGTA
405641 TATATATATATATATATATATATATTATTTTGAAAATGTGTGGTTTTAAAAAACAATATGTATAT
1 TATATATATATATATATATATATATTATTTTGAAAATGTGTGGTTTTAAAAAACAATATGTATAT
*
405706 ACATTATGTTAAAAATGAGTAACTTATTTTAAAATAAATAAATATATATTATATTTTTTGAAAAC
66 ACATAATGTTAAAAATGAGTAACTTATTTTAAAATAAATAAATATATATTATA----TT---AAC
* *
405771 ATATAATATTTAAAATAAATATATATTATATTTTGAAATATATAATATTTAAAATAAATATATAT
124 ATATAATATATAAAATAAATATATATTATATTTTGAAACATATAATATTTAAAATAAATATATAT
405836 TATATTTTGAAATATATATAGTTTTCAAGAAAAATATACGTAT-AAT
189 TATATTTTGAAATATATATAGTTTTCAAGAAAAATATACGTATAAAT
*
405882 TATATATATATATATATATATATATTATTTTGAAAATGTGTGGTTTT-AAAAAC-ATTTGTATAT
1 TATATATATATATATATATATATATTATTTTGAAAATGTGTGGTTTTAAAAAACAATATGTATAT
* *
405945 ACATAATGTTAAAAATGAGTAATTTATTTTAAAATAAATAAATATATA-TATA-T-ATATAT-AT
66 ACATAATGTTAAAAATGAGTAACTTATTTTAAAATAAATAAATATATATTATATTAACATATAAT
* * *
406006 ATAT-ATATATATATATA-TATATTTTGAAAACATATAATTTTTAAAATAAATATATATTATATT
131 ATATAAAATAAATATATATTATATTTTG-AAACATATAATATTTAAAATAAATATATATTATATT
406069 TTGAAATATATATAGTTTTCAAGAAAAATATACGTATAAAT
195 TTGAAATATATATAGTTTTCAAGAAAAATATACGTATAAAT
*
406110 T-TTTA-ATATATATATATATATAGTTAT
1 TATATATATATATATATATATATA-TTAT
406137 GGATATATTA
Statistics
Matches: 242, Mismatches: 10, Indels: 20
0.89 0.04 0.07
Matches are distributed among these distances:
226 26 0.11
227 89 0.37
228 9 0.04
229 5 0.02
233 1 0.00
238 4 0.02
239 55 0.23
240 6 0.02
241 47 0.19
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (235 bp):
TATATATATATATATATATATATATTATTTTGAAAATGTGTGGTTTTAAAAAACAATATGTATAT
ACATAATGTTAAAAATGAGTAACTTATTTTAAAATAAATAAATATATATTATATTAACATATAAT
ATATAAAATAAATATATATTATATTTTGAAACATATAATATTTAAAATAAATATATATTATATTT
TGAAATATATATAGTTTTCAAGAAAAATATACGTATAAAT
Found at i:406059 original size:41 final size:41
Alignment explanation
Indices: 406014--406100 Score: 115
Period size: 41 Copynumber: 2.1 Consensus size: 41
406004 ATATATATAT
*
406014 ATATATATATATATTTTGAAA-ACATATAATTTTTAA-AATAA
1 ATATATAT-TATATTTTGAAATACATATAATTTTCAAGAA-AA
* *
406055 ATATATATTATATTTTGAAATATATATAGTTTTCAAGAAAA
1 ATATATATTATATTTTGAAATACATATAATTTTCAAGAAAA
406096 ATATA
1 ATATA
406101 CGTATAAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
40 12 0.29
41 27 0.66
42 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (41 bp):
ATATATATTATATTTTGAAATACATATAATTTTCAAGAAAA
Found at i:406151 original size:18 final size:16
Alignment explanation
Indices: 406116--406171 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 16
406106 AAATTTTTAA
406116 TATATATATATATATAGT
1 TATATATAT-TAT-TAGT
406134 TATGGATATATTATTAGT
1 TAT--ATATATTATTAGT
406152 GTATATATTATTATTA-T
1 -TATATA-TATTATTAGT
406169 TAT
1 TAT
406172 TAATATTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
16 3 0.09
17 4 0.12
18 15 0.44
19 6 0.18
20 6 0.18
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.54
Consensus pattern (16 bp):
TATATATATTATTAGT
Found at i:409802 original size:55 final size:55
Alignment explanation
Indices: 409718--409828 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
409708 GTCCCATTTG
409718 AGTTAGAGATAACAAGGGGTAAATTTGAGACAGAGCGGAAAGAATTAGAGGATAA
1 AGTTAGAGATAACAAGGGGTAAATTTGAGACAGAGCGGAAAGAATTAGAGGATAA
409773 AGTTAGAGATAACAAGGGGTAAATTTGAGACAGAGCGGAAAGAATTAGAGGATAA
1 AGTTAGAGATAACAAGGGGTAAATTTGAGACAGAGCGGAAAGAATTAGAGGATAA
409828 A
1 A
409829 ATGAAAAAGC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.46, C:0.05, G:0.31, T:0.18
Consensus pattern (55 bp):
AGTTAGAGATAACAAGGGGTAAATTTGAGACAGAGCGGAAAGAATTAGAGGATAA
Found at i:411356 original size:21 final size:22
Alignment explanation
Indices: 411330--411370 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
411320 CTAAGATAGG
411330 GAGTATCGATAC-TCCTTTAAT
1 GAGTATCGATACTTCCTTTAAT
*
411351 GAGTATCGGTACTTCCTTTA
1 GAGTATCGATACTTCCTTTA
411371 TACTTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (22 bp):
GAGTATCGATACTTCCTTTAAT
Found at i:414831 original size:21 final size:22
Alignment explanation
Indices: 414805--414845 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
414795 CTAAGACAGG
*
414805 GAGTATCGGTAC-TCCTTTAAT
1 GAGTATCGATACTTCCTTTAAT
414826 GAGTATCGATACTTCCTTTA
1 GAGTATCGATACTTCCTTTA
414846 TACTATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (22 bp):
GAGTATCGATACTTCCTTTAAT
Found at i:415122 original size:20 final size:20
Alignment explanation
Indices: 415055--415110 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
415045 TTATACGTGA
*
415055 ACAATATCAGTACTGTTCAT
1 ACAATATCAATACTGTTCAT
*
415075 ACAGTATCAATACTGTTCAT
1 ACAATATCAATACTGTTCAT
415095 ACAATATCAATACTGT
1 ACAATATCAATACTGT
415111 ACGAACAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.34
Consensus pattern (20 bp):
ACAATATCAATACTGTTCAT
Found at i:416493 original size:21 final size:22
Alignment explanation
Indices: 416468--416516 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 22
416458 TTTAAAAGTT
*
416468 TCATTTTGTTTTTCAAAAT-AAA
1 TCATTTTG-ATTTCAAAATCAAA
416490 -CA-TTTGATTTCAAAATCAAA
1 TCATTTTGATTTCAAAATCAAA
416510 TCATTTT
1 TCATTTT
416517 CAACTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
19 9 0.39
20 7 0.30
21 4 0.17
22 3 0.13
ACGTcount: A:0.37, C:0.12, G:0.04, T:0.47
Consensus pattern (22 bp):
TCATTTTGATTTCAAAATCAAA
Found at i:416495 original size:20 final size:21
Alignment explanation
Indices: 416478--416515 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 21
416468 TCATTTTGTT
416478 TTTCAAAAT-AAA-CATTTGA
1 TTTCAAAATCAAATCATTTGA
416497 TTTCAAAATCAAATCATTT
1 TTTCAAAATCAAATCATTT
416516 TCAACTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (21 bp):
TTTCAAAATCAAATCATTTGA
Found at i:418313 original size:21 final size:22
Alignment explanation
Indices: 418287--418327 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
418277 CTAAGACAGG
*
418287 GAGTATCGGTAC-TCCTTTAAT
1 GAGTATCGATACTTCCTTTAAT
418308 GAGTATCGATACTTCCTTTA
1 GAGTATCGATACTTCCTTTA
418328 TACTATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (22 bp):
GAGTATCGATACTTCCTTTAAT
Found at i:430264 original size:219 final size:218
Alignment explanation
Indices: 429902--430515 Score: 660
Period size: 219 Copynumber: 2.8 Consensus size: 218
429892 AACTGACTGT
* * * * *
429902 ATTTTGGCTTAACTCAACGAAGAGGAGCCATCTTCCAGTTAACCCTTTTCAAAGTCAATCTCAAT
1 ATTTTGGCTTAACTCATCGAAGAGGAGCCATCTTCCAGTCAACCCTTTTCGAAGTCAATTTCAAC
* * * * ** * *
429967 TCCACGGAGGAGGATATTGGGTTCAAAAACCAAATCAACTACGCTCTAGCATAACTCAGTAGCGA
66 TCCACGGTGGAGGATATTGAGTTCAAAAGCCAAATCAACTGCAATCTAGCTTAACTCAGTAGTGA
* * * * * *
430032 GGAGCAAGTTTCCAGTTAAAGTTTTCAGG-CTAGGTTTTAACTTCATGACGAAGGATACTTGACT
131 GGAGCTAGTTTCCAGTTAAAGTTTTCAGGTC-AAGTTTCAACTTCACGACGAAGAATACTTAACT
** * *
430096 GGGAA-ACACATCCA-AAATTGAATGC
195 CAGAAGA-AAAT-AATAAATT-AATGC
* * *
430121 ATTTTGGCTTAACTCATCAAAGATGAGCCATCTTCTAGTCAACCCTTTTCGAAGTCAATTTCAAC
1 ATTTTGGCTTAACTCATCGAAGAGGAGCCATCTTCCAGTCAACCCTTTTCGAAGTCAATTTCAAC
* ** *
430186 TCCACGGTGGAGGATATTGTGTTCAAAAGCCAAATGGACTGCATTCTAGCTTAACTCAGTAGTGA
66 TCCACGGTGGAGGATATTGAGTTCAAAAGCCAAATCAACTGCAATCTAGCTTAACTCAGTAGTGA
* * * * *
430251 GGAGCTGGTTTCCAATTAAAATTTTCAGGTCAAGTTTCAATTTCACGATGAAGAATACTTAACTC
131 GGAGCTAGTTTCCAGTTAAAGTTTTCAGGTCAAGTTTCAACTTCACGACGAAGAATACTTAACTC
430316 AGAAGGAAAATAATAAATTAATGC
196 AGAA-GAAAATAATAAATTAATGC
** * * * *
430340 ATTTTGGCTTAACTCAGT-GGCGAGGCGACATATTCCAGTCAACCCTTTTCGAAGTTAATTTCAA
1 ATTTTGGCTTAACTCA-TCGAAGAGGAGCCATCTTCCAGTCAACCCTTTTCGAAGTCAATTTCAA
* * ** * * * **
430404 CTCTACGGTGGAGGACATTGAGTTTGAATGCCAAATCAACTGCAATATAGCTTAACTAAGCGGTG
65 CTCCACGGTGGAGGATATTGAGTTCAAAAGCCAAATCAACTGCAATCTAGCTTAACTCAGTAGTG
* ** *
430469 AGGAGCTAGTTTCCAGTTAAAGTTTTTAGACCATGTTTCAACTTCAC
130 AGGAGCTAGTTTCCAGTTAAAGTTTTCAGGTCAAGTTTCAACTTCAC
430516 AATGAAGGAT
Statistics
Matches: 327, Mismatches: 63, Indels: 10
0.82 0.16 0.03
Matches are distributed among these distances:
219 316 0.97
220 10 0.03
221 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (218 bp):
ATTTTGGCTTAACTCATCGAAGAGGAGCCATCTTCCAGTCAACCCTTTTCGAAGTCAATTTCAAC
TCCACGGTGGAGGATATTGAGTTCAAAAGCCAAATCAACTGCAATCTAGCTTAACTCAGTAGTGA
GGAGCTAGTTTCCAGTTAAAGTTTTCAGGTCAAGTTTCAACTTCACGACGAAGAATACTTAACTC
AGAAGAAAATAATAAATTAATGC
Found at i:431133 original size:16 final size:16
Alignment explanation
Indices: 431095--431139 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
431085 TTTCGATATA
431095 TATATATATAGTT-TT
1 TATATATATAGTTATT
* *
431110 TA-AAATATTGTTATT
1 TATATATATAGTTATT
431125 TATATATATAGTTAT
1 TATATATATAGTTAT
431140 CCGTATATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 8 0.33
15 6 0.25
16 10 0.42
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (16 bp):
TATATATATAGTTATT
Found at i:442558 original size:23 final size:23
Alignment explanation
Indices: 442532--442576 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
442522 AAAAACCTTG
442532 TTTACCAAAACCAAAAAACTCTA
1 TTTACCAAAACCAAAAAACTCTA
* * *
442555 TTTAGCAGAACCGAAAAACTCT
1 TTTACCAAAACCAAAAAACTCT
442577 GTTTCTACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.47, C:0.24, G:0.07, T:0.22
Consensus pattern (23 bp):
TTTACCAAAACCAAAAAACTCTA
Found at i:445017 original size:20 final size:20
Alignment explanation
Indices: 444992--445038 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
444982 ATGATATAAT
444992 TAGCTCATGACCTTCAAACA
1 TAGCTCATGACCTTCAAACA
445012 TAGCTCATGACCTTCAAACA
1 TAGCTCATGACCTTCAAACA
445032 TAGCTCA
1 TAGCTCA
445039 CATCACCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.34, C:0.30, G:0.11, T:0.26
Consensus pattern (20 bp):
TAGCTCATGACCTTCAAACA
Found at i:450343 original size:90 final size:90
Alignment explanation
Indices: 450179--450343 Score: 287
Period size: 90 Copynumber: 1.8 Consensus size: 90
450169 CTAACACACC
450179 CTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATAT
1 CTTTTATA-CCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATAT
*
450244 TTAATTAATTGGAATTTAATAATCCT
65 TTAAATAATTGGAATTTAATAATCCT
*
450270 CTTTTAT-CCAAGTTACCCTAATCATATTGGGGATTTTATTATTTCAAATTAATTAAATCTATAT
1 CTTTTATACCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATAT
450334 TTAAATAATT
65 TTAAATAATT
450344 AATTAAAATT
Statistics
Matches: 71, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
89 24 0.34
90 40 0.56
91 7 0.10
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.45
Consensus pattern (90 bp):
CTTTTATACCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATT
TAAATAATTGGAATTTAATAATCCT
Found at i:466167 original size:20 final size:20
Alignment explanation
Indices: 466115--466175 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
466105 TCCCCTGTGG
* *
466115 GGGGGGATCGATTCCCATTCAAA
1 GGGGGAATCGATTCCC--TC-AT
*
466138 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
466158 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
466176 TGCACCAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
20 17 0.52
21 2 0.06
23 14 0.42
ACGTcount: A:0.18, C:0.25, G:0.33, T:0.25
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:466223 original size:29 final size:29
Alignment explanation
Indices: 466181--466250 Score: 131
Period size: 29 Copynumber: 2.4 Consensus size: 29
466171 CCCTCTGCAC
*
466181 CAAAATGCTAAAATCTGATTTTAAACACA
1 CAAAATGCTAAAATCTGATTTTAAACAAA
466210 CAAAATGCTAAAATCTGATTTTAAACAAA
1 CAAAATGCTAAAATCTGATTTTAAACAAA
466239 CAAAATGCTAAA
1 CAAAATGCTAAA
466251 TTAATTTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.51, C:0.16, G:0.07, T:0.26
Consensus pattern (29 bp):
CAAAATGCTAAAATCTGATTTTAAACAAA
Found at i:466260 original size:29 final size:29
Alignment explanation
Indices: 466181--466258 Score: 115
Period size: 29 Copynumber: 2.8 Consensus size: 29
466171 CCCTCTGCAC
* *
466181 CAAAATGCTAAAATCTGATTTTAAACACA
1 CAAAATGCTAAAATCTAATTTTAAACAAA
*
466210 CAAAATGCTAAAATCTGATTTTAAACAAA
1 CAAAATGCTAAAATCTAATTTTAAACAAA
466239 CAAAATGCT-AAAT-TAATTTT
1 CAAAATGCTAAAATCTAATTTT
466259 TTCTAGTGGT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
27 6 0.13
28 4 0.09
29 37 0.79
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.31
Consensus pattern (29 bp):
CAAAATGCTAAAATCTAATTTTAAACAAA
Found at i:470037 original size:22 final size:21
Alignment explanation
Indices: 469998--470038 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
469988 GTTTATTTTC
**
469998 ATTTTTTATTTTTGAAACATT
1 ATTTTTTATTTTAAAAACATT
470019 ATTTTTATATTTTAAAAACA
1 ATTTTT-TATTTTAAAAACA
470039 ATTTCTCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTTTTTATTTTAAAAACATT
Found at i:475250 original size:24 final size:23
Alignment explanation
Indices: 475223--475338 Score: 84
Period size: 24 Copynumber: 5.0 Consensus size: 23
475213 TAACCATAAC
*
475223 TAATACAATATAATACTATAATAT
1 TAATATAATATAATA-TATAATAT
*
475247 TAATATAATATACA-ATATAGTAT
1 TAATATAATATA-ATATATAATAT
*
475270 AATATATAATATAATATATAATA-
1 TA-ATATAATATAATATATAATAT
475293 TAAGTAT--TATAATATACTTTAATA-
1 TAA-TATAATATAATATA---TAATAT
475317 T-ATACT-ATATAATATATAATAT
1 TAATA-TAATATAATATATAATAT
475339 ATATTTTATA
Statistics
Matches: 77, Mismatches: 5, Indels: 22
0.74 0.05 0.21
Matches are distributed among these distances:
21 14 0.18
22 3 0.04
23 15 0.19
24 44 0.57
25 1 0.01
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (23 bp):
TAATATAATATAATATATAATAT
Found at i:475261 original size:31 final size:30
Alignment explanation
Indices: 475174--475338 Score: 115
Period size: 33 Copynumber: 5.2 Consensus size: 30
475164 AAATGAAAAA
*
475174 ATAATATTAATATAATA-ACAAATAATAATAA
1 ATAATATTAATATAATATAC-AAT-ATAATAT
*
475205 ATAGA-ATATAACCATAACTAATACAATATAATACT
1 ATA-ATAT-TAA-TATAA-T-ATACAATATAATA-T
*
475240 ATAATATTAATATAATATACAATAT-A-GT
1 ATAATATTAATATAATATACAATATAATAT
*
475268 ATAATATATAATATAATATATAATATAAGTATT
1 ATAATAT-TAATATAATATACAATATAA-TA-T
* * *
475301 ATAATA-TACTTTAATATATACTATATAATAT
1 ATAATATTAATAT-A-ATATACAATATAATAT
475332 ATAATAT
1 ATAATAT
475339 ATATTTTATA
Statistics
Matches: 108, Mismatches: 10, Indels: 31
0.72 0.07 0.21
Matches are distributed among these distances:
28 8 0.07
29 17 0.16
30 2 0.02
31 25 0.23
32 8 0.07
33 26 0.24
34 11 0.10
35 9 0.08
36 2 0.02
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (30 bp):
ATAATATTAATATAATATACAATATAATAT
Found at i:475265 original size:12 final size:12
Alignment explanation
Indices: 475182--475339 Score: 63
Period size: 12 Copynumber: 13.5 Consensus size: 12
475172 AAATAATATT
475182 AATATAATA-AC
1 AATATAATATAC
475193 AA-ATAATAATA-
1 AATATAAT-ATAC
*
475204 AATAGAATATAAC
1 AATATAATAT-AC
* *
475217 CATA-ACTAATAC
1 AATATAAT-ATAC
475229 AATAT-A-ATAC
1 AATATAATATAC
*
475239 --TATAATAT-T
1 AATATAATATAC
475248 AATATAATATAC
1 AATATAATATAC
*
475260 AATATAGTATA-
1 AATATAATATAC
475271 ATATATAATATA-
1 A-ATATAATATAC
475283 ATATATAATATA-
1 A-ATATAATATAC
475295 AGTATTATAATATAC
1 A--A-TATAATATAC
**
475310 TTTA-ATATATAC
1 AATATA-ATATAC
* *
475322 TATATAATATAT
1 AATATAATATAC
475334 AATATA
1 AATATA
475340 TATTTTATAA
Statistics
Matches: 115, Mismatches: 14, Indels: 35
0.70 0.09 0.21
Matches are distributed among these distances:
8 3 0.03
9 1 0.01
10 11 0.10
11 17 0.15
12 66 0.57
13 8 0.07
14 9 0.08
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (12 bp):
AATATAATATAC
Found at i:475272 original size:17 final size:17
Alignment explanation
Indices: 475223--475381 Score: 100
Period size: 19 Copynumber: 9.3 Consensus size: 17
475213 TAACCATAAC
*
475223 TAATACAATATAATACTA
1 TAATATAATATAATA-TA
475241 TAATATTAATATAATATA
1 TAATA-TAATATAATATA
* *
475259 CAATATAGTATAATATA
1 TAATATAATATAATATA
475276 TAATATAATATATAATATAA
1 TAATAT-A-ATATAATAT-A
* * *
475296 GTATTATAATATACTTTA
1 -TAATATAATATAATATA
475314 -ATATATACTATATAATATA
1 TA-ATATA--ATATAATATA
*
475333 TAATAT-ATAT--TTTA
1 TAATATAATATAATATA
* *
475347 TAATGT-ATATGATATA
1 TAATATAATATAATATA
475363 T-A-AT-ATATAATATA
1 TAATATAATATAATATA
475377 TAATA
1 TAATA
475382 CACACACACA
Statistics
Matches: 112, Mismatches: 16, Indels: 28
0.72 0.10 0.18
Matches are distributed among these distances:
14 23 0.21
15 2 0.02
16 10 0.09
17 20 0.18
18 13 0.12
19 36 0.32
20 3 0.03
21 5 0.04
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.43
Consensus pattern (17 bp):
TAATATAATATAATATA
Found at i:475277 original size:7 final size:7
Alignment explanation
Indices: 475230--475381 Score: 118
Period size: 7 Copynumber: 21.1 Consensus size: 7
475220 AACTAATACA
475230 ATATAAT
1 ATATAAT
475237 ACTATAAT
1 A-TATAAT
475245 AT-T-A-
1 ATATAAT
475249 ATATAAT
1 ATATAAT
*
475256 ATACAAT
1 ATATAAT
475263 ATAGT-AT
1 ATA-TAAT
475270 A-ATATAT
1 ATATA-AT
475277 AATATAAT
1 -ATATAAT
475285 ATATAAT
1 ATATAAT
*
475292 ATA-AGT
1 ATATAAT
475298 ATTATAAT
1 A-TATAAT
475306 ATACTTTAAT
1 ATA---TAAT
*
475316 ATATACT
1 ATATAAT
475323 ATATAAT
1 ATATAAT
475330 ATATAAT
1 ATATAAT
*
475337 ATATATT
1 ATATAAT
*
475344 TTATAATGT
1 ATATAA--T
*
475353 ATATGAT
1 ATATAAT
475360 ATATAAT
1 ATATAAT
475367 ATATAAT
1 ATATAAT
475374 ATATAAT
1 ATATAAT
475381 A
1 A
475382 CACACACACA
Statistics
Matches: 117, Mismatches: 12, Indels: 32
0.73 0.07 0.20
Matches are distributed among these distances:
4 2 0.02
5 3 0.03
6 6 0.05
7 78 0.67
8 13 0.11
9 8 0.07
10 7 0.06
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (7 bp):
ATATAAT
Found at i:475288 original size:2 final size:2
Alignment explanation
Indices: 475230--475415 Score: 72
Period size: 2 Copynumber: 100.5 Consensus size: 2
475220 AACTAATACA
*
475230 AT AT A- AT ACT AT A- AT AT -T A- AT AT A- AT AT AC A- AT AT AGT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
475268 AT A- AT AT AT A- AT AT A- AT AT AT A- AT AT A- AGT AT -T AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
*
475304 AT AT ACT TT A- AT AT AT ACT AT AT A- AT AT AT A- AT AT AT AT -T
1 AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
* * *
475344 TT AT A- AT GT AT AT GAT AT AT A- AT AT AT A- AT AT AT A- AT AC
1 AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
475383 AC AC AC AC AC AT AC AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
475416 ATTGTAGACA
Statistics
Matches: 147, Mismatches: 10, Indels: 54
0.70 0.05 0.26
Matches are distributed among these distances:
1 21 0.14
2 116 0.79
3 10 0.07
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (2 bp):
AT
Found at i:475339 original size:5 final size:5
Alignment explanation
Indices: 475174--475332 Score: 55
Period size: 5 Copynumber: 30.6 Consensus size: 5
475164 AAATGAAAAA
* * *
475174 ATAAT ATTAAT ATAAT A-ACAA ATAAT AATAAAT AGAAT ATAACC ATAA-
1 ATAAT A-TAAT ATAAT ATA-AT ATAAT -AT-AAT ATAAT ATAA-T ATAAT
* * * *
475222 CTAAT ACAAT AT-A- ATACT ATAAT ATTAAT ATAAT ATACAAT ATAGT
1 ATAAT ATAAT ATAAT ATAAT ATAAT A-TAAT ATAAT AT--AAT ATAAT
* *
475268 ATAATAT ATAAT ATAATAT ATAAT ATAAGT AT--T ATAAT ATACT TTAAT
1 AT-A-AT ATAAT AT-A-AT ATAAT ATAA-T ATAAT ATAAT ATAAT ATAAT
475316 AT-AT ACT-AT ATAAT ATA
1 ATAAT A-TAAT ATAAT ATA
475333 TAATATATAT
Statistics
Matches: 116, Mismatches: 17, Indels: 42
0.66 0.10 0.24
Matches are distributed among these distances:
3 5 0.04
4 9 0.08
5 62 0.53
6 25 0.22
7 15 0.13
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (5 bp):
ATAAT
Found at i:475362 original size:30 final size:30
Alignment explanation
Indices: 475230--475380 Score: 100
Period size: 30 Copynumber: 4.9 Consensus size: 30
475220 AACTAATACA
*
475230 ATATAATACTATAATAT-T-A-ATATAATAT
1 ATATAATA-TATAATATATAATATATAATGT
* *
475258 ACA-ATATAGTATAATATATAATATAATATAT-A
1 ATATA-ATA-TATAATATATAATAT-ATA-ATGT
*
475290 ATATAAGTATTATAATATACTTTAATATAT-A-CT
1 ATATAA-TA-TATAATATA---TAATATATAATGT
* *
475323 ATATAATATATAATATATATTTTATAATGT
1 ATATAATATATAATATATAATATATAATGT
*
475353 ATATGATATATAATATATAATATATAAT
1 ATATAATATATAATATATAATATATAAT
475381 ACACACACAC
Statistics
Matches: 97, Mismatches: 12, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
27 1 0.01
28 19 0.20
29 2 0.02
30 27 0.28
31 11 0.11
32 8 0.08
33 21 0.22
35 2 0.02
36 6 0.06
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (30 bp):
ATATAATATATAATATATAATATATAATGT
Found at i:475465 original size:5 final size:5
Alignment explanation
Indices: 475448--475543 Score: 58
Period size: 5 Copynumber: 18.6 Consensus size: 5
475438 CGGGATAAAA
* *
475448 TATAT TATA- TATAT TATA- TAGCAT TAT-T ATATAT TATAG TATA- T-TAT
1 TATAT TATAT TATAT TATAT TA-TAT TATAT -TATAT TATAT TATAT TATAT
*
475495 TATACT TATATT ATATAT TATAG TATATT GTATAT TATAT TAATAT TAT
1 TATA-T TATA-T -TATAT TATAT TATA-T -TATAT TATAT T-ATAT TAT
475544 TTTTTCATTT
Statistics
Matches: 73, Mismatches: 6, Indels: 24
0.71 0.06 0.23
Matches are distributed among these distances:
3 2 0.03
4 9 0.12
5 38 0.52
6 16 0.22
7 8 0.11
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (5 bp):
TATAT
Found at i:475480 original size:20 final size:20
Alignment explanation
Indices: 475451--475498 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
475441 GATAAAATAT
475451 ATTA-TATATATTATA-TAGC
1 ATTATTATATATTATAGTA-C
*
475470 ATTATTATATATTATAGTAT
1 ATTATTATATATTATAGTAC
475490 ATTATTATA
1 ATTATTATA
475499 CTTATATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 4 0.15
20 20 0.77
21 2 0.08
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (20 bp):
ATTATTATATATTATAGTAC
Found at i:475504 original size:24 final size:24
Alignment explanation
Indices: 475477--475544 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
475467 AGCATTATTA
475477 TATATTATAGTATATTATTATACT-
1 TATATTATA-TATATTATTATACTG
* *
475501 TATATTATATAT-TATAGTATATTG
1 TATATTATATATAT-TATTATACTG
475525 TATATTATATTAATATTATT
1 TATATTATA-T-ATATTATT
475545 TTTTCATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
22 1 0.03
23 10 0.28
24 18 0.50
25 1 0.03
26 5 0.14
27 1 0.03
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.56
Consensus pattern (24 bp):
TATATTATATATATTATTATACTG
Found at i:475510 original size:31 final size:30
Alignment explanation
Indices: 475447--475543 Score: 130
Period size: 31 Copynumber: 3.3 Consensus size: 30
475437 CCGGGATAAA
*
475447 ATATATTATA-TATATTATATAGCAT-TATT
1 ATATATTATAGTATATTATATA-CTTATATT
475476 ATATATTATAGTATATTATTATACTTATATT
1 ATATATTATAGTATATTA-TATACTTATATT
*
475507 ATATATTATAGTATATTGTATA-TTATATT
1 ATATATTATAGTATATTATATACTTATATT
475536 A-ATATTAT
1 ATATATTAT
475544 TTTTTCATTT
Statistics
Matches: 63, Mismatches: 2, Indels: 7
0.88 0.03 0.10
Matches are distributed among these distances:
28 7 0.11
29 18 0.29
30 13 0.21
31 25 0.40
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (30 bp):
ATATATTATAGTATATTATATACTTATATT
Found at i:477770 original size:16 final size:16
Alignment explanation
Indices: 477751--477792 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
477741 CTATTTTGCT
*
477751 ATTTTATTTTTTTTCA
1 ATTTTATTTTATTTCA
*
477767 ATTTTATTTTATTTCC
1 ATTTTATTTTATTTCA
*
477783 TTTTTATTTT
1 ATTTTATTTT
477793 CATTCGCATC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (16 bp):
ATTTTATTTTATTTCA
Found at i:483453 original size:2 final size:2
Alignment explanation
Indices: 483446--483519 Score: 53
Period size: 2 Copynumber: 37.5 Consensus size: 2
483436 CATTTCTTAT
* * * * * *
483446 TA TA TA TA TA TA TA TA TA TT TG TT TC TA CA T- TC TA TA TA TGA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
* *
483488 TA T- TT TG TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
483520 CGATTTTTAG
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
1 2 0.03
2 55 0.93
3 2 0.03
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (2 bp):
TA
Found at i:483950 original size:6 final size:6
Alignment explanation
Indices: 483939--483966 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
483929 TAACATAATA
483939 CCAATG CCAATG CCAATG CCAATG CCAA
1 CCAATG CCAATG CCAATG CCAATG CCAA
483967 AGAAGGATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.36, G:0.14, T:0.14
Consensus pattern (6 bp):
CCAATG
Found at i:501296 original size:18 final size:18
Alignment explanation
Indices: 501270--501306 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
501260 GGAAAGATAA
501270 AACTAAATCTAGGGCTTG
1 AACTAAATCTAGGGCTTG
*
501288 AACTGAATCTAGGGCTTG
1 AACTAAATCTAGGGCTTG
501306 A
1 A
501307 TGCTTTGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.27
Consensus pattern (18 bp):
AACTAAATCTAGGGCTTG
Found at i:501364 original size:9 final size:9
Alignment explanation
Indices: 501350--501378 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
501340 TTCTCTATAC
501350 TTAGGAAAT
1 TTAGGAAAT
501359 TTAGGAAAT
1 TTAGGAAAT
501368 TTAGGAAAT
1 TTAGGAAAT
501377 TT
1 TT
501379 TTATGAAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (9 bp):
TTAGGAAAT
Found at i:509478 original size:17 final size:17
Alignment explanation
Indices: 509457--509652 Score: 101
Period size: 17 Copynumber: 11.4 Consensus size: 17
509447 AAAATAATGT
509457 TAATATAATAATAAATA
1 TAATATAATAATAAATA
*
509474 GAATATAACTATAAGTAAA-A
1 TAATAT-A--ATAA-TAAATA
*
509494 TAATATAATACTATAATA
1 TAATATAATAATA-AATA
509512 TTAATATAAT-ATACAATA
1 -TAATATAATAATA-AATA
*
509530 TACTATAAT-ATATAATA
1 TAATATAATAATA-AATA
* *
509547 TAAGTATAATAATATACTT
1 TAA-TATAATAATA-AATA
**
509566 TAATAT-AT-AT-TGTA
1 TAATATAATAATAAATA
509580 TAATAT-AT-ATAATATA
1 TAATATAATAATAA-ATA
*
509596 TAATAT-ATACT--ATA
1 TAATATAATAATAAATA
509610 TAATATGTAAT-ATAATATA
1 TAATA--TAATAATAA-ATA
*
509629 TAATATAATAATATATA
1 TAATATAATAATAAATA
509646 TAATATA
1 TAATATA
509653 TACTATCCCG
Statistics
Matches: 142, Mismatches: 18, Indels: 38
0.72 0.09 0.19
Matches are distributed among these distances:
14 19 0.13
16 16 0.11
17 46 0.32
18 20 0.14
19 27 0.19
20 10 0.07
21 4 0.03
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (17 bp):
TAATATAATAATAAATA
Found at i:509503 original size:5 final size:5
Alignment explanation
Indices: 509457--509652 Score: 88
Period size: 5 Copynumber: 37.4 Consensus size: 5
509447 AAAATAATGT
*
509457 TAATA TAATAA TAAATA GAATA TAACTA TAAGTA -AA-A TAATA T-A-A
1 TAATA TAAT-A T-AATA TAATA TAA-TA TAA-TA TAATA TAATA TAATA
* *
509502 TACTA TAATA TTAATA TAATA TACAATA TACTA TAATATA TAATA TAAGTA
1 TAATA TAATA -TAATA TAATA T--AATA TAATA T-A-ATA TAATA TAA-TA
* * **
509553 T-A-A TAATA TACTT TAATA T-ATA TTGTA TAATA T-ATA TAATA T-ATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
509598 -ATATA TACTATA TAATA TGTAATA TAATATA TAATA TAATAA TATATA
1 TA-ATA TA--ATA TAATA --TAATA T-A-ATA TAATA TAAT-A TA-ATA
509646 TAATA TA
1 TAATA TA
509653 TACTATCCCG
Statistics
Matches: 150, Mismatches: 14, Indels: 54
0.69 0.06 0.25
Matches are distributed among these distances:
3 5 0.03
4 15 0.10
5 73 0.49
6 29 0.19
7 28 0.19
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:509519 original size:56 final size:53
Alignment explanation
Indices: 509450--509648 Score: 137
Period size: 56 Copynumber: 3.7 Consensus size: 53
509440 AAACCAAAAA
*
509450 ATAATGTTAATATAATAATA-AATAGAATATAACTATAAGTAAAATAA-TATAATACT
1 ATAAT-TTAATATAAT-ATACAATAGAATATAA-TAT-A-TAAAATAAGTATAATAAT
* * *
509506 ATAATATTAATATAATATACAATATACTATAATATATAATATAAGTATAATAAT
1 ATAAT-TTAATATAATATACAATAGAATATAATATATAAAATAAGTATAATAAT
* * * * *
509560 ATACTTTAATATATATTGTATAATA-TATATAATATAT--AAT-A-TATACT-AT
1 ATAATTTAATATA-A-TATACAATAGAATATAATATATAAAATAAGTATAATAAT
* *
509609 ATAATATGTAATATAATATATAATATAATA-ATATATATAA
1 ATAAT-T-TAATATAATATACAATAGAATATA-ATATATAA
509649 TATATACTAT
Statistics
Matches: 118, Mismatches: 15, Indels: 24
0.75 0.10 0.15
Matches are distributed among these distances:
49 15 0.13
50 16 0.14
51 8 0.07
52 2 0.02
53 15 0.13
54 24 0.20
55 13 0.11
56 25 0.21
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (53 bp):
ATAATTTAATATAATATACAATAGAATATAATATATAAAATAAGTATAATAAT
Found at i:509531 original size:12 final size:11
Alignment explanation
Indices: 509458--509652 Score: 114
Period size: 12 Copynumber: 17.0 Consensus size: 11
509448 AAATAATGTT
509458 AATATAATAATA
1 AATATAAT-ATA
*
509470 AATAGAATATA
1 AATATAATATA
* *
509481 ACTATAA-GTA
1 AATATAATATA
509491 AA-ATAATATA
1 AATATAATATA
*
509501 ATACTATAATATT
1 A-A-TATAATATA
509514 AATATAATATA
1 AATATAATATA
*
509525 CAATATACTATA
1 -AATATAATATA
509537 ATATATAATATA
1 A-ATATAATATA
*
509549 AGTAT-A-AT-
1 AATATAATATA
* *
509557 AATATACTTTA
1 AATATAATATA
* *
509568 ATATATATTGTA
1 A-ATATAATATA
509580 TAATAT-ATATA
1 -AATATAATATA
509591 ATATATAATATA
1 A-ATATAATATA
*
509603 TACTATATAATATGT
1 -A--ATATAATAT-A
509618 AATATAATATA
1 AATATAATATA
509629 TAATATAATAATA
1 -AATATAAT-ATA
*
509642 TATATAATATA
1 AATATAATATA
509653 TACTATCCCG
Statistics
Matches: 144, Mismatches: 21, Indels: 37
0.71 0.10 0.18
Matches are distributed among these distances:
8 4 0.03
9 6 0.04
10 9 0.06
11 32 0.22
12 69 0.48
13 13 0.09
14 11 0.08
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (11 bp):
AATATAATATA
Found at i:509575 original size:2 final size:2
Alignment explanation
Indices: 509568--509654 Score: 70
Period size: 2 Copynumber: 48.5 Consensus size: 2
509558 ATATACTTTA
*
509568 AT AT AT AT -T GT AT A- AT AT AT AT A- AT AT AT A- AT AT AT ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
*
509607 AT AT A- AT AT GT A- AT AT A- AT AT AT A- AT AT A- AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
509643 AT AT A- AT AT AT A
1 AT AT AT AT AT AT A
509655 CTATCCCGGA
Statistics
Matches: 70, Mismatches: 3, Indels: 24
0.72 0.03 0.25
Matches are distributed among these distances:
1 11 0.16
2 57 0.81
3 2 0.03
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:509582 original size:33 final size:31
Alignment explanation
Indices: 509493--509654 Score: 91
Period size: 29 Copynumber: 5.3 Consensus size: 31
509483 TATAAGTAAA
* *
509493 ATAATATAATACTATAATATTAATATAATATACA
1 ATAATAT-ATAATATAATA-T-ATATAATATACT
509527 AT-ATACTATAATAT-ATA-ATATAAGTATA--
1 ATAATA-TATAATATAATATATATAA-TATACT
*
509555 ATAATATACTTTAATAT-ATATTGTATAATATA-T
1 ATAATATA---TAATATAATA-TATATAATATACT
509588 ATAATATATAATAT-ATACTATAT-A-ATA-T
1 ATAATATATAATATAATA-TATATAATATACT
*
509616 GTAATATA-ATATATAATATA-ATAATATA-T
1 ATAATATATA-ATATAATATATATAATATACT
509645 ATAATATATA
1 ATAATATATA
509655 CTATCCCGGA
Statistics
Matches: 108, Mismatches: 6, Indels: 32
0.74 0.04 0.22
Matches are distributed among these distances:
27 3 0.03
28 22 0.20
29 24 0.22
30 18 0.17
31 9 0.08
32 7 0.06
33 22 0.20
34 3 0.03
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (31 bp):
ATAATATATAATATAATATATATAATATACT
Found at i:509654 original size:7 final size:7
Alignment explanation
Indices: 509496--509645 Score: 105
Period size: 7 Copynumber: 20.7 Consensus size: 7
509486 AAGTAAAATA
509496 ATATAAT
1 ATATAAT
509503 ACTATAAT
1 A-TATAAT
509511 AT-T-A-
1 ATATAAT
509515 ATATAAT
1 ATATAAT
*
509522 ATACAATAT
1 ATA-TA-AT
509531 ACTATAAT
1 A-TATAAT
509539 ATATAAT
1 ATATAAT
*
509546 ATA-AGT
1 ATATAAT
509552 ATAATAAT
1 AT-ATAAT
509560 ATACTTTAAT
1 ATA---TAAT
*
509570 ATATATT
1 ATATAAT
*
509577 GTATAATAT
1 ATAT-A-AT
509586 ATATAAT
1 ATATAAT
509593 ATATAAT
1 ATATAAT
*
509600 ATATACT
1 ATATAAT
509607 ATATAAT
1 ATATAAT
*
509614 ATGT-A-
1 ATATAAT
509619 ATATAAT
1 ATATAAT
509626 ATATAAT
1 ATATAAT
509633 ATAATAAT
1 AT-ATAAT
509641 ATATA
1 ATATA
509646 TAATATATAC
Statistics
Matches: 114, Mismatches: 12, Indels: 34
0.71 0.08 0.21
Matches are distributed among these distances:
4 2 0.02
5 5 0.04
6 8 0.07
7 58 0.51
8 24 0.21
9 8 0.07
10 9 0.08
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (7 bp):
ATATAAT
Found at i:510009 original size:6 final size:6
Alignment explanation
Indices: 509998--510023 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
509988 GCGGAAGGTG
509998 AATGGA AATGGA AATGGA AATGGA AA
1 AATGGA AATGGA AATGGA AATGGA AA
510024 GAATTTGGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.31, T:0.15
Consensus pattern (6 bp):
AATGGA
Found at i:512614 original size:21 final size:21
Alignment explanation
Indices: 512590--512640 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
512580 CATTCATTTA
512590 ATTCATTTTGTAGCATGTATC
1 ATTCATTTTGTAGCATGTATC
*
512611 ATTCATTTTGTAGCGTGTATC
1 ATTCATTTTGTAGCATGTATC
512632 ATTCATTTT
1 ATTCATTTT
512641 CATCTCATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.51
Consensus pattern (21 bp):
ATTCATTTTGTAGCATGTATC
Found at i:512821 original size:48 final size:49
Alignment explanation
Indices: 512762--512857 Score: 140
Period size: 49 Copynumber: 2.0 Consensus size: 49
512752 ATCAGTAACG
** *
512762 TCAGACGTGCTAGGT-AACATTGATAATAGCACCACCATCACAAAGACA
1 TCAGACGTGCTAAATCAACATTAATAATAGCACCACCATCACAAAGACA
* *
512810 TCAGACGTGCTAAATCATCATTAATAGTAGCACCACCATCACAAAGAC
1 TCAGACGTGCTAAATCAACATTAATAATAGCACCACCATCACAAAGAC
512858 TCCAAACGTA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
48 13 0.31
49 29 0.69
ACGTcount: A:0.40, C:0.26, G:0.15, T:0.20
Consensus pattern (49 bp):
TCAGACGTGCTAAATCAACATTAATAATAGCACCACCATCACAAAGACA
Found at i:512872 original size:49 final size:49
Alignment explanation
Indices: 512779--512873 Score: 138
Period size: 49 Copynumber: 1.9 Consensus size: 49
512769 TGCTAGGTAA
* * *
512779 CATTGATAATAGCACCACCATCACAAAGACATCAGACGTGCTAAATCAT
1 CATTAATAATAGCACCACCATCACAAAGACATCAAACGTACTAAATCAT
*
512828 CATTAATAGTAGCACCACCATCACAAAGAC-TCCAAACGTACTAAAT
1 CATTAATAATAGCACCACCATCACAAAGACAT-CAAACGTACTAAAT
512874 GCTCCACATC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 1 0.02
49 40 0.98
ACGTcount: A:0.42, C:0.27, G:0.11, T:0.20
Consensus pattern (49 bp):
CATTAATAATAGCACCACCATCACAAAGACATCAAACGTACTAAATCAT
Found at i:516135 original size:6 final size:6
Alignment explanation
Indices: 516124--516148 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
516114 GTTACTTTGA
516124 TTTATT TTTATT TTTATT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT T
516149 CATTTGAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:516148 original size:22 final size:22
Alignment explanation
Indices: 516096--516153 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
516086 AGACAACCCG
*
516096 TTTTTATTT-TATTTTCTTGTTA
1 TTTTTATTTAT-TTTTATTGTTA
* * *
516118 CTTTGATTTATTTTTATTTTTA
1 TTTTTATTTATTTTTATTGTTA
516140 TTTTTATTTCATTT
1 TTTTTATTT-ATTT
516154 GAGTATTTCT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
22 23 0.82
23 5 0.18
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (22 bp):
TTTTTATTTATTTTTATTGTTA
Found at i:516653 original size:21 final size:22
Alignment explanation
Indices: 516627--516682 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
516617 CGGACATATT
*
516627 CATTTTAGGTAGAGAAAT-TAA
1 CATTTTAGGTAGAAAAATATAA
*
516648 CATTTTCGGTAGAAAAATAATAA
1 CATTTTAGGTAGAAAAAT-ATAA
*
516671 TATTTTAGGTAG
1 CATTTTAGGTAG
516683 CGTTCTATCG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 16 0.55
23 13 0.45
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.36
Consensus pattern (22 bp):
CATTTTAGGTAGAAAAATATAA
Found at i:517669 original size:27 final size:27
Alignment explanation
Indices: 517614--517720 Score: 110
Period size: 27 Copynumber: 3.9 Consensus size: 27
517604 TAAAAGGTAG
*
517614 AACTTTTTGAAATTTACACTAAA-AGAC
1 AACTTTTTGAAATTTACAATAAATA-AC
517641 AACTTTTTGAAATTTACAATAAATAAC
1 AACTTTTTGAAATTTACAATAAATAAC
** *
517668 AAACTAATTGTAATTTACAATAAAGGATAA-
1 -AACTTTTTGAAATTTACAAT-AA--ATAAC
*
517698 AACTTTTTGGAATTTACAATAAA
1 AACTTTTTGAAATTTACAATAAA
517721 GTACAAAATA
Statistics
Matches: 68, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
26 1 0.01
27 24 0.35
28 20 0.29
29 19 0.28
31 4 0.06
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.35
Consensus pattern (27 bp):
AACTTTTTGAAATTTACAATAAATAAC
Found at i:517711 original size:29 final size:29
Alignment explanation
Indices: 517598--517721 Score: 114
Period size: 29 Copynumber: 4.4 Consensus size: 29
517588 AAATATAAAA
*
517598 TTACAATAAAAGG-TAGAACTTTTTGAAAT
1 TTACAAT-AAAGGATAAAACTTTTTGAAAT
* * *
517627 TTACACTAAA--AGACAACTTTTTGAAAT
1 TTACAATAAAGGATAAAACTTTTTGAAAT
* ** *
517654 TTACAATAAA-TA-ACAAACTAATTGTAAT
1 TTACAATAAAGGATA-AAACTTTTTGAAAT
*
517682 TTACAATAAAGGATAAAACTTTTTGGAAT
1 TTACAATAAAGGATAAAACTTTTTGAAAT
517711 TTACAATAAAG
1 TTACAATAAAG
517722 TACAAAATAT
Statistics
Matches: 78, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
27 24 0.31
28 24 0.31
29 29 0.37
30 1 0.01
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.33
Consensus pattern (29 bp):
TTACAATAAAGGATAAAACTTTTTGAAAT
Found at i:517728 original size:29 final size:29
Alignment explanation
Indices: 517614--517777 Score: 128
Period size: 29 Copynumber: 5.8 Consensus size: 29
517604 TAAAAGGTAG
*
517614 AACTTTTTGAAATTTACACTAAAAG-AC--
1 AACTTTTTGAAATTTACAAT-AAAGTACAA
517641 AACTTTTTGAAATTTACAATAAA-TA-ACA
1 AACTTTTTGAAATTTACAATAAAGTACA-A
** * * *
517669 AACTAATTGTAATTTACAATAAAGGATAA
1 AACTTTTTGAAATTTACAATAAAGTACAA
*
517698 AACTTTTTGGAATTTACAATAAAGTACAA
1 AACTTTTTGAAATTTACAATAAAGTACAA
* *
517727 AA-TATTTT-ATAAATTACAATAAAATACAA
1 AACT-TTTTGA-AATTTACAATAAAGTACAA
* *
517756 AACTTCATAGAAA-TTACAATAA
1 AACTT-TTTGAAATTTACAATAA
517778 TGATATTTCT
Statistics
Matches: 111, Mismatches: 15, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
26 4 0.04
27 19 0.17
28 21 0.19
29 61 0.55
30 5 0.05
31 1 0.01
ACGTcount: A:0.51, C:0.10, G:0.06, T:0.33
Consensus pattern (29 bp):
AACTTTTTGAAATTTACAATAAAGTACAA
Found at i:520959 original size:137 final size:136
Alignment explanation
Indices: 520447--520960 Score: 688
Period size: 137 Copynumber: 3.8 Consensus size: 136
520437 CAACTGGTGT
* * * * *
520447 ATGAAATTGTTCCTTCGTGATGAGGATGTCTGGCCATCTTTGAAGATATTTGAAATAACACGGTT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTAGCCATCTTTAAAGATATTTGAGATAACACGGTT
* * * * * *
520512 CCTTCGTGATGAAGACGTTTGATTATCTGAGGATGACT-CGGCTCCTACGTGATGAGGAGTTCTG
66 CCTTCGTGATGAGGATGTCTGGTTATCTAAGGATGA-TGC-GCTCCTACGTGATGAAGAGTTCTG
*
520576 GTCAGTGG
129 GTCAATGG
* * * *
520584 ATGACATTGTTCCTTCATGATGAGGATGTCTAGCAATCTTTAAAGATATTTAAGATAACACGGTT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTAGCCATCTTTAAAGATATTTGAGATAACACGGTT
* ** *
520649 CCTTCGTGATGAGGATGTCTAGTTATCTAAGGATGACACGACTCCTACGTGATGAAGAGTTATGG
66 CCTTCGTGATGAGGATGTCTGGTTATCTAAGGATGATGCG-CTCCTACGTGATGAAGAGTTCTGG
520714 TCAATGG
130 TCAATGG
* *
520721 ATGACATTGTTCCTTCGTGATGAGGACGTCTAGCCATCTTTAAAGATATTTGAGATAGCATGGTT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTAGCCATCTTTAAAGATATTTGAGATAACACGGTT
* * *** * **
520786 CATTCGTGATGAGGATGTCTGGCTATCTAAGGATGATGCTGCTCCTTTATGATGAAGAATTCTAA
66 CCTTCGTGATGAGGATGTCTGGTTATCTAAGGATGATGC-GCTCCTACGTGATGAAGAGTTCTGG
520851 TCAATGG
130 TCAATGG
*
520858 ATGACATTGTTCCTTCGTGATGAGGACGTCTAGCCATCTTTAAAGATATTTGAGATAACACAGTT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTAGCCATCTTTAAAGATATTTGAGATAACACGGTT
* *
520923 CCTTTGTGATGAGGATATCTGGTTATCTAAGGATGATG
66 CCTTCGTGATGAGGATGTCTGGTTATCTAAGGATGATG
520961 TTGTTTCTTC
Statistics
Matches: 332, Mismatches: 42, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
136 1 0.00
137 330 0.99
138 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.33
Consensus pattern (136 bp):
ATGACATTGTTCCTTCGTGATGAGGACGTCTAGCCATCTTTAAAGATATTTGAGATAACACGGTT
CCTTCGTGATGAGGATGTCTGGTTATCTAAGGATGATGCGCTCCTACGTGATGAAGAGTTCTGGT
CAATGG
Found at i:521077 original size:120 final size:120
Alignment explanation
Indices: 520864--521082 Score: 348
Period size: 120 Copynumber: 1.8 Consensus size: 120
520854 ATGGATGACA
* *
520864 TTGTTCCTTCGTGATGAGGACGTCTAGCCATCTTTAAAGATATTTGAGATAACACAGTTCCTTTG
1 TTGTTCATTCGTGATGAGGACGTCTAGCCATCTTTAAAGATATTTGAGATAACACAGTTCCTTCG
* * *
520929 TGATGAGGATATCTGGTTATCTAAGGATGATGTTGTTTCTTCGTGATGAGGAGTT
66 TGATAAAGACATCTGGTTATCTAAGGATGATGTTGTTTCTTCGTGATGAGGAGTT
* * **
520984 TTGTTCATTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAGCATGGTTCCTTCG
1 TTGTTCATTCGTGATGAGGACGTCTAGCCATCTTTAAAGATATTTGAGATAACACAGTTCCTTCG
*
521049 TGATAAAGACGTCTGGTTATCTAAGGATGATGTT
66 TGATAAAGACATCTGGTTATCTAAGGATGATGTT
521083 TCCTAAAATA
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
120 89 1.00
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.37
Consensus pattern (120 bp):
TTGTTCATTCGTGATGAGGACGTCTAGCCATCTTTAAAGATATTTGAGATAACACAGTTCCTTCG
TGATAAAGACATCTGGTTATCTAAGGATGATGTTGTTTCTTCGTGATGAGGAGTT
Found at i:530656 original size:16 final size:16
Alignment explanation
Indices: 530635--530675 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 16
530625 TCCCATGTTG
530635 ATTTTATTATCAATAT
1 ATTTTATTATCAATAT
530651 ATTTTA-TAT-AATAT
1 ATTTTATTATCAATAT
*
530665 AATTT-TTATCA
1 ATTTTATTATCA
530676 CCTAACATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
14 12 0.55
15 4 0.18
16 6 0.27
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTTATTATCAATAT
Found at i:530665 original size:14 final size:17
Alignment explanation
Indices: 530635--530670 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
530625 TCCCATGTTG
530635 ATTTTATTATCAATAT-
1 ATTTTATTATCAATATA
530651 ATTTTA-TAT-AATATA
1 ATTTTATTATCAATATA
530666 ATTTT
1 ATTTT
530671 TATCACCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 5 0.26
15 8 0.42
16 6 0.32
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTTATTATCAATATA
Found at i:530810 original size:45 final size:42
Alignment explanation
Indices: 530754--530850 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 42
530744 TATAAGGAAT
* *
530754 TAAAATAAAAATTATT-AAAAATATAGGGGATAAAAATTAAAATA
1 TAAAATAAAAA-TATTGAAAAATAAAGGAG-TAAAAA-TAAAATA
* *
530798 CTAAATTAAAAATATTGAAAAATAAAGGAGTAATAATAAAATA
1 -TAAAATAAAAATATTGAAAAATAAAGGAGTAAAAATAAAATA
530841 TAAAATAAAA
1 TAAAATAAAA
530851 TAGTGACCAA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
42 9 0.20
43 7 0.15
44 9 0.20
45 21 0.46
ACGTcount: A:0.65, C:0.01, G:0.08, T:0.26
Consensus pattern (42 bp):
TAAAATAAAAATATTGAAAAATAAAGGAGTAAAAATAAAATA
Found at i:531381 original size:22 final size:22
Alignment explanation
Indices: 531341--531409 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 22
531331 CGGAGGGAGC
* *
531341 TCCGACCACCGGTCGGTCACTAT
1 TCCGGCCA-CGGTCAGTCACTAT
531364 TCCGGCCACGGTCAGTCACTAT
1 TCCGGCCACGGTCAGTCACTAT
* * *
531386 TCCGGCTACCGCCAGTCACTAT
1 TCCGGCCACGGTCAGTCACTAT
531408 TC
1 TC
531410 ATCGCCACTG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
22 34 0.83
23 7 0.17
ACGTcount: A:0.17, C:0.39, G:0.20, T:0.23
Consensus pattern (22 bp):
TCCGGCCACGGTCAGTCACTAT
Found at i:534331 original size:2 final size:2
Alignment explanation
Indices: 534326--534358 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
534316 AAGGTCTTCA
534326 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
534359 AAAGTTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:536606 original size:46 final size:46
Alignment explanation
Indices: 536534--536735 Score: 269
Period size: 46 Copynumber: 4.6 Consensus size: 46
536524 TTTAAATTTT
*
536534 ATTTTATTTAT-AGCACCCTTTCATGCCTTCATGCATCCTTTCATGC
1 ATTTTATTTATGA-CATCCTTTCATGCCTTCATGCATCCTTTCATGC
* * *
536580 ATTTTATTTATGACATCCTTTAATGCCTTCGTGCATCATTTCATGC
1 ATTTTATTTATGACATCCTTTCATGCCTTCATGCATCCTTTCATGC
*
536626 ATTTTATTTATGGCATCCTTTCATG------T-C-TCCTTTCATGC
1 ATTTTATTTATGACATCCTTTCATGCCTTCATGCATCCTTTCATGC
* *
536664 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTTATTTATGACATCCTTTCATGCCTTCATGCATCCTTTCATGC
536710 ATTTTATTTATGACATCCTTTCATGC
1 ATTTTATTTATGACATCCTTTCATGC
536736 ATTTTATTTA
Statistics
Matches: 139, Mismatches: 8, Indels: 18
0.84 0.05 0.11
Matches are distributed among these distances:
38 35 0.25
39 1 0.01
40 1 0.01
44 1 0.01
45 1 0.01
46 99 0.71
47 1 0.01
ACGTcount: A:0.20, C:0.24, G:0.10, T:0.47
Consensus pattern (46 bp):
ATTTTATTTATGACATCCTTTCATGCCTTCATGCATCCTTTCATGC
Found at i:536650 original size:72 final size:72
Alignment explanation
Indices: 536566--536943 Score: 348
Period size: 72 Copynumber: 5.2 Consensus size: 72
536556 ATGCCTTCAT
* * **
536566 GCATCCTTTCATGCATTTTATTTATGACATCCTTTAATGCCTTCGTGCATCATTTCATGCATTTT
1 GCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTT
536631 ATTTATG
66 ATTTATG
*
536638 GCATCCTTTCATGTCTCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCT
1 G--------CA----TCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCAT
536703 TTCATGCATTTTATTTATG
54 TTCATGCATTTTATTTATG
* ** * * **
536722 ACATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATAAATCCTTTCCTATATTTT
1 GCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTT
536787 ATTTATG
66 ATTTATG
* * *
536794 GCATCCTTTCATGC--CTTA---AT-GCATCCTTTCATGCATTTTATTTATGACATCCTTTCATG
1 GCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGC--CTTA---ATG-CATCATTTCATG
*
536853 -A-CTTA---AT-
60 CATTTTATTTATG
* *
536860 GCATCCTTTCATGTATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCTTTTCATGCATTTT
1 GCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTT
536925 ATTTATG
66 ATTTATG
536932 GCATCCTTTCAT
1 GCATCCTTTCAT
536944 ACCTTAATGT
Statistics
Matches: 252, Mismatches: 24, Indels: 60
0.75 0.07 0.18
Matches are distributed among these distances:
66 38 0.15
67 8 0.03
68 9 0.04
70 9 0.04
71 7 0.03
72 113 0.45
76 2 0.01
80 2 0.01
84 64 0.25
ACGTcount: A:0.21, C:0.22, G:0.10, T:0.47
Consensus pattern (72 bp):
GCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTT
ATTTATG
Found at i:536690 original size:84 final size:84
Alignment explanation
Indices: 536561--536737 Score: 284
Period size: 84 Copynumber: 2.1 Consensus size: 84
536551 CTTTCATGCC
**
536561 TTCATGCATCCTTTCATGCATTTTATTTATGACATCCTTTAATGCCTTCGTGCATCATTTCATGC
1 TTCATGCATCCTTTCATGCATTTTATTTATGACATCCTTTAATGCCTTAATGCATCATTTCATGC
*
536626 ATTTTATTTATGGCATCCT
66 ATTTTATTTATGACATCCT
* * *
536645 TTCATGTC-TCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
1 TTCATG-CATCCTTTCATGCATTTTATTTATGACATCCTTTAATGCCTTAATGCATCATTTCATG
536709 CATTTTATTTATGACATCCT
65 CATTTTATTTATGACATCCT
536729 TTCATGCAT
1 TTCATGCAT
536738 TTTATTTATG
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
83 1 0.01
84 83 0.98
85 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.10, T:0.47
Consensus pattern (84 bp):
TTCATGCATCCTTTCATGCATTTTATTTATGACATCCTTTAATGCCTTAATGCATCATTTCATGC
ATTTTATTTATGACATCCT
Found at i:536774 original size:46 final size:46
Alignment explanation
Indices: 536723--537001 Score: 423
Period size: 46 Copynumber: 6.0 Consensus size: 46
536713 TTATTTATGA
*
536723 CATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATA
1 CATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATG
* * **
536769 AATCCTTTCCTATATTTTATTTATGGCATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATG
* *
536815 CATCCTTTCATGCATTTTATTTATGACATCCTTTCATGACTTAATG
1 CATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATG
*
536861 CATCCTTTCATGTATTTTATTTATGGCATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATG
* *
536907 CATCTTTTCATGCATTTTATTTATGGCATCCTTTCATACCTTAATG
1 CATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATG
* * * *
536953 TATCATTTCATGCATTTTATTTATGGCATCCTTGCATGCCAATAATG
1 CATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCC-TTAATG
537000 CA
1 CA
537002 CCCATATGCA
Statistics
Matches: 209, Mismatches: 23, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
46 203 0.97
47 6 0.03
ACGTcount: A:0.23, C:0.22, G:0.10, T:0.46
Consensus pattern (46 bp):
CATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATG
Found at i:536776 original size:92 final size:88
Alignment explanation
Indices: 536678--537001 Score: 328
Period size: 92 Copynumber: 3.5 Consensus size: 88
536668 TATTTATGGC
* *
536678 ATCCTTTCATGCCTTA-AT-GCATCCTTTCATGCATTTTATTTATGACATCCTTTCATGCATTTT
1 ATCCTTTCATGCTTTATATGGCATCCTTTCATGC--CTTA---ATG-CATCCTTTCATGCATTTT
*
536741 ATTTATGGCATCCTTTCATGCCTTAATAA
60 ATTTATGGCATCCTTTCATGCCTTAATGA
**
536770 ATCCTTTCCTATATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAT
1 ATCCTTT-C-ATGCTTTA--TATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAT
* * *
536835 TTATGACATCCTTTCATGACTTAATGC
62 TTATGGCATCCTTTCATGCCTTAATGA
* *
536862 ATCCTTTCATGTATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCTTTTCATGCATTTTAT
1 ATCCTTTCATG--CTTTA--TATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAT
* *
536927 TTATGGCATCCTTTCATACCTTAATGT
62 TTATGGCATCCTTTCATGCCTTAATGA
* * *
536954 ATCATTTCATGCATTTTATTTATGGCATCCTTGCATGCCAATAATGCA
1 ATCCTTTCATGC--TTTA--TATGGCATCCTTTCATGCC-TTAATGCA
537002 CCCATATGCA
Statistics
Matches: 203, Mismatches: 18, Indels: 21
0.84 0.07 0.09
Matches are distributed among these distances:
90 2 0.01
91 1 0.00
92 165 0.81
93 11 0.05
94 5 0.02
96 3 0.01
97 2 0.01
98 14 0.07
ACGTcount: A:0.23, C:0.22, G:0.10, T:0.46
Consensus pattern (88 bp):
ATCCTTTCATGCTTTATATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTATTTAT
GGCATCCTTTCATGCCTTAATGA
Found at i:536895 original size:118 final size:116
Alignment explanation
Indices: 536664--536872 Score: 363
Period size: 118 Copynumber: 1.8 Consensus size: 116
536654 CCTTTCATGC
536664 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGACATCCT
1 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGACATCCT
*
536729 TTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATAAATCCTTTCCTAT
66 TTCATGCATCTTA--TATGGCATCCTTTCATGCCTTAATAAATCCTTTCCTAT
536782 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGACATCCT
1 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGACATCCT
536847 TTCATG-A-CTTA-AT-GCATCCTTTCATG
66 TTCATGCATCTTATATGGCATCCTTTCATG
536873 TATTTTATTT
Statistics
Matches: 90, Mismatches: 1, Indels: 6
0.93 0.01 0.06
Matches are distributed among these distances:
112 13 0.14
113 2 0.02
116 3 0.03
117 1 0.01
118 71 0.79
ACGTcount: A:0.22, C:0.22, G:0.09, T:0.47
Consensus pattern (116 bp):
ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGACATCCT
TTCATGCATCTTATATGGCATCCTTTCATGCCTTAATAAATCCTTTCCTAT
Found at i:537573 original size:31 final size:31
Alignment explanation
Indices: 537524--537583 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
537514 TCTTTGAAAT
*
537524 GGTATCGATACCTTCCCTT-AGGTATCGATTA
1 GGTATCGATACCTCCCCTTCA-GTATCGATTA
537555 GGTATCGATA-CTACCCCTTCAGTATCGAT
1 GGTATCGATACCT-CCCCTTCAGTATCGAT
537584 ACCGATTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 2 0.08
31 23 0.88
32 1 0.04
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.33
Consensus pattern (31 bp):
GGTATCGATACCTCCCCTTCAGTATCGATTA
Found at i:538931 original size:9 final size:9
Alignment explanation
Indices: 538910--538942 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
538900 GTCTCATTTT
538910 TATTATT-A
1 TATTATTAA
538918 TATTATTAA
1 TATTATTAA
538927 TATTATTAA
1 TATTATTAA
*
538936 TACTATT
1 TATTATT
538943 TATTTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (9 bp):
TATTATTAA
Found at i:541043 original size:2 final size:2
Alignment explanation
Indices: 541032--541062 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
541022 TTCCATGTTA
541032 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
541063 TCCTTTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:546713 original size:84 final size:84
Alignment explanation
Indices: 546572--546741 Score: 277
Period size: 84 Copynumber: 2.0 Consensus size: 84
546562 AGCCTCATTG
* * *
546572 ACAAAGGAGTTCTGACAAGAGACATGATCGAGAAATAGGGAATAAGTAAGGGTAAAAACCCTAAT
1 ACAAAGGAGTCCTGACAAGAGACATGATCAAGAAATAGGGAATAAGTAAAGGTAAAAACCCTAAT
*
546637 CTGACTGGGCACCCATCAT
66 CCGACTGGGCACCCATCAT
* *
546656 ACAAATGAGTCCTGACAAGAGACATGATCAAGAAATAGGGAGTAAGTAAAGGTAAAAACCCTAAT
1 ACAAAGGAGTCCTGACAAGAGACATGATCAAGAAATAGGGAATAAGTAAAGGTAAAAACCCTAAT
*
546721 CCGACTGGGCACCCTTCAT
66 CCGACTGGGCACCCATCAT
546740 AC
1 AC
546742 TAGGTAAAAT
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
84 79 1.00
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.18
Consensus pattern (84 bp):
ACAAAGGAGTCCTGACAAGAGACATGATCAAGAAATAGGGAATAAGTAAAGGTAAAAACCCTAAT
CCGACTGGGCACCCATCAT
Found at i:549641 original size:34 final size:34
Alignment explanation
Indices: 549522--549723 Score: 320
Period size: 34 Copynumber: 6.0 Consensus size: 34
549512 TCCTTCGGGT
*
549522 CATCAGTAAGTCTTCCGAGCATTATGATCAAATC
1 CATCAGTAAGTCTTCCGAGCATGATGATCAAATC
549556 CATC--TAAGTCTTCCGAGCATGATGATCAAATC
1 CATCAGTAAGTCTTCCGAGCATGATGATCAAATC
549588 CATC-GTAAGTCTTCCGAGCATGATGATCAAATC
1 CATCAGTAAGTCTTCCGAGCATGATGATCAAATC
** *
549621 CATCAGTAAGTCTTTAGAGCATGATGGTCAAATC
1 CATCAGTAAGTCTTCCGAGCATGATGATCAAATC
549655 CATCAGTAAGTCTTCCGAGCATGATGATCAAATC
1 CATCAGTAAGTCTTCCGAGCATGATGATCAAATC
* * *
549689 CATCAGTAAGTCTTTCGAGCATGATGCTTAAATC
1 CATCAGTAAGTCTTCCGAGCATGATGATCAAATC
549723 C
1 C
549724 TTTGGGCCAT
Statistics
Matches: 156, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
32 31 0.20
33 32 0.21
34 93 0.60
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (34 bp):
CATCAGTAAGTCTTCCGAGCATGATGATCAAATC
Found at i:549823 original size:79 final size:79
Alignment explanation
Indices: 549683--549850 Score: 246
Period size: 79 Copynumber: 2.1 Consensus size: 79
549673 GCATGATGAT
* * * *
549683 CAAATCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTTGGGCCATCTTAAACCTTCACC
1 CAAATCCATCAGTAAGCCTTTCGAGCATGACGATTAAATCCTTCGGGCCATCTTAAACCTTCACC
**
549748 GAAGTGTAGTGAAG
66 GAAGAATAGTGAAG
* * * *
549762 CAAATCCATCAGTAAGCCTTTCGAGCATGACGATTAAGTCCTTCGGGCCATTTTAAGCCTTCACG
1 CAAATCCATCAGTAAGCCTTTCGAGCATGACGATTAAATCCTTCGGGCCATCTTAAACCTTCACC
549827 GAAGAATAGTGAAG
66 GAAGAATAGTGAAG
549841 CAAATCCATC
1 CAAATCCATC
549851 TATCTGATAT
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (79 bp):
CAAATCCATCAGTAAGCCTTTCGAGCATGACGATTAAATCCTTCGGGCCATCTTAAACCTTCACC
GAAGAATAGTGAAG
Found at i:550047 original size:111 final size:111
Alignment explanation
Indices: 549896--550596 Score: 1154
Period size: 111 Copynumber: 6.3 Consensus size: 111
549886 AATTTTTTTC
* *
549896 TCAATATTTGATATTCTCTGAGTGACAGCGGAACAAGTCTACCCTGATTCAATGGATCAACTTTC
1 TCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCTGATTCAATGGATCAACTTTC
* *
549961 CCATATCTGATATTACCTCAGAGAAAGCGGAACAGATCCCTCTCTT
66 CCAGATCTGATATTCCCTCAGAGAAAGCGGAACAGATCCCTCTCTT
* *
550007 TCAAGCTTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACTTTC
1 TCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCTGATTCAATGGATCAACTTTC
* * *
550072 CCAAATCTGATATTCCCTCAGAGGAAGCAGAACAGATCCCTCTCTT
66 CCAGATCTGATATTCCCTCAGAGAAAGCGGAACAGATCCCTCTCTT
* ** *
550118 TCAAGATTTGATATTCCCTGAGTGAAAGTAGAACAAGTCTACCCTGATTCAATGAATCAACTTTC
1 TCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCTGATTCAATGGATCAACTTTC
550183 CCAGATCTGATATTCCCTCAGAGGAAA-CGGAACAGATCCCTCTCTT
66 CCAGATCTGATATTCCCTCAGA-GAAAGCGGAACAGATCCCTCTCTT
550229 TCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCTGATTCAATGGATCAACTTTC
1 TCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCTGATTCAATGGATCAACTTTC
* *
550294 CCAGATCTGATATTCCCTCAGAGGAAGCGGAACAAATCCCTCTCTT
66 CCAGATCTGATATTCCCTCAGAGAAAGCGGAACAGATCCCTCTCTT
*
550340 TCAAGATTTGATATTCACTGAGTGACAGCGGAACAAGTCTACCCTGATTCAATGGATCAACTTTC
1 TCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCTGATTCAATGGATCAACTTTC
* *
550405 CCAGATCTGATATTCCCTCAGAGGAAGCGGAACATATCCCTCTCTT
66 CCAGATCTGATATTCCCTCAGAGAAAGCGGAACAGATCCCTCTCTT
* *
550451 TCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAGTCTACCCTGATTCAAAGGATCAACTTTC
1 TCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCTGATTCAATGGATCAACTTTC
* *
550516 CTAGATCTGATATTCCCTCAGA-AGAAGCAGAACAGATCCCTCTCTT
66 CCAGATCTGATATTCCCTCAGAGA-AAGCGGAACAGATCCCTCTCTT
* *
550562 TCAATATTTGATATTCCCTGAGTGACAACGGAACA
1 TCAAGATTTGATATTCCCTGAGTGACAGCGGAACA
550597 TATCCTTTAT
Statistics
Matches: 554, Mismatches: 33, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
110 3 0.01
111 548 0.99
112 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (111 bp):
TCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCTGATTCAATGGATCAACTTTC
CCAGATCTGATATTCCCTCAGAGAAAGCGGAACAGATCCCTCTCTT
Found at i:552811 original size:2 final size:2
Alignment explanation
Indices: 552799--552869 Score: 135
Period size: 2 Copynumber: 36.0 Consensus size: 2
552789 TTCCATGTTA
552799 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
552840 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
552870 TGCTTTATTA
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 67 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:554784 original size:2 final size:2
Alignment explanation
Indices: 554777--554819 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
554767 CCATAAAAGC
*
554777 TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
554819 T
1 T
554820 CTTTCTGACA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:557012 original size:46 final size:46
Alignment explanation
Indices: 556961--557552 Score: 891
Period size: 46 Copynumber: 12.8 Consensus size: 46
556951 CGTTAAATTT
* *
556961 CATTTTATTTTTGGCATCCTTTCATGCCTTCATGCATCCTTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
* *
557007 CATTTTATTTATGGAATCCTTTCATGCCTTCATGCATCCTTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
* *
557053 CATTTTATTTATGGAATCCTTTCATGCCTTCATGCATCCTTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
*
557099 CATTTTATTTATGGCGTCCTTTCATGCCTTAATGCATCCTTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
*
557145 CATTTTATTTATGGGATCCTTTCATGCCTTAATGCATCCTTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
* *
557191 CATTTGATTTATGGCATCCATTCATGCCTTAATGCATCCTTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
* *
557237 CATTTGATTTATGGCATCCATTCATGCCTTAATGCATCCTTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
* * *
557283 CATTTTATTTATGGTATCCTTTCATACCTTAACGCATTCC-TTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCA-TCCTTTCATG
* * *
557329 CATTTTATTTTTGGCATCCTTTTATGCCTTAATGCATCATTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
557375 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
*
557421 CATTTTATTTATGGCATCCTTTCATGCCTTAATAG-ATCCGTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAAT-GCATCCTTTCATG
* * * * * *
557467 CAATTTATTTATGGAATCTTTTCATTCCTTAATACATCATTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
* * *
557513 TATTTTATTTATGGTATCCTTTCATGCCAATAATGCATCC
1 CATTTTATTTATGGCATCCTTTCATGCC-TTAATGCATCC
557553 ATGTGTATTA
Statistics
Matches: 501, Mismatches: 40, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
45 2 0.00
46 487 0.97
47 12 0.02
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.45
Consensus pattern (46 bp):
CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
Found at i:557375 original size:20 final size:20
Alignment explanation
Indices: 557342--557467 Score: 83
Period size: 20 Copynumber: 5.7 Consensus size: 20
557332 TTTATTTTTG
*
557342 GCATCCTTTTATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
* *
557362 GCATCATTTCATGCATTTTATTTAT
1 GCATCCTTTCATGC--CTTA---AT
557387 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
557408 GCATCCTTTCATGCATTTTATTTAT
1 GCATCCTTTCATGC--CTTA---AT
557433 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
557454 AG-ATCCGTTCATGC
1 -GCATCCTTTCATGC
557468 AATTTATTTA
Statistics
Matches: 85, Mismatches: 9, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
20 37 0.44
21 5 0.06
22 6 0.07
24 6 0.07
25 4 0.05
26 27 0.32
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.44
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:558046 original size:19 final size:19
Alignment explanation
Indices: 557977--558047 Score: 81
Period size: 19 Copynumber: 3.5 Consensus size: 19
557967 TGACTCCATA
*
557977 GTATCGATACCTCTACCATG
1 GTATCGATA-CTCTACTATG
557997 GTATCGATACTACTATACTATG
1 GTATCGATACT-C--TACTATG
558019 GTA-CTGATACTCTACTATG
1 GTATC-GATACTCTACTATG
558038 GTATCGATAC
1 GTATCGATAC
558048 CATTTTTGCA
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
19 17 0.38
20 11 0.24
21 2 0.04
22 15 0.33
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (19 bp):
GTATCGATACTCTACTATG
Found at i:558109 original size:20 final size:20
Alignment explanation
Indices: 558086--558123 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
558076 TTGATACCTT
*
558086 CCCTTAGGTATCTATACTAC
1 CCCTTAGGTATCGATACTAC
*
558106 CCCTTCGGTATCGATACT
1 CCCTTAGGTATCGATACT
558124 GATTAAATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.34
Consensus pattern (20 bp):
CCCTTAGGTATCGATACTAC
Done.