Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008423.1 Hibiscus syriacus cultivar Beakdansim tig00111206_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: 1633377
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 8
Found at i:813227 original size:24 final size:24
Alignment explanation
Indices: 813195--813324 Score: 206
Period size: 24 Copynumber: 5.4 Consensus size: 24
813185 CAAATCCTAT
*
813195 ATTTACATTTTATTCTGCCTTTAC
1 ATTTCCATTTTATTCTGCCTTTAC
813219 ATTTCCATTTTATTCTGCCTTTAC
1 ATTTCCATTTTATTCTGCCTTTAC
* *
813243 ATTTCCATTTTGTTTTGCCTTTAC
1 ATTTCCATTTTATTCTGCCTTTAC
*
813267 ATTTCCATTTTATTATGCCTTTAC
1 ATTTCCATTTTATTCTGCCTTTAC
* *
813291 ATTTCCATTTTATTTTGCCTGTAC
1 ATTTCCATTTTATTCTGCCTTTAC
813315 ATTTCCATTT
1 ATTTCCATTT
813325 GTTTGCACTC
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 99 1.00
ACGTcount: A:0.18, C:0.22, G:0.05, T:0.55
Consensus pattern (24 bp):
ATTTCCATTTTATTCTGCCTTTAC
Found at i:821430 original size:157 final size:156
Alignment explanation
Indices: 821145--821455 Score: 491
Period size: 157 Copynumber: 2.0 Consensus size: 156
821135 GAGGGGAGAA
** *
821145 TTGTAATACCCCAAAAATTTGGATAATGACCAAAATGAAAATTTAGAAAGCTTGATGGTCAAAGT
1 TTGTAATACCCCAAAAAAATAGATAATGACCAAAATGAAAATTTAGAAAGCTTGATGGTCAAAGT
* *
821210 AGAAAATTAGGAAAAAGTTTAGGGAATTAAGTGATAATTTCCTAAAAATAATTTTATTCCATAAA
66 AGAAAATTAGGAAAAAGTGTAGGGAATTAAGTGATAATTTCCTAAAAAGAATTTTATTCCATAAA
821275 TAGATGGTTTACTCTTGAGAGTGGAG
131 TAGATGGTTTACTCTTGAGAGTGGAG
* * *
821301 TTGTAATACCCCCAAAAAAATAGATAATGACCAAAAT-ACAAATTTTGAAAGTTTGATGGTTAAA
1 TTGTAATA-CCCCAAAAAAATAGATAATGACCAAAATGA-AAATTTAGAAAGCTTGATGGTCAAA
* *
821365 GTGGAAAATT-GGGAAAAGTGTAGGGAATTAAGTGATAAATTTCCTAAAAAGAATTTTATTCCAT
64 GTAGAAAATTAGGAAAAAGTGTAGGGAATTAAGTGAT-AATTTCCTAAAAAGAATTTTATTCCAT
821429 AAATAGATGGTTTACTCTTGAGAGTGG
128 AAATAGATGGTTTACTCTTGAGAGTGG
821456 GGTTTTATAG
Statistics
Matches: 142, Mismatches: 10, Indels: 5
0.90 0.06 0.03
Matches are distributed among these distances:
156 33 0.23
157 109 0.77
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.31
Consensus pattern (156 bp):
TTGTAATACCCCAAAAAAATAGATAATGACCAAAATGAAAATTTAGAAAGCTTGATGGTCAAAGT
AGAAAATTAGGAAAAAGTGTAGGGAATTAAGTGATAATTTCCTAAAAAGAATTTTATTCCATAAA
TAGATGGTTTACTCTTGAGAGTGGAG
Found at i:823898 original size:45 final size:45
Alignment explanation
Indices: 823809--823987 Score: 218
Period size: 45 Copynumber: 4.0 Consensus size: 45
823799 GTAAGCATAC
* * * *
823809 AAATAAGCTTACAAGCTTATGGAAT-AATGGCAAATATATGGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
823853 AAATAAGCTTATGAGCTTATGGGATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * * *
823898 AAATAAGCTTACGAGCTTATAGTACAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
823943 AAATAAGCTTACGAGCATATGGTTAATAAATGGTAA-AATATTGGT
1 AAATAAGCTTACGAGCTTATGG--AATAAATGGTAAGTATATTGGT
823988 GATGCAAATA
Statistics
Matches: 115, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
44 22 0.19
45 76 0.66
46 7 0.06
47 10 0.09
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:825048 original size:20 final size:22
Alignment explanation
Indices: 825025--825070 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
825015 TGAATTGGAA
825025 GAATCGATTA-AA-AAAAGTTT
1 GAATCGATTATAAGAAAAGTTT
*
825045 GAATGGATTATAAGAAAAGTTT
1 GAATCGATTATAAGAAAAGTTT
825067 -AATC
1 GAATC
825071 AGATGAAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 9 0.41
21 5 0.23
22 8 0.36
ACGTcount: A:0.48, C:0.04, G:0.17, T:0.30
Consensus pattern (22 bp):
GAATCGATTATAAGAAAAGTTT
Found at i:826856 original size:23 final size:22
Alignment explanation
Indices: 826810--826879 Score: 70
Period size: 23 Copynumber: 3.1 Consensus size: 22
826800 AAAAAACAGG
* *
826810 AAACAGAAA-AAAAATAGAATAA
1 AAACAAAAAGAAAAAGAGAA-AA
* *
826832 AAAGAAAAAGAAAACGAAGAAAA
1 AAACAAAAAGAAAAAG-AGAAAA
*
826855 AAACAAATAGAAAAAGAGAAAA
1 AAACAAAAAGAAAAAGAGAAAA
826877 AAA
1 AAA
826880 ATGAGAGATG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
22 16 0.41
23 19 0.49
24 4 0.10
ACGTcount: A:0.79, C:0.04, G:0.13, T:0.04
Consensus pattern (22 bp):
AAACAAAAAGAAAAAGAGAAAA
Found at i:831030 original size:25 final size:25
Alignment explanation
Indices: 831001--831075 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
830991 ATGGCAAGTA
831001 TATGGGTAAAATAAGCTTACGAGCT
1 TATGGGTAAAATAAGCTTACGAGCT
* **
831026 TATGGG-ATAAAT--G-GTA--AGTA
1 TATGGGTA-AAATAAGCTTACGAGCT
*
831046 TATTGGTAAAATAAGCTTACGAGCT
1 TATGGGTAAAATAAGCTTACGAGCT
831071 TATGG
1 TATGG
831076 TACAAATGGT
Statistics
Matches: 35, Mismatches: 8, Indels: 14
0.61 0.14 0.25
Matches are distributed among these distances:
20 11 0.31
21 1 0.03
22 3 0.09
23 3 0.09
24 1 0.03
25 16 0.46
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.31
Consensus pattern (25 bp):
TATGGGTAAAATAAGCTTACGAGCT
Found at i:831054 original size:45 final size:45
Alignment explanation
Indices: 830965--831143 Score: 236
Period size: 45 Copynumber: 4.0 Consensus size: 45
830955 GTAAGCATGC
* * * *
830965 AAATAAGCTTTCAAGCTTATGGAAT-AATGGCAAGTATATGGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
831009 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * *
831054 AAATAAGCTTACGAGCTTATGGTACAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
831099 AAATAAGCTTACGAGCATATGGTTAATAAATGGTAA-AATATTGGT
1 AAATAAGCTTACGAGCTTATGG--AATAAATGGTAAGTATATTGGT
831144 GATGCAAATA
Statistics
Matches: 119, Mismatches: 13, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
44 22 0.18
45 80 0.67
46 7 0.06
47 10 0.08
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:831513 original size:12 final size:12
Alignment explanation
Indices: 831496--831520 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
831486 TTTTCGGAAA
831496 TTACTGTAGCAG
1 TTACTGTAGCAG
831508 TTACTGTAGCAG
1 TTACTGTAGCAG
831520 T
1 T
831521 GCATCGATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (12 bp):
TTACTGTAGCAG
Found at i:833771 original size:45 final size:45
Alignment explanation
Indices: 833678--833855 Score: 288
Period size: 45 Copynumber: 4.0 Consensus size: 45
833668 GGTAATCATG
*
833678 AAAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
* *
833722 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTGTATTTGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
833767 AAAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAA-TAAATGGTAAGTATATTGGT
* *
833813 -AAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATTTTGG
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGG
833856 ATATGCTAGT
Statistics
Matches: 125, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
44 44 0.35
45 63 0.50
46 18 0.14
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
Found at i:834229 original size:65 final size:65
Alignment explanation
Indices: 834156--834294 Score: 253
Period size: 65 Copynumber: 2.2 Consensus size: 65
834146 AAATTGATAA
834156 ATTG-ATAGTGATGAAAGGTTAATTTTTATGAGTTTTATATGTAATTTTCGGAAGTTACTGTAGC
1 ATTGAATAGTGATGAAAGGTTAATTTTTATGAGTTTTATATGTAATTTTCGGAAGTTACTGTAGC
*
834220 ATTGAATAGTGATGAAAGGTTAATTTTTATGATTTTTATATGTAATTTTCGGAAGTTACTGTAGC
1 ATTGAATAGTGATGAAAGGTTAATTTTTATGAGTTTTATATGTAATTTTCGGAAGTTACTGTAGC
*
834285 AGTGAATAGT
1 ATTGAATAGT
834295 AACGAACAGT
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
64 4 0.06
65 68 0.94
ACGTcount: A:0.31, C:0.04, G:0.22, T:0.43
Consensus pattern (65 bp):
ATTGAATAGTGATGAAAGGTTAATTTTTATGAGTTTTATATGTAATTTTCGGAAGTTACTGTAGC
Found at i:835200 original size:20 final size:20
Alignment explanation
Indices: 835171--835213 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
835161 ATTCCATTAC
*
835171 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
835191 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
835211 ATG
1 ATG
835214 GGCTTTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:836054 original size:23 final size:23
Alignment explanation
Indices: 836028--836107 Score: 81
Period size: 23 Copynumber: 3.4 Consensus size: 23
836018 TCTTTGGGAC
836028 AATTCTATGTGGTCCTTCGGCAT
1 AATTCTATGTGGTCCTTCGGCAT
* * *
836051 AATTCTACGTGGTCCTTCGGGAC
1 AATTCTATGTGGTCCTTCGGCAT
* **
836074 AAATCTATGTGG-CACTTCGGTGT
1 AATTCTATGTGGTC-CTTCGGCAT
836097 ATATTCTATGT
1 A-ATTCTATGT
836108 TGCACTTCAG
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
22 1 0.02
23 37 0.80
24 8 0.17
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (23 bp):
AATTCTATGTGGTCCTTCGGCAT
Found at i:836112 original size:24 final size:24
Alignment explanation
Indices: 836028--836129 Score: 72
Period size: 23 Copynumber: 4.3 Consensus size: 24
836018 TCTTTGGGAC
836028 AATTCTATGTGGTC-CTTC-G-GCA
1 AATTCTATGTGG-CACTTCAGTGCA
* *
836050 TAATTCTACGTGGTC-CTTC-GGGACA
1 -AATTCTATGTGG-CACTTCAGTG-CA
* *
836075 AA-TCTATGTGGCACTTCGGTGTA
1 AATTCTATGTGGCACTTCAGTGCA
* *
836098 TATTCTATGTTGCACTTCAGTGCA
1 AATTCTATGTGGCACTTCAGTGCA
836122 AATTCTAT
1 AATTCTAT
836130 ACGGCAGTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
22 1 0.02
23 32 0.49
24 30 0.46
25 2 0.03
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.37
Consensus pattern (24 bp):
AATTCTATGTGGCACTTCAGTGCA
Found at i:837194 original size:14 final size:14
Alignment explanation
Indices: 837177--837204 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
837167 CTAAATAAAA
837177 CTAAAATAAACAAT
1 CTAAAATAAACAAT
837191 CTAAAATAAACAAT
1 CTAAAATAAACAAT
837205 AAACATGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.21
Consensus pattern (14 bp):
CTAAAATAAACAAT
Found at i:838857 original size:23 final size:23
Alignment explanation
Indices: 838816--838859 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
838806 GGTGGTTTGA
* *
838816 ATAATAATATTTATAATATGGCT
1 ATAATAATAATAATAATATGGCT
*
838839 ATAATAATAATAATTATATGG
1 ATAATAATAATAATAATATGG
838860 GTAGGTTGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (23 bp):
ATAATAATAATAATAATATGGCT
Found at i:844227 original size:21 final size:21
Alignment explanation
Indices: 844185--844228 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
844175 ACCACGGGAG
* *
844185 CTAGCTCTTCACGAGTTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
844206 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
844227 CT
1 CT
844229 CCGGAACCAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.39, G:0.16, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:845427 original size:65 final size:63
Alignment explanation
Indices: 845308--845509 Score: 230
Period size: 65 Copynumber: 3.1 Consensus size: 63
845298 AGTGATGGAC
** *
845308 CGATGCACCAATCCATGCATCGATGCAC-CATGAATTAAATTG-AACATCGAATGCATTTCATGC
1 CGATGCA-CAA-CCATGCATCGATGCACTCA-GAA-TATTTTGAAACATCGAATGCATTTGATGC
845371 AT
62 AT
*
845373 CGATGCACATACCATGCATCGATGCACTGAGAAT-TTTATGAAAACATCGAATGCATTTGATGCA
1 CGATGCACA-ACCATGCATCGATGCACTCAGAATATTT-TG-AAACATCGAATGCATTTGATGCA
845437 T
63 T
* * ** *
845438 CGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGATGCAT
1 CGATGCA-CAACCATGCATCGATGCACTCAGAATATTTTGAAACATCGAATGCATTTGATGCAT
845502 CGATGCAC
1 CGATGCAC
845510 TCTTAGTGCA
Statistics
Matches: 120, Mismatches: 10, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 51 0.43
65 59 0.49
66 5 0.04
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.26
Consensus pattern (63 bp):
CGATGCACAACCATGCATCGATGCACTCAGAATATTTTGAAACATCGAATGCATTTGATGCAT
Found at i:845509 original size:17 final size:19
Alignment explanation
Indices: 845481--845529 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
845471 TATTTTGAAA
845481 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
845499 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
845518 CACCGATGCACT
1 CATCGATGCACT
845530 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:846303 original size:22 final size:21
Alignment explanation
Indices: 846267--846309 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
846257 AGTAAAAAAT
846267 AAATATTAAATTT-AATTTAA
1 AAATATTAAATTTAAATTTAA
846287 AAATATATAAATCTTAAATTTAA
1 AAATAT-TAAAT-TTAAATTTAA
846310 TTTTTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 5 0.25
22 2 0.10
23 7 0.35
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATATTAAATTTAAATTTAA
Found at i:846318 original size:6 final size:6
Alignment explanation
Indices: 846309--846337 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
846299 CTTAAATTTA
846309 ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
846338 AATCTTGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:847025 original size:2 final size:2
Alignment explanation
Indices: 847018--847048 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
847008 CCCGAGAAAA
*
847018 AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
847049 TGAAACCCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:847030 original size:14 final size:14
Alignment explanation
Indices: 847011--847042 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
847001 CGCAAGTCCC
847011 GAGAAAAAGAGAGA
1 GAGAAAAAGAGAGA
*
847025 GAGAAAGAGAGAGA
1 GAGAAAAAGAGAGA
847039 GAGA
1 GAGA
847043 GAGAGATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (14 bp):
GAGAAAAAGAGAGA
Found at i:847031 original size:12 final size:12
Alignment explanation
Indices: 847011--847048 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
847001 CGCAAGTCCC
*
847011 GAGAAAAAGAGA
1 GAGAGAAAGAGA
847023 GAGAGAAAGAGA
1 GAGAGAAAGAGA
*
847035 GAGAGAGAGAGA
1 GAGAGAAAGAGA
847047 GA
1 GA
847049 TGAAACCCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (12 bp):
GAGAGAAAGAGA
Found at i:857313 original size:16 final size:16
Alignment explanation
Indices: 857292--857323 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
857282 CTGTAACACA
857292 CCCATGCAAAAGAGGC
1 CCCATGCAAAAGAGGC
857308 CCCATGCAAAAGAGGC
1 CCCATGCAAAAGAGGC
857324 ACCCCAAGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.31, G:0.25, T:0.06
Consensus pattern (16 bp):
CCCATGCAAAAGAGGC
Found at i:859037 original size:21 final size:21
Alignment explanation
Indices: 859012--859057 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
859002 AGTTATAATT
859012 TAAACATTTTTTTATATCAAG
1 TAAACATTTTTTTATATCAAG
859033 TAAACATTTTTTTATATCAAG
1 TAAACATTTTTTTATATCAAG
859054 TAAA
1 TAAA
859058 AGATATAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (21 bp):
TAAACATTTTTTTATATCAAG
Found at i:862068 original size:29 final size:25
Alignment explanation
Indices: 862011--862069 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 25
862001 TGAGTCCGAT
*
862011 ATATACATAAATAAAAACATATAAT
1 ATATACATAAATAAAAACATATAAG
*
862036 ATATACATAACATAAGTAAACGATATAGG
1 ATATACATAA-ATAA--AAAC-ATATAAG
862065 ATATA
1 ATATA
862070 TTTAATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 10 0.36
26 4 0.14
28 4 0.14
29 10 0.36
ACGTcount: A:0.58, C:0.08, G:0.07, T:0.27
Consensus pattern (25 bp):
ATATACATAAATAAAAACATATAAG
Found at i:862767 original size:29 final size:29
Alignment explanation
Indices: 862735--862790 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
862725 AAAAAAAATA
862735 AAAGGATAGAAATATAAATACATAAAAGT
1 AAAGGATAGAAATATAAATACATAAAAGT
* *
862764 AAAGGGTAGAAATGTAAATACATAAAA
1 AAAGGATAGAAATATAAATACATAAAA
862791 TTAATGTGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.61, C:0.04, G:0.16, T:0.20
Consensus pattern (29 bp):
AAAGGATAGAAATATAAATACATAAAAGT
Found at i:863206 original size:23 final size:21
Alignment explanation
Indices: 863146--863208 Score: 54
Period size: 23 Copynumber: 2.8 Consensus size: 21
863136 AACTGAATCG
* *
863146 TTTAAAAAATATTTTTTTAAT
1 TTTAAAAAATATATTTTCAAT
*
863167 TTTAAAAATAATTTATTTTCATAT
1 TTT-AAAA-AATATATTTTCA-AT
*
863191 ATTTAAAAAATCTATTTT
1 -TTTAAAAAATATATTTT
863209 TTTAGAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 3 0.09
22 4 0.12
23 18 0.53
24 6 0.18
25 3 0.09
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTAAAAAATATATTTTCAAT
Found at i:865617 original size:36 final size:36
Alignment explanation
Indices: 865570--865642 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
865560 AGTTCTGGAA
* *
865570 TTAAGTGATAAAAGAATCAGCCATGGATATGTAGAT
1 TTAAGTGATAAAAAAATCAACCATGGATATGTAGAT
865606 TTAAGTGATAAAAAAATCAACCATGGATATGTAGAT
1 TTAAGTGATAAAAAAATCAACCATGGATATGTAGAT
865642 T
1 T
865643 ATAATTTATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.29
Consensus pattern (36 bp):
TTAAGTGATAAAAAAATCAACCATGGATATGTAGAT
Found at i:869973 original size:16 final size:15
Alignment explanation
Indices: 869946--869977 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
869936 TTAAATAAAG
869946 AAATACAATGGAAAT
1 AAATACAATGGAAAT
869961 AAATACGAATGGAAAT
1 AAATAC-AATGGAAAT
869977 A
1 A
869978 TGCGAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.59, C:0.06, G:0.16, T:0.19
Consensus pattern (15 bp):
AAATACAATGGAAAT
Found at i:870193 original size:30 final size:29
Alignment explanation
Indices: 870160--870341 Score: 161
Period size: 30 Copynumber: 6.0 Consensus size: 29
870150 CCAAAATAAC
870160 AAAAACAAG-AACTTAAAGGACTAAAATAG
1 AAAAA-AAGAAACTTAAAGGACTAAAATAG
* * *
870189 CAAAAATAA-AAATTTAAAAGACTAAAATTG
1 -AAAAA-AAGAAACTTAAAGGACTAAAATAG
* *
870219 TAAGAAAAAGAAATTTAAAGGACCAAAATAG
1 -AA-AAAAAGAAACTTAAAGGACTAAAATAG
*
870250 AAAAAATAGAAACTTAAAGGATTAAAATAG
1 AAAAAA-AGAAACTTAAAGGACTAAAATAG
* * *
870280 AAAAAAATAGAAAGTTAAGGGATTAAAATAG
1 -AAAAAA-AGAAACTTAAAGGACTAAAATAG
*
870311 AAAAAAAATAAAAACTTAAAGGACTAAAATA
1 --AAAAAA-AGAAACTTAAAGGACTAAAATA
870342 CAGAAAGTTA
Statistics
Matches: 129, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
29 4 0.03
30 50 0.39
31 49 0.38
32 26 0.20
ACGTcount: A:0.64, C:0.05, G:0.13, T:0.18
Consensus pattern (29 bp):
AAAAAAAGAAACTTAAAGGACTAAAATAG
Found at i:870236 original size:31 final size:29
Alignment explanation
Indices: 870172--870341 Score: 153
Period size: 31 Copynumber: 5.6 Consensus size: 29
870162 AAACAAGAAC
870172 TTAAAGGACTAAAATAGCAAAAATAA-AAAT
1 TTAAAGGACTAAAATAG-AAAAA-AAGAAAT
* *
870202 TTAAAAGACTAAAATTGTAAGAAAAAGAAAT
1 TTAAAGGACTAAAATAG-AA-AAAAAGAAAT
* *
870233 TTAAAGGACCAAAATAGAAAAAATAGAAAC
1 TTAAAGGACTAAAATAGAAAAAA-AGAAAT
* *
870263 TTAAAGGATTAAAATAGAAAAAAATAGAAAG
1 TTAAAGGACTAAAATAG-AAAAAA-AGAAAT
* * * *
870294 TTAAGGGATTAAAATAGAAAAAAAATAAAAAC
1 TTAAAGGACTAAAATAG--AAAAAA-AGAAAT
870326 TTAAAGGACTAAAATA
1 TTAAAGGACTAAAATA
870342 CAGAAAGTTA
Statistics
Matches: 120, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
29 4 0.03
30 41 0.34
31 49 0.41
32 26 0.22
ACGTcount: A:0.63, C:0.05, G:0.13, T:0.19
Consensus pattern (29 bp):
TTAAAGGACTAAAATAGAAAAAAAGAAAT
Found at i:870248 original size:61 final size:61
Alignment explanation
Indices: 870172--870341 Score: 207
Period size: 61 Copynumber: 2.8 Consensus size: 61
870162 AAACAAGAAC
* * * * * *
870172 TTAAAGGACTAAAATAGCAAAAATAAAAATTTAAAAGACTAAAATTGTAAGAAAA-AGAAAT
1 TTAAAGGACTAAAATAGAAAAAATAAAAACTTAAAGGACTAAAATAG-AAAAAAATAGAAAG
* * *
870233 TTAAAGGACCAAAATAGAAAAAATAGAAACTTAAAGGATTAAAATAGAAAAAAATAGAAAG
1 TTAAAGGACTAAAATAGAAAAAATAAAAACTTAAAGGACTAAAATAGAAAAAAATAGAAAG
* *
870294 TTAAGGGATTAAAATAGAAAAAAAATAAAAACTTAAAGGACTAAAATA
1 TTAAAGGACTAAAATAG--AAAAAATAAAAACTTAAAGGACTAAAATA
870342 CAGAAAGTTA
Statistics
Matches: 92, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
60 6 0.07
61 59 0.64
63 27 0.29
ACGTcount: A:0.63, C:0.05, G:0.13, T:0.19
Consensus pattern (61 bp):
TTAAAGGACTAAAATAGAAAAAATAAAAACTTAAAGGACTAAAATAGAAAAAAATAGAAAG
Found at i:871743 original size:3 final size:3
Alignment explanation
Indices: 871735--871773 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
871725 AAATTAATTA
*
871735 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT ACT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
871774 TTTTTGTAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:874757 original size:2 final size:2
Alignment explanation
Indices: 874750--874783 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
874740 ATGGATTTCA
874750 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
874784 TAAAAAACGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:877921 original size:3 final size:3
Alignment explanation
Indices: 877911--877970 Score: 104
Period size: 3 Copynumber: 20.0 Consensus size: 3
877901 AAAATATTAT
877911 TAA T-A TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
877956 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
877971 ACAATTAAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 50 0.91
4 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:878691 original size:43 final size:43
Alignment explanation
Indices: 878643--878729 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 43
878633 TATCTGGATG
* *
878643 ACACTGCTCCTTTACGTTGAGGAGATCTAGTCGGATGGAGACA
1 ACACTGCTCCTTCACGTTGAGGAGATATAGTCGGATGGAGACA
* * * *
878686 ACACTGCTCCTTCGCGTTGAGGAGATATGGTTGTATGGAGACA
1 ACACTGCTCCTTCACGTTGAGGAGATATAGTCGGATGGAGACA
878729 A
1 A
878730 AACAGTTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (43 bp):
ACACTGCTCCTTCACGTTGAGGAGATATAGTCGGATGGAGACA
Found at i:880713 original size:13 final size:13
Alignment explanation
Indices: 880695--880733 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
880685 ATCTATTTTC
880695 TTTCTTTTCCTTT
1 TTTCTTTTCCTTT
880708 TTTC--TT-CTTT
1 TTTCTTTTCCTTT
880718 TTTCTTTTCCTTT
1 TTTCTTTTCCTTT
880731 TTT
1 TTT
880734 TCGCATTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
10 8 0.35
11 2 0.09
12 2 0.09
13 11 0.48
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTCTTTTCCTTT
Found at i:883341 original size:16 final size:16
Alignment explanation
Indices: 883320--883353 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
883310 CCTAGACGTT
883320 GAGTTTGAAAGGGGTC
1 GAGTTTGAAAGGGGTC
883336 GAGTTTGAAAGGGGTC
1 GAGTTTGAAAGGGGTC
883352 GA
1 GA
883354 TACTTTATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.06, G:0.44, T:0.24
Consensus pattern (16 bp):
GAGTTTGAAAGGGGTC
Found at i:884588 original size:20 final size:20
Alignment explanation
Indices: 884563--884625 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
884553 CCGTTAGACA
*
884563 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCTGTACCCCCT
884583 GGGGGGAATCTGTACCCCCT
1 GGGGGGAATCTGTACCCCCT
884603 GGGGGGGAATCTGTACCCCCT
1 -GGGGGGAATCTGTACCCCCT
884624 GG
1 GG
884626 ACAATCTGAT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
20 21 0.51
21 20 0.49
ACGTcount: A:0.14, C:0.29, G:0.40, T:0.17
Consensus pattern (20 bp):
GGGGGGAATCTGTACCCCCT
Found at i:884601 original size:21 final size:21
Alignment explanation
Indices: 884563--884625 Score: 110
Period size: 21 Copynumber: 3.0 Consensus size: 21
884553 CCGTTAGACA
*
884563 GGGGGGAATCGGTACCCCCT-
1 GGGGGGAATCTGTACCCCCTG
884583 GGGGGGAATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
884604 GGGGGGAATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
884625 G
1 G
884626 ACAATCTGAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
20 19 0.46
21 22 0.54
ACGTcount: A:0.14, C:0.29, G:0.40, T:0.17
Consensus pattern (21 bp):
GGGGGGAATCTGTACCCCCTG
Found at i:886089 original size:19 final size:20
Alignment explanation
Indices: 886046--886095 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
886036 TCTAAATCAT
*
886046 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATATCATTTTGG
* *
886066 CTTTCAAAATAT-ATTTTTG
1 TTTTCAAAATATCATTTTGG
886085 TTTTCAAAATA
1 TTTTCAAAATA
886096 AAATCATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATATCATTTTGG
Found at i:887015 original size:34 final size:32
Alignment explanation
Indices: 886953--887022 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
886943 ACCTTACAAC
* *
886953 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
886985 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
887019 TCCC
1 TCCC
887023 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:887396 original size:21 final size:21
Alignment explanation
Indices: 887370--887473 Score: 147
Period size: 21 Copynumber: 4.9 Consensus size: 21
887360 CGTTAAACAA
* *
887370 GGGGAATCGGTACCCCCTGGT
1 GGGGAATCTGTACCCCCTGGG
*
887391 GGGGAATCTGTTCCCCCTGGG
1 GGGGAATCTGTACCCCCTGGG
*
887412 GGGGAATCGGTACCCCCT-GG
1 GGGGAATCTGTACCCCCTGGG
887432 GGGGAATCTGTACCCCCTAGGG
1 GGGGAATCTGTACCCCCT-GGG
887454 GAGGGAATCTGTACCCCCTG
1 G-GGGAATCTGTACCCCCTG
887474 AACAATCTGA
Statistics
Matches: 74, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
20 19 0.26
21 34 0.46
22 4 0.05
23 17 0.23
ACGTcount: A:0.15, C:0.29, G:0.37, T:0.19
Consensus pattern (21 bp):
GGGGAATCTGTACCCCCTGGG
Found at i:887422 original size:42 final size:42
Alignment explanation
Indices: 887370--887473 Score: 165
Period size: 42 Copynumber: 2.5 Consensus size: 42
887360 CGTTAAACAA
*
887370 GGGGAATCGGTACCCCCTGGTGGGGAATCTGTTCCCCCT-GGG
1 GGGGAATCGGTACCCCCTGG-GGGGAATCTGTACCCCCTAGGG
887412 GGGGAATCGGTACCCCCTGGGGGGAATCTGTACCCCCTAGGG
1 GGGGAATCGGTACCCCCTGGGGGGAATCTGTACCCCCTAGGG
*
887454 GAGGGAATCTGTACCCCCTG
1 G-GGGAATCGGTACCCCCTG
887474 AACAATCTGA
Statistics
Matches: 58, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
41 17 0.29
42 24 0.41
43 17 0.29
ACGTcount: A:0.15, C:0.29, G:0.37, T:0.19
Consensus pattern (42 bp):
GGGGAATCGGTACCCCCTGGGGGGAATCTGTACCCCCTAGGG
Found at i:887481 original size:41 final size:40
Alignment explanation
Indices: 887370--887482 Score: 102
Period size: 41 Copynumber: 2.7 Consensus size: 40
887360 CGTTAAACAA
*** *
887370 GGGGAATCGGTACCCCCTGGTGGGGAATCTGTTCCCCCTGGG
1 GGGGAATCGGTACCCCCT-G-GAACAATCTGTACCCCCTGGG
***
887412 GGGGAATCGGTACCCCCTGGGGGGAATCTGTACCCCCTAGGG
1 GGGGAATCGGTACCCCCT-GGAACAATCTGTACCCCCT-GGG
*
887454 GAGGGAATCTGTACCCCCT-GAACAATCTG
1 G-GGGAATCGGTACCCCCTGGAACAATCTG
887483 ATTTTTCTTG
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
41 24 0.38
42 24 0.38
43 16 0.25
ACGTcount: A:0.18, C:0.28, G:0.35, T:0.19
Consensus pattern (40 bp):
GGGGAATCGGTACCCCCTGGAACAATCTGTACCCCCTGGG
Found at i:890969 original size:18 final size:19
Alignment explanation
Indices: 890929--890971 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
890919 TTAAAAAATA
* **
890929 AAAAATAATATTTTTTATT
1 AAAAATAATATTTTTAAAG
890948 AAAAAT-ATATTTTTAAAG
1 AAAAATAATATTTTTAAAG
890966 AAAAAT
1 AAAAAT
890972 TCTCCTCCCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
AAAAATAATATTTTTAAAG
Found at i:892048 original size:3 final size:3
Alignment explanation
Indices: 892042--892080 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
892032 TGATGATGAT
892042 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
892081 ATGGGTTTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:897255 original size:14 final size:14
Alignment explanation
Indices: 897227--897267 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
897217 TTTTAATTAT
* *
897227 ATTTAAAATTTAAA
1 ATTTAAAAATAAAA
897241 ATTTAAAAATAAAA
1 ATTTAAAAATAAAA
897255 A--TAAAAATAAAA
1 ATTTAAAAATAAAA
897267 A
1 A
897268 ATTATGATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 12 0.48
14 13 0.52
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
ATTTAAAAATAAAA
Found at i:899947 original size:131 final size:131
Alignment explanation
Indices: 899671--900037 Score: 574
Period size: 131 Copynumber: 2.8 Consensus size: 131
899661 TAATTCTAAA
* *
899671 AGAGAAAATGATAATATCTAATTATTTCCGATCGAGAATAAATGACCTCTCATGCCTTAAAGCAG
1 AGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAG
* * * * *
899736 TCA-TTCTTACTCCAACCGAAATGAAGAGATATCACTATTTCATCTTAAAATTCAATATTGATTC
66 TCATTTATTACTCCAACCGAAATGAAGAGATATCACTATTCCATCTTAAAAATCAATATTAATTA
899800 G
131 G
* * *
899801 AGTGAAAACGATAATATCTAATGATTTCCAATTGAGAATAAATGACCTCTCATGCCTTAAAGCAG
1 AGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAG
* *
899866 TCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAAATCAATATTAATTA
66 TCATTTATTACTCCAACCGAAATGAAGAGATATCACTATTCCATCTTAAAAATCAATATTAATTA
899931 G
131 G
* * *
899932 AGAGAAAACGGTAATATCTAATTATTTCCAATCGAGAATAAACGACCTCTCATGACTTAAAGCAG
1 AGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAG
* *
899997 TCATTTATTACTCCAACCGAAATGAAAAGATATTACTATTC
66 TCATTTATTACTCCAACCGAAATGAAGAGATATCACTATTC
900038 TTAATATCGA
Statistics
Matches: 215, Mismatches: 21, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
130 63 0.29
131 152 0.71
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (131 bp):
AGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAG
TCATTTATTACTCCAACCGAAATGAAGAGATATCACTATTCCATCTTAAAAATCAATATTAATTA
G
Found at i:900514 original size:16 final size:17
Alignment explanation
Indices: 900493--900535 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
900483 ACAACATGCA
900493 AAAATTAAAATAAAAC-
1 AAAATTAAAATAAAACT
* *
900509 AAAATTTAAATAGAACT
1 AAAATTAAAATAAAACT
900526 AAAATATAAA
1 AAAAT-TAAA
900536 CAATCACATC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 14 0.64
17 5 0.23
18 3 0.14
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (17 bp):
AAAATTAAAATAAAACT
Found at i:902649 original size:20 final size:18
Alignment explanation
Indices: 902607--902654 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 18
902597 GATGCAATAA
* *
902607 GTATCGATACTGATAAGG
1 GTATCGATACTGAGAAAG
902625 GTATCGATACTAAGAGAAAG
1 GTATCGATACT--GAGAAAG
*
902645 GTATCTATAC
1 GTATCGATAC
902655 CATGGATTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 11 0.44
20 14 0.56
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (18 bp):
GTATCGATACTGAGAAAG
Found at i:903484 original size:44 final size:44
Alignment explanation
Indices: 903436--903797 Score: 397
Period size: 44 Copynumber: 8.0 Consensus size: 44
903426 AAATAAATGA
* * * *
903436 ATAAATGAAAATACATAACGATACATTATTGGCAGAAATGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* *
903480 ATAAATGAAAATGCATAACGGTGCATTATTGGCATAAAGGTACC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* * * * *
903524 ATAAATGAATATGTATAACGGTGCATTATTGGCAAAAAATGTACC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGC-AGAAAGGTGCC
* *
903569 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTGAC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* *
903613 ATAAATGAAAATGCATAACGTTGCATTATTGGCAGAACGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* * *
903657 ATAAATGAAAATGCATAACGATGCATT-TTGGTATAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* *
903700 ACAAATGAAACTTAAATGCATAAAGGTGCATT-TTGGCAGAAAGGTGCC
1 ATAAATG--A---AAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* **
903748 ACAAATGAAACTTAAATGCATAACAATGCATT-TTGGCAGAAAGGTGCC
1 ATAAATG--A---AAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
903796 AT
1 AT
903798 TCATGGTTTA
Statistics
Matches: 280, Mismatches: 32, Indels: 8
0.88 0.10 0.03
Matches are distributed among these distances:
43 19 0.07
44 143 0.51
45 41 0.15
48 77 0.28
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
Found at i:903586 original size:89 final size:88
Alignment explanation
Indices: 903436--903757 Score: 380
Period size: 89 Copynumber: 3.6 Consensus size: 88
903426 AAATAAATGA
* *
903436 ATAAATGAAAATACATAACGATACATTATTGGCAGAAATGTGCCATAAATGAAAATGCATAACGG
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAATGTGCCATAAATGAAAATGCATAACGG
903501 TGCATTATTGGCATAAAGGTACC
66 TGCATTATTGGCATAAAGGTACC
* * * * *
903524 ATAAATGAATATGTATAACGGTGCATTATTGGCAAAAAATGTACCATAAATGAAAATGCATAACG
1 ATAAATGAAAATGCATAACGATGCATTATTGGC-AGAAATGTGCCATAAATGAAAATGCATAACG
* *
903589 GTGCATTATTGGCAGAAATGTGA-C
65 GTGCATTATTGGCATAAAGGT-ACC
* ** *
903613 ATAAATGAAAATGCATAACGTTGCATTATTGGCAGAACGGTGCCATAAATGAAAATGCATAACGA
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAATGTGCCATAAATGAAAATGCATAACGG
* *
903678 TGCATT-TTGGTATAAAGGTGCC
66 TGCATTATTGGCATAAAGGTACC
* * * * *
903700 ACAAATGAAACTTAAATGCATAAAGGTGCATT-TTGGCAGAAAGGTGCCACAAATGAAA
1 ATAAATG--A---AAATGCATAACGATGCATTATTGGCAGAAATGTGCCATAAATGAAA
903758 CTTAAATGCA
Statistics
Matches: 200, Mismatches: 26, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
87 17 0.09
88 61 0.31
89 80 0.40
90 1 0.00
91 24 0.12
92 17 0.09
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (88 bp):
ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAATGTGCCATAAATGAAAATGCATAACGG
TGCATTATTGGCATAAAGGTACC
Found at i:903638 original size:133 final size:131
Alignment explanation
Indices: 903436--903797 Score: 404
Period size: 133 Copynumber: 2.7 Consensus size: 131
903426 AAATAAATGA
* * *
903436 ATAAATGAAAATACATAACGATACATTATTGGCAGAAATGTGCCATAAATGAAAATGCATAACGG
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTGCCATAAATGAAAATGCATAACGG
* * * * *
903501 TGCATTATTGGCATAAAGGTACCATAAATGAATATGTATAACGGTGCATTATTGGCAAAAAATGT
66 TGCATTATTGGCAGAAAGGTACCATAAATGAAAATGCATAACGATGCATT-TTGG-AAAAAAGGT
903566 ACC
129 ACC
* *
903569 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTGACATAAATGAAAATGCATAACGT
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTGCCATAAATGAAAATGCATAACGG
* * * * *
903634 TGCATTATTGGCAGAACGGTGCCATAAATGAAAATGCATAACGATGCATTTTGGTATAAAGGTGC
66 TGCATTATTGGCAGAAAGGTACCATAAATGAAAATGCATAACGATGCATTTTGGAAAAAAGGTAC
903699 C
131 C
* * * *
903700 ACAAATGAAACTTAAATGCATAAAGGTGCATT-TTGGCAGAAAGGTGCCACAAATGAAACTTAAA
1 ATAAATG--A---AAATGCATAACGGTGCATTATTGGCAGAAATGTGCCATAAATG--A---AAA
** *
903764 TGCATAACAATGCATT-TTGGCAGAAAGGTGCCAT
56 TGCATAACGGTGCATTATTGGCAGAAAGGTACCAT
903798 TCATGGTTTA
Statistics
Matches: 196, Mismatches: 23, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
131 14 0.07
132 4 0.02
133 105 0.54
135 20 0.10
136 18 0.09
137 1 0.01
139 17 0.09
140 17 0.09
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (131 bp):
ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTGCCATAAATGAAAATGCATAACGG
TGCATTATTGGCAGAAAGGTACCATAAATGAAAATGCATAACGATGCATTTTGGAAAAAAGGTAC
C
Found at i:903730 original size:48 final size:48
Alignment explanation
Indices: 903621--903796 Score: 220
Period size: 48 Copynumber: 3.8 Consensus size: 48
903611 ACATAAATGA
* * * *
903621 AAATGCATAACGTTGCATTATTGGCAGAACGGTGCCATAAATG--A---
1 AAATGCATAAAGATGCATT-TTGGCAGAAAGGTGCCACAAATGAAACTT
* * *
903665 AAATGCATAACGATGCATTTTGGTATAAAGGTGCCACAAATGAAACTT
1 AAATGCATAAAGATGCATTTTGGCAGAAAGGTGCCACAAATGAAACTT
*
903713 AAATGCATAAAGGTGCATTTTGGCAGAAAGGTGCCACAAATGAAACTT
1 AAATGCATAAAGATGCATTTTGGCAGAAAGGTGCCACAAATGAAACTT
903761 AAATGCATAACA-ATGCATTTTGGCAGAAAGGTGCCA
1 AAATGCATAA-AGATGCATTTTGGCAGAAAGGTGCCA
903797 TTCATGGTTT
Statistics
Matches: 116, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
43 19 0.16
44 18 0.16
45 1 0.01
48 77 0.66
49 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (48 bp):
AAATGCATAAAGATGCATTTTGGCAGAAAGGTGCCACAAATGAAACTT
Found at i:903791 original size:96 final size:92
Alignment explanation
Indices: 903459--903796 Score: 302
Period size: 89 Copynumber: 3.7 Consensus size: 92
903449 CATAACGATA
* * ** * *
903459 CATTATTGGCAGAAATGTGCCATAAATGAAAATGCATAACGGTGCATTATTGGCATAAAGGTACC
1 CATTATTGGCAGAAAGGTGCCACAAATGAAAATGCATAACAATGCATT-TTGGCAGAAAGGTGCC
* * *
903524 ATAAATG-AA--T--ATGTATAACGGTG
65 ACAAATGAAACTTAAATGCATAAAGGTG
* * * * ** * *
903547 CATTATTGGCAAAAAATGTACCATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTGA
1 CATTATTGGC-AGAAAGGTGCCACAAATGAAAATGCATAACAATGCATT-TTGGCAGAAAGGTGC
* * *
903612 CATAAATG--A---AAATGCATAACGTTG
64 CACAAATGAAACTTAAATGCATAAAGGTG
* * * * *
903636 CATTATTGGCAGAACGGTGCCATAAATGAAAATGCATAACGATGCATTTTGGTATAAAGGTGCCA
1 CATTATTGGCAGAAAGGTGCCACAAATGAAAATGCATAACAATGCATTTTGGCAGAAAGGTGCCA
903701 CAAATGAAACTTAAATGCATAAAGGTG
66 CAAATGAAACTTAAATGCATAAAGGTG
903728 CATT-TTGGCAGAAAGGTGCCACAAATGAAACTTAAATGCATAACAATGCATTTTGGCAGAAAGG
1 CATTATTGGCAGAAAGGTGCCACAAATG--A---AAATGCATAACAATGCATTTTGGCAGAAAGG
903792 TGCCA
61 TGCCA
903797 TTCATGGTTT
Statistics
Matches: 212, Mismatches: 25, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
87 18 0.08
88 44 0.21
89 78 0.37
91 21 0.10
92 17 0.08
93 1 0.00
96 33 0.16
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (92 bp):
CATTATTGGCAGAAAGGTGCCACAAATGAAAATGCATAACAATGCATTTTGGCAGAAAGGTGCCA
CAAATGAAACTTAAATGCATAAAGGTG
Found at i:909043 original size:22 final size:22
Alignment explanation
Indices: 909015--909063 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
909005 TACCCTCGAG
909015 TTAAAGAATTTTCCAAAGCATC
1 TTAAAGAATTTTCCAAAGCATC
*
909037 TTAAAGAATTTTCCAAATCATC
1 TTAAAGAATTTTCCAAAGCATC
909059 TTAAA
1 TTAAA
909064 TATGTTTATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.43, C:0.16, G:0.06, T:0.35
Consensus pattern (22 bp):
TTAAAGAATTTTCCAAAGCATC
Found at i:912105 original size:21 final size:21
Alignment explanation
Indices: 912080--912120 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
912070 GGAGGGAAAG
912080 TTTTTAACTTTTTAACTTTTT
1 TTTTTAACTTTTTAACTTTTT
* * *
912101 TTTTTGATTTTTTTACTTTT
1 TTTTTAACTTTTTAACTTTT
912121 ACTTTAGGGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTTAACTTTTTAACTTTTT
Found at i:914825 original size:20 final size:20
Alignment explanation
Indices: 914800--914842 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
914790 TCTAAGATCC
**
914800 CATTTAGGATCATATAGATG
1 CATTTAGGAGAATATAGATG
*
914820 CATTTAGGAGAATATAGTTG
1 CATTTAGGAGAATATAGATG
914840 CAT
1 CAT
914843 GTGGTGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGAGAATATAGATG
Found at i:915152 original size:30 final size:30
Alignment explanation
Indices: 915116--915192 Score: 127
Period size: 30 Copynumber: 2.6 Consensus size: 30
915106 GGACCAATCA
915116 CTACTGTAGCTGATTCTGTTATACCTCAAC
1 CTACTGTAGCTGATTCTGTTATACCTCAAC
*
915146 CTACTGTAGCTAATTCTGTTATACCTCAAC
1 CTACTGTAGCTGATTCTGTTATACCTCAAC
* *
915176 TTACTGCAGCTGATTCT
1 CTACTGTAGCTGATTCT
915193 ACTATTGCAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (30 bp):
CTACTGTAGCTGATTCTGTTATACCTCAAC
Found at i:919389 original size:22 final size:22
Alignment explanation
Indices: 919361--919409 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
919351 TACCCTCGAG
919361 TTAAAGAATTTTCCAAAGCATC
1 TTAAAGAATTTTCCAAAGCATC
*
919383 TTAAAGAATTTTCCAAATCATC
1 TTAAAGAATTTTCCAAAGCATC
919405 TTAAA
1 TTAAA
919410 TATGTTTATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.43, C:0.16, G:0.06, T:0.35
Consensus pattern (22 bp):
TTAAAGAATTTTCCAAAGCATC
Found at i:927217 original size:16 final size:16
Alignment explanation
Indices: 927193--927225 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
927183 TTGATCCCAA
*
927193 AAGGTCTGAAGAGTTT
1 AAGGGCTGAAGAGTTT
927209 AAGGGCTGAAGAGTTT
1 AAGGGCTGAAGAGTTT
927225 A
1 A
927226 GGAGCTCCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.33, T:0.27
Consensus pattern (16 bp):
AAGGGCTGAAGAGTTT
Found at i:932690 original size:44 final size:44
Alignment explanation
Indices: 932640--932868 Score: 309
Period size: 44 Copynumber: 5.2 Consensus size: 44
932630 AAATGAATGA
932640 ATAAATGAAAATGCATAACAATGCATTATTGACAGAAAGGTGCC
1 ATAAATGAAAATGCATAACAATGCATTATTGACAGAAAGGTGCC
* *
932684 ATAAATGAAAATGCATAACAATGCATTATTTACATAAAGGTGCC
1 ATAAATGAAAATGCATAACAATGCATTATTGACAGAAAGGTGCC
* * * *
932728 ATAAATGAAAATGCATAACAGTGCATTATTGGCAGAATGGTTCC
1 ATAAATGAAAATGCATAACAATGCATTATTGACAGAAAGGTGCC
*** * **
932772 ATAAATGAAAATGCATAATGGTACATTATTGGTAGAAAGGTGCC
1 ATAAATGAAAATGCATAACAATGCATTATTGACAGAAAGGTGCC
* *
932816 ATAAATGAAAATGGATAACAATGCATT-TTGTCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACAATGCATTATTGACAGAAAGGTGCC
*
932859 ACAAAT-AAAA
1 ATAAATGAAAA
932869 CTTAAATGCA
Statistics
Matches: 163, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
42 4 0.02
43 19 0.12
44 140 0.86
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.25
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACAATGCATTATTGACAGAAAGGTGCC
Found at i:932812 original size:132 final size:132
Alignment explanation
Indices: 932640--932916 Score: 355
Period size: 132 Copynumber: 2.1 Consensus size: 132
932630 AAATGAATGA
*
932640 ATAAATGAAAATGCATAACAATGCATTATTGACAGAAAGGTGCCATAAATGAAAATGCATAACAA
1 ATAAATGAAAATGCATAACAATACATTATTGACAGAAAGGTGCCATAAATGAAAATGCATAACAA
* * * *
932705 TGCATTATT-TACATAAAGGTGCCATAAAT-GA-AAATGCATAACA-GTGCATTATTGGCAGAAT
66 TGCATT-TTGT-CAGAAAGGTGCCACAAATAAATAAATGCATAA-AGGTGCATT-TTGGCAGAAA
*
932766 GGTTCC
127 AGTTCC
*** ** *
932772 ATAAATGAAAATGCATAATGGTACATTATTGGTAGAAAGGTGCCATAAATGAAAATGGATAACAA
1 ATAAATGAAAATGCATAACAATACATTATTGACAGAAAGGTGCCATAAATGAAAATGCATAACAA
932837 TGCATTTTGTCAGAAAGGTGCCACAAATAAAACTTAAATGCATAAAGGTGCATTTTGGCAGAAAA
66 TGCATTTTGTCAGAAAGGTGCCACAAAT-AAA--TAAATGCATAAAGGTGCATTTTGGCAGAAAA
932902 GTTCC
128 GTTCC
932907 ATAAATGAAA
1 ATAAATGAAA
932917 CATAAATGCA
Statistics
Matches: 126, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
131 18 0.14
132 65 0.52
133 1 0.01
135 25 0.20
136 17 0.13
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.26
Consensus pattern (132 bp):
ATAAATGAAAATGCATAACAATACATTATTGACAGAAAGGTGCCATAAATGAAAATGCATAACAA
TGCATTTTGTCAGAAAGGTGCCACAAATAAATAAATGCATAAAGGTGCATTTTGGCAGAAAAGTT
CC
Found at i:932891 original size:48 final size:48
Alignment explanation
Indices: 932837--932944 Score: 144
Period size: 48 Copynumber: 2.2 Consensus size: 48
932827 TGGATAACAA
* * * *
932837 TGCATTTTGTCAGAAAGGTGCCACAAATAAAACTTAAATGCATAAAGG
1 TGCATTTTGGCAGAAAAGTGCCACAAATAAAACATAAATGCACAAAGG
* * * *
932885 TGCATTTTGGCAGAAAAGTTCCATAAATGAAACATAAATGCACAACGG
1 TGCATTTTGGCAGAAAAGTGCCACAAATAAAACATAAATGCACAAAGG
932933 TGCATTTTGGCA
1 TGCATTTTGGCA
932945 TAAATGTGTC
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (48 bp):
TGCATTTTGGCAGAAAAGTGCCACAAATAAAACATAAATGCACAAAGG
Found at i:937458 original size:6 final size:6
Alignment explanation
Indices: 937447--937523 Score: 154
Period size: 6 Copynumber: 12.8 Consensus size: 6
937437 GAGAGGATAT
937447 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
937495 ATATAC ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATA
937524 TAGGAGAATC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 71 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:941837 original size:132 final size:131
Alignment explanation
Indices: 941487--941855 Score: 603
Period size: 131 Copynumber: 2.8 Consensus size: 131
941477 ATAATTCTAA
* *
941487 GAGAGAAAACGATAATATCTAATTATTTCCAATTGAGAATAAATGACCTCTCATGTCTTAAAGCA
1 GAGAGAAAATGATAATATCTAATTATTTCCAATTGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * *
941552 GTCATTTATTACTCCAATCAAAATGAAGAGATATCACTATTTCGTCTTAAAATTCAATATTGGTT
66 GTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCGTCTTAAAAATCAATATTGATT
941617 C
131 C
* *
941618 GAGTGAAAATGATAATATCTAATGATTTCCAATTGAGAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAATGATAATATCTAATTATTTCCAATTGAGAATAAATGACCTCTCATGCCTTAAAGCA
*
941683 GTCATTTATTACTCCAATCGAAATGAAGATATATCACTATTTCGTCTTAAAAATCAATATTGATT
66 GTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCGTCTTAAAAATCAATATTGATT
941748 C
131 C
* *
941749 GAGAGAAAATGGTAATTTTCTAATTATTTCCAATTGAGAATAAATGACCTCTCATGCCTTAAAGC
1 GAGAGAAAATGATAA-TATCTAATTATTTCCAATTGAGAATAAATGACCTCTCATGCCTTAAAGC
* * * *
941814 AATCATTTATTACTCCAACCGAAATGAAAAGATATTACTATT
65 AGTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATT
941856 CTCATTATCG
Statistics
Matches: 220, Mismatches: 17, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
131 136 0.62
132 84 0.38
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.33
Consensus pattern (131 bp):
GAGAGAAAATGATAATATCTAATTATTTCCAATTGAGAATAAATGACCTCTCATGCCTTAAAGCA
GTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCGTCTTAAAAATCAATATTGATT
C
Found at i:942742 original size:24 final size:25
Alignment explanation
Indices: 942690--942751 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
942680 TAGTTTTATA
*
942690 AAGTTCTTTA-TTTTCTTTTATTTTC
1 AAGTT-TTTATTTTTATTTTATTTTC
942715 AAGTTTTTATTTTTATTTTATTTT-
1 AAGTTTTTATTTTTATTTTATTTTC
942739 AAG-TTTTATTTTT
1 AAGTTTTTATTTTT
942752 GAACATGCTA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
23 10 0.29
24 7 0.20
25 18 0.51
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.71
Consensus pattern (25 bp):
AAGTTTTTATTTTTATTTTATTTTC
Found at i:942745 original size:12 final size:12
Alignment explanation
Indices: 942705--942750 Score: 58
Period size: 11 Copynumber: 3.8 Consensus size: 12
942695 CTTTATTTTC
942705 TTTTATTTTCAAG
1 TTTTATTTT-AAG
*
942718 TTTTTATTTTTA-
1 -TTTTATTTTAAG
942730 TTTTATTTTAAG
1 TTTTATTTTAAG
942742 TTTTATTTT
1 TTTTATTTT
942751 TGAACATGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 10 0.34
12 9 0.31
13 1 0.03
14 9 0.31
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (12 bp):
TTTTATTTTAAG
Found at i:948611 original size:90 final size:89
Alignment explanation
Indices: 948456--948632 Score: 309
Period size: 90 Copynumber: 2.0 Consensus size: 89
948446 CCTAACACAC
948456 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATA
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATA
* *
948521 TTTAATTAATTGGAATTTAATAAT
66 TTTAATTAATTGAAATTAAATAAT
* *
948545 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTATATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTA-GGATTTTATTATTTCAAATTAATTAAATCTAT
948610 ATTTAATTAATTGAAATTAAATA
65 ATTTAATTAATTGAAATTAAATA
948633 TTCAGGATTA
Statistics
Matches: 83, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 31 0.37
90 52 0.63
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTGAAATTAAATAAT
Found at i:954540 original size:25 final size:23
Alignment explanation
Indices: 954506--954557 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 23
954496 CTTTCTTTTC
* *
954506 TTTTCTTTTATTTTCAAGTTTTCAT
1 TTTTATTTTATTTT-AAATTTT-AT
954531 TTTTATTTTATTTTAAATTTTAT
1 TTTTATTTTATTTTAAATTTTAT
954554 TTTT
1 TTTT
954558 GAACATGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 6 0.24
24 6 0.24
25 13 0.52
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.73
Consensus pattern (23 bp):
TTTTATTTTATTTTAAATTTTAT
Found at i:956962 original size:3 final size:3
Alignment explanation
Indices: 956956--957026 Score: 135
Period size: 3 Copynumber: 24.0 Consensus size: 3
956946 AAAGATGATG
956956 ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
957003 ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA
957027 TCGGGATGAA
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 65 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:960899 original size:21 final size:20
Alignment explanation
Indices: 960869--960915 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
960859 ACCAATAATA
*
960869 TTCTTTATTATCCT-TTTATT
1 TTCTTTATTA-CATCTTTATT
960889 TTCTTATATTACATCTTTATT
1 TTCTT-TATTACATCTTTATT
960910 TTCTTT
1 TTCTTT
960916 TTCTTGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.17, C:0.15, G:0.00, T:0.68
Consensus pattern (20 bp):
TTCTTTATTACATCTTTATT
Found at i:962089 original size:3 final size:3
Alignment explanation
Indices: 962083--962153 Score: 135
Period size: 3 Copynumber: 24.0 Consensus size: 3
962073 ATCATCATTG
962083 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
962130 TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
962154 AATAAAAATA
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 65 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:969819 original size:44 final size:42
Alignment explanation
Indices: 969769--969863 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 42
969759 GGCCTTGTGC
*
969769 ATCGATGCACATTCAAGG-TGTGCATCGGTGCACCT-TCATGGTGT
1 ATCGATGCACATTCAAGGATGT--ATCGATGCA-CTGTCA-GGTGT
*
969813 ATCGATGCACATTCAAGGATGTATCGATGCACTGTTAGGTGT
1 ATCGATGCACATTCAAGGATGTATCGATGCACTGTCAGGTGT
969855 ATCGATGCA
1 ATCGATGCA
969864 TTAAGCACAA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
42 16 0.34
43 10 0.21
44 18 0.38
45 3 0.06
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.29
Consensus pattern (42 bp):
ATCGATGCACATTCAAGGATGTATCGATGCACTGTCAGGTGT
Found at i:969857 original size:20 final size:21
Alignment explanation
Indices: 969769--969863 Score: 104
Period size: 21 Copynumber: 4.4 Consensus size: 21
969759 GGCCTTGTGC
969769 ATCGATGCACATTCAAGGTGT
1 ATCGATGCACATTCAAGGTGT
* * *
969790 GCATCGGTGCACCTTCATGGTGT
1 --ATCGATGCACATTCAAGGTGT
969813 ATCGATGCACATTCAAGGATGT
1 ATCGATGCACATTCAAGG-TGT
*
969835 ATCGATGCAC-TGT-TAGGTGT
1 ATCGATGCACAT-TCAAGGTGT
969855 ATCGATGCA
1 ATCGATGCA
969864 TTAAGCACAA
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
20 12 0.19
21 19 0.30
22 14 0.22
23 18 0.29
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.29
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:976527 original size:28 final size:27
Alignment explanation
Indices: 976483--976536 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
976473 GCATTTTTTG
976483 CATTTTCATTTTACATTCGCATCTTTA
1 CATTTTCATTTTACATTCGCATCTTTA
* *
976510 CATTTTCATTTTTGCATTTGCATCTTT
1 CATTTTCA-TTTTACATTCGCATCTTT
976537 GCATACTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.19, C:0.20, G:0.06, T:0.56
Consensus pattern (27 bp):
CATTTTCATTTTACATTCGCATCTTTA
Found at i:976537 original size:8 final size:7
Alignment explanation
Indices: 976461--976540 Score: 51
Period size: 6 Copynumber: 11.1 Consensus size: 7
976451 GCATACTTAT
976461 TTTTGCA
1 TTTTGCA
976468 TTTATGCA
1 TTT-TGCA
976476 TTTTTTGCA
1 --TTTTGCA
976485 TTTT-CA
1 TTTTGCA
*
976491 TTTTACA
1 TTTTGCA
*
976498 -TTCGCA
1 TTTTGCA
*
976504 TCTTTACA
1 T-TTTGCA
976512 TTTT-CA
1 TTTTGCA
976518 TTTTTGCA
1 -TTTTGCA
976526 -TTTGCA
1 TTTTGCA
976532 TCTTTGCA
1 T-TTTGCA
976540 T
1 T
976541 ACTTACATTT
Statistics
Matches: 59, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
6 18 0.31
7 16 0.27
8 18 0.31
9 4 0.07
10 3 0.05
ACGTcount: A:0.17, C:0.17, G:0.09, T:0.56
Consensus pattern (7 bp):
TTTTGCA
Found at i:976537 original size:14 final size:14
Alignment explanation
Indices: 976479--976540 Score: 63
Period size: 14 Copynumber: 4.5 Consensus size: 14
976469 TTATGCATTT
*
976479 TTTGCATTTTCAT-
1 TTTGCATTTGCATC
* *
976492 TTTACATTCGCATC
1 TTTGCATTTGCATC
* * *
976506 TTTACATTTTCATT
1 TTTGCATTTGCATC
976520 TTTGCATTTGCATC
1 TTTGCATTTGCATC
976534 TTTGCAT
1 TTTGCAT
976541 ACTTACATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
13 10 0.26
14 29 0.74
ACGTcount: A:0.18, C:0.19, G:0.08, T:0.55
Consensus pattern (14 bp):
TTTGCATTTGCATC
Found at i:979224 original size:89 final size:89
Alignment explanation
Indices: 979071--979236 Score: 269
Period size: 89 Copynumber: 1.9 Consensus size: 89
979061 CATATACTCA
* **
979071 TATTATATATACAATAAAGCTTGAGCTATCCCCCTAAAACAATTGGTTAATCGCCCCGGTTTTAT
1 TATTATATATACAATAAAGCTTGAGCTATCCCCCTAAAACAATTGGTTAATAGCCCCGACTTTAT
979136 GAATAATATTCAACTAACCTATAT
66 GAATAATATTCAACTAACCTATAT
* * *
979160 TATTATATATACAATAAAGCTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCTGACTTTAT
1 TATTATATATACAATAAAGCTTGAGCTATCCCCCTAAAACAATTGGTTAATAGCCCCGACTTTAT
*
979225 GGATAATATTCA
66 GAATAATATTCA
979237 GCTAGTCTGT
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
89 70 1.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (89 bp):
TATTATATATACAATAAAGCTTGAGCTATCCCCCTAAAACAATTGGTTAATAGCCCCGACTTTAT
GAATAATATTCAACTAACCTATAT
Found at i:981478 original size:123 final size:123
Alignment explanation
Indices: 981315--981737 Score: 458
Period size: 123 Copynumber: 3.5 Consensus size: 123
981305 CACTCGAGGT
** * * *
981315 ATCAACATTTTTAGAAAGAGTTCGTAATAAGAAGAACTCATCTGAAGTGAAAGAATAAGTTCATA
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGAAAGAACAAGTTCATA
* **
981380 ATCTGAAGAACTTATTCAACCTTTTGCTTGACTCTATCACAGAAGGAGATAGAGCAAC
66 ATCTGAAAAACTTATTCAACCTTTTGCTCAACTCTATCACAGAAGGAGATAGAGCAAC
* * * * *
981438 ATCAACATTTGCAGAAGGAGTTCATAATAAAAATAACTCATCTGAAGAGGAAGAACAAGTTCATA
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGAAAGAACAAGTTCATA
* * * *
981503 ATTTGAAAAACTTATTCAACCTTTTGCTCAACTCTATTACAGAAGGGGATAGAGCAGC
66 ATCTGAAAAACTTATTCAACCTTTTGCTCAACTCTATCACAGAAGGAGATAGAGCAAC
* * * * * *
981561 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCGTCTGAAAAGGAGGAAGAAGTTTATA
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGAAAGAACAAGTTCATA
** * * * * * * ** *
981626 ATGAGAAGAAA-TTGTTCAACC-TTAGCTCAATTC-ATCGCAGAATGAAATAGATTACC
66 ATCTGAA-AAACTTATTCAACCTTTTGCTCAACTCTATCACAGAAGGAGATAGAGCAAC
* * * *
981682 ATCAACATTTCCAGAATGAGTTCATAATGAGAAGAACTCATCTAAAGA-AGAAGAAC
1 ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGA-AAGAAC
981738 TTGTTCAACA
Statistics
Matches: 251, Mismatches: 47, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
121 61 0.24
122 10 0.04
123 177 0.71
124 3 0.01
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.26
Consensus pattern (123 bp):
ATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGAAAGAACAAGTTCATA
ATCTGAAAAACTTATTCAACCTTTTGCTCAACTCTATCACAGAAGGAGATAGAGCAAC
Found at i:981890 original size:3 final size:3
Alignment explanation
Indices: 981869--981933 Score: 87
Period size: 3 Copynumber: 21.7 Consensus size: 3
981859 GTTTTTTGTC
* *
981869 TAT TAT T-T TTT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
981916 TAT ATAT TTT TAT TAT TA
1 TAT -TAT TAT TAT TAT TA
981934 AATAAAATAT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
2 2 0.04
3 50 0.91
4 3 0.05
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:983167 original size:22 final size:21
Alignment explanation
Indices: 983131--983171 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
983121 AATTAAGGCC
*
983131 TTTTAATTTTGATATTTTACG
1 TTTTAATCTTGATATTTTACG
983152 TTTTAATCCTTGATATTTTA
1 TTTTAAT-CTTGATATTTTA
983172 ATAATTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.61
Consensus pattern (21 bp):
TTTTAATCTTGATATTTTACG
Found at i:987239 original size:14 final size:15
Alignment explanation
Indices: 987220--987248 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
987210 TAGTGTATCA
987220 AAATTAAAAA-AAAT
1 AAATTAAAAATAAAT
987234 AAATTAAAAATAAAT
1 AAATTAAAAATAAAT
987249 TGTAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATTAAAAATAAAT
Found at i:988827 original size:40 final size:42
Alignment explanation
Indices: 988776--988891 Score: 146
Period size: 40 Copynumber: 2.8 Consensus size: 42
988766 TGGTTGATCC
* *
988776 ATGGTGATGTTGATCCAACTCCTTACGTGATGGACGAGC-CA
1 ATGGTGATGTTGATCCAACTCCTTAAGTGATGGACGAGCAAA
*
988817 A-GGTGATGTTGATCCAACTCCTTAAGTGATGGATGAGCAAA
1 ATGGTGATGTTGATCCAACTCCTTAAGTGATGGACGAGCAAA
* * * * *
988858 ATGATGGTGTTGTTCCAACTCTTTATGTGATGGA
1 ATGGTGATGTTGATCCAACTCCTTAAGTGATGGA
988892 AACGAGCTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
40 35 0.54
41 3 0.05
42 27 0.42
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (42 bp):
ATGGTGATGTTGATCCAACTCCTTAAGTGATGGACGAGCAAA
Found at i:990717 original size:54 final size:54
Alignment explanation
Indices: 990659--990770 Score: 145
Period size: 54 Copynumber: 2.1 Consensus size: 54
990649 ATCAGAATTA
*
990659 ATCAAGAAACCCCTAAAAATCAGGCTTAG-CTCACTTCCAAATCCATTTGAAAAC
1 ATCAAGAAACCCCTAAAAATCAGGCTTAGTCTC-CTTCAAAATCCATTTGAAAAC
* * * * * *
990713 ATCAAGAAACCCTTGAAAATCGGGCTTAGTTTCTTTCAAAATTCATTTGAAAAC
1 ATCAAGAAACCCCTAAAAATCAGGCTTAGTCTCCTTCAAAATCCATTTGAAAAC
990767 ATCA
1 ATCA
990771 TATTGTTTGG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 48 0.96
55 2 0.04
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (54 bp):
ATCAAGAAACCCCTAAAAATCAGGCTTAGTCTCCTTCAAAATCCATTTGAAAAC
Found at i:992112 original size:27 final size:28
Alignment explanation
Indices: 992046--992112 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
992036 GTTATAAGGC
992046 TTAGGTTGACTTGGGAAGGTAATGTGTT
1 TTAGGTTGACTTGGGAAGGTAATGTGTT
* * * *
992074 TCAGATTAACTTGGGGAGGTAATG-GTT
1 TTAGGTTGACTTGGGAAGGTAATGTGTT
992101 TTAGGTTGACTT
1 TTAGGTTGACTT
992113 CTTTGGTTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
27 12 0.38
28 20 0.62
ACGTcount: A:0.22, C:0.06, G:0.33, T:0.39
Consensus pattern (28 bp):
TTAGGTTGACTTGGGAAGGTAATGTGTT
Found at i:992870 original size:11 final size:11
Alignment explanation
Indices: 992854--992951 Score: 86
Period size: 11 Copynumber: 9.5 Consensus size: 11
992844 TTTGAACTAT
992854 TTTTTTCTCTC
1 TTTTTTCTCTC
*
992865 TTTTTTC-CTT
1 TTTTTTCTCTC
992875 TTTTTTCTC-C
1 TTTTTTCTCTC
992885 TTTTTTCT-T-
1 TTTTTTCTCTC
992894 TTTTTTC-CT-
1 TTTTTTCTCTC
*
992903 TTTGCTT-TCT-
1 TTT-TTTCTCTC
*
992913 TTTTCTCTCTC
1 TTTTTTCTCTC
* *
992924 TTTCTTCTATC
1 TTTTTTCTCTC
992935 TTTTTTCTCTC
1 TTTTTTCTCTC
992946 TTTTTT
1 TTTTTT
992952 ATTTTTTTCT
Statistics
Matches: 70, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
9 12 0.17
10 27 0.39
11 31 0.44
ACGTcount: A:0.01, C:0.23, G:0.01, T:0.74
Consensus pattern (11 bp):
TTTTTTCTCTC
Found at i:992878 original size:10 final size:10
Alignment explanation
Indices: 992853--992905 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
992843 ATTTGAACTA
992853 TTTTTTTCTCT
1 TTTTTTTC-CT
*
992864 CTTTTTTCCT
1 TTTTTTTCCT
992874 TTTTTTT-CT
1 TTTTTTTCCT
*
992883 CCTTTTTT-CT
1 -TTTTTTTCCT
992893 TTTTTTTCCT
1 TTTTTTTCCT
992903 TTT
1 TTT
992906 GCTTTCTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 8 0.22
10 21 0.58
11 7 0.19
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTTTCCT
Found at i:992878 original size:20 final size:19
Alignment explanation
Indices: 992853--992961 Score: 98
Period size: 20 Copynumber: 5.5 Consensus size: 19
992843 ATTTGAACTA
992853 TTTTTTTCTCTCTTTTTTCC
1 TTTTTTTCTCTCTTTTTT-C
992873 TTTTTTT-TCTCCTTTTTTC
1 TTTTTTTCTCT-CTTTTTTC
992892 TTTTTTT-TC-CTTTTGCTTTC
1 TTTTTTTCTCTC-TTT--TTTC
* *
992912 TTTTTCTCTCTCTTTCTTCTA
1 TTTTTTTCTCTCTTT-TT-TC
*
992933 TCTTTTTTCTCTCTTTTTTA
1 T-TTTTTTCTCTCTTTTTTC
992953 TTTTTTTCT
1 TTTTTTTCT
992962 TTTTCTTATT
Statistics
Matches: 78, Mismatches: 3, Indels: 17
0.80 0.03 0.17
Matches are distributed among these distances:
17 1 0.01
18 3 0.04
19 21 0.27
20 30 0.38
21 9 0.12
22 14 0.18
ACGTcount: A:0.02, C:0.22, G:0.01, T:0.75
Consensus pattern (19 bp):
TTTTTTTCTCTCTTTTTTC
Found at i:992965 original size:9 final size:9
Alignment explanation
Indices: 992853--992994 Score: 81
Period size: 9 Copynumber: 15.1 Consensus size: 9
992843 ATTTGAACTA
992853 TTTTTTTCTC
1 TTTTTTT-TC
*
992863 TCTTTTTTCC
1 T-TTTTTTTC
992873 TTTTTTTTC
1 TTTTTTTTC
*
992882 TCCTTTTTTC
1 T-TTTTTTTC
992892 TTTTTTTTCC
1 TTTTTTTT-C
*
992902 TTTTGCTTTC
1 TTTT-TTTTC
*
992912 TTTTTCTCTC
1 TTTTT-TTTC
* *
992922 TCTTTCTTC
1 TTTTTTTTC
992931 TATCTTTTTTC
1 T-T-TTTTTTC
* *
992942 TCTCTTTT-
1 TTTTTTTTC
*
992950 TTATTTTT-
1 TTTTTTTTC
*
992958 TTCTTTTTC
1 TTTTTTTTC
* *
992967 TTATTCTTC
1 TTTTTTTTC
992976 TTTTTTTTC
1 TTTTTTTTC
*
992985 TTTTCTTTC
1 TTTTTTTTC
992994 T
1 T
992995 GTGTTAGCGA
Statistics
Matches: 101, Mismatches: 23, Indels: 17
0.72 0.16 0.12
Matches are distributed among these distances:
8 12 0.12
9 45 0.45
10 28 0.28
11 16 0.16
ACGTcount: A:0.02, C:0.21, G:0.01, T:0.76
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:996146 original size:14 final size:14
Alignment explanation
Indices: 996127--996162 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
996117 AGAAAATAGT
*
996127 AAATTAAAGTAATG
1 AAATTAAAGGAATG
*
996141 AAATTAAAGGACTG
1 AAATTAAAGGAATG
996155 AAATTAAA
1 AAATTAAA
996163 TAAATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.58, C:0.03, G:0.14, T:0.25
Consensus pattern (14 bp):
AAATTAAAGGAATG
Found at i:999528 original size:77 final size:77
Alignment explanation
Indices: 999442--999591 Score: 300
Period size: 77 Copynumber: 1.9 Consensus size: 77
999432 ATTTAAAAAA
999442 ATATTTGGGTTAAAAAACTAAAGCCTTAAACGTGACTGAATGGAAACAAGAAGAGGAAATGTGGT
1 ATATTTGGGTTAAAAAACTAAAGCCTTAAACGTGACTGAATGGAAACAAGAAGAGGAAATGTGGT
999507 GGTGTGAGAAAT
66 GGTGTGAGAAAT
999519 ATATTTGGGTTAAAAAACTAAAGCCTTAAACGTGACTGAATGGAAACAAGAAGAGGAAATGTGGT
1 ATATTTGGGTTAAAAAACTAAAGCCTTAAACGTGACTGAATGGAAACAAGAAGAGGAAATGTGGT
999584 GGTGTGAG
66 GGTGTGAG
999592 CCCTAAATCA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 73 1.00
ACGTcount: A:0.41, C:0.08, G:0.28, T:0.23
Consensus pattern (77 bp):
ATATTTGGGTTAAAAAACTAAAGCCTTAAACGTGACTGAATGGAAACAAGAAGAGGAAATGTGGT
GGTGTGAGAAAT
Found at i:1002300 original size:60 final size:60
Alignment explanation
Indices: 1002227--1002369 Score: 182
Period size: 60 Copynumber: 2.4 Consensus size: 60
1002217 AAAATAGGGT
** *
1002227 AAAG-TACACAAATGGTCCCCTGACTATAGA-ATATTATTTTGTTGAGTCCATCGACTATTA
1 AAAGTTACA-AAATGGTCCCCCAACTATAGAGA-ATTACTTTGTTGAGTCCATCGACTATTA
* * *
1002287 AAAGTTACAAAATGGTCCCCCAACTATAGAGAGTTGCTTTGTTGAGTCCCTCGACTATTA
1 AAAGTTACAAAATGGTCCCCCAACTATAGAGAATTACTTTGTTGAGTCCATCGACTATTA
*
1002347 AATGTTACAAAATGGTCACCCCA
1 AAAGTTACAAAATGGTC-CCCCA
1002370 CTACTTATTA
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
60 63 0.86
61 10 0.14
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (60 bp):
AAAGTTACAAAATGGTCCCCCAACTATAGAGAATTACTTTGTTGAGTCCATCGACTATTA
Found at i:1012666 original size:22 final size:21
Alignment explanation
Indices: 1012641--1012735 Score: 66
Period size: 23 Copynumber: 4.2 Consensus size: 21
1012631 TCATTATAGA
* *
1012641 CATTTTATATGGCAGTTCGGTG
1 CATTTTA-ACGGCACTTCGGTG
*
1012663 CATTTCTACCGGCACTTCGGTG
1 CATTT-TAACGGCACTTCGGTG
*
1012685 CATTTTTACGCGGCACTTCGGTG
1 CA-TTTTA-ACGGCACTTCGGTG
* *
1012708 TAATTCT-ACGTGGCACTTCGGTG
1 -CATTTTAAC--GGCACTTCGGTG
1012731 CATTT
1 CATTT
1012736 ATATGAGCTA
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
21 1 0.02
22 23 0.40
23 33 0.57
24 1 0.02
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.37
Consensus pattern (21 bp):
CATTTTAACGGCACTTCGGTG
Found at i:1012702 original size:23 final size:23
Alignment explanation
Indices: 1012651--1012735 Score: 118
Period size: 23 Copynumber: 3.7 Consensus size: 23
1012641 CATTTTATAT
*
1012651 GGCAGTTCGGTGCATTTCTAC-C
1 GGCACTTCGGTGCATTTCTACGC
*
1012673 GGCACTTCGGTGCATTTTTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
1012696 GGCACTTCGGTGTAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
1012719 GGCACTTCGGTGCATTT
1 GGCACTTCGGTGCATTT
1012736 ATATGAGCTA
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
22 19 0.35
23 35 0.65
ACGTcount: A:0.14, C:0.25, G:0.27, T:0.34
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:1013101 original size:18 final size:18
Alignment explanation
Indices: 1013075--1013112 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1013065 GTAGGTCATT
*
1013075 TTGTTATGTAAATC-AATG
1 TTGTCATGT-AATCAAATG
1013093 TTGTCATGTAATCAAATG
1 TTGTCATGTAATCAAATG
1013111 TT
1 TT
1013113 TAAGTTGTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.45
Consensus pattern (18 bp):
TTGTCATGTAATCAAATG
Found at i:1013596 original size:2 final size:2
Alignment explanation
Indices: 1013589--1013646 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
1013579 GGGCGACCAA
1013589 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
1013631 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
1013647 TATTTTTCAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1014181 original size:14 final size:14
Alignment explanation
Indices: 1014162--1014193 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1014152 TATCTATTTT
1014162 AATATTAAACTCTA
1 AATATTAAACTCTA
*
1014176 AATATTAAACTTTA
1 AATATTAAACTCTA
1014190 AATA
1 AATA
1014194 AGATCAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (14 bp):
AATATTAAACTCTA
Found at i:1020217 original size:49 final size:49
Alignment explanation
Indices: 1020142--1020479 Score: 334
Period size: 49 Copynumber: 6.9 Consensus size: 49
1020132 ATTGCTCTAA
* * *
1020142 AATGCAAGTTAAATTCCTAACGGTGCATTTTTAGCATAAAGGTGCCACT
1 AATGCAAGTTAAATGCCTAACGGTGCATTTTTGGCAGAAAGGTGCCACT
* * * *
1020191 AATGCAAGTTAAATGCCTAACTGTGCATTTTTTGTAGAAATGTGCCACT
1 AATGCAAGTTAAATGCCTAACGGTGCATTTTTGGCAGAAAGGTGCCACT
* * ** * * * * *
1020240 AGTGCAAGTTAGATTACAAATGGTGCATTTATGGAATAAAGGTGCCACT
1 AATGCAAGTTAAATGCCTAACGGTGCATTTTTGGCAGAAAGGTGCCACT
* * * * * ** *
1020289 AATGAAAGGTAAATGCTTAACGATGCATTTTTGGCAGAAATGTGTAATT
1 AATGCAAGTTAAATGCCTAACGGTGCATTTTTGGCAGAAAGGTGCCACT
* * * * ** *
1020338 AATACAAGTTAGATGACAAATTGTGCATTTATGGCAGAAAGGTGCCACT
1 AATGCAAGTTAAATGCCTAACGGTGCATTTTTGGCAGAAAGGTGCCACT
* * **
1020387 AATGCAAGTTAAATACCTAACGGTGAATTTTTTACAGAAAGGTGCCACT
1 AATGCAAGTTAAATGCCTAACGGTGCATTTTTGGCAGAAAGGTGCCACT
* *
1020436 AATGCAAGTTAAATGTCTAACGGTGCATTTTTTGGTAGAAAGGT
1 AATGCAAGTTAAATGCCTAACGGTGCA-TTTTTGGCAGAAAGGT
1020480 ACCATTATCG
Statistics
Matches: 221, Mismatches: 67, Indels: 1
0.76 0.23 0.00
Matches are distributed among these distances:
49 208 0.94
50 13 0.06
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (49 bp):
AATGCAAGTTAAATGCCTAACGGTGCATTTTTGGCAGAAAGGTGCCACT
Found at i:1020554 original size:46 final size:46
Alignment explanation
Indices: 1020482--1020734 Score: 301
Period size: 46 Copynumber: 5.5 Consensus size: 46
1020472 AGAAAGGTAC
* * *
1020482 CATTATCGGCATGAAAGAATGTCATAAATGAAAATGCATAATGGTG
1 CATTATCGACATGAAAGGATGCCATAAATGAAAATGCATAATGGTG
* * *
1020528 CATTATCAACATGAAATGATGCCATAAATGAAAATGCATAACGGTG
1 CATTATCGACATGAAAGGATGCCATAAATGAAAATGCATAATGGTG
* ** * * *
1020574 CATAATCGGTATGAAAAGATGTCGTAAATGAAAATGCATAATGGTG
1 CATTATCGACATGAAAGGATGCCATAAATGAAAATGCATAATGGTG
* *
1020620 CATTATCGACATGAAAGGATGCCATAAATTAAAATGCACAATGGTG
1 CATTATCGACATGAAAGGATGCCATAAATGAAAATGCATAATGGTG
* * * * *
1020666 CATAATAGACATGAAAGGATGCCATAAATAAAAATACATAACGGTG
1 CATTATCGACATGAAAGGATGCCATAAATGAAAATGCATAATGGTG
* * *
1020712 TATTAACGACATAAAAGG-TGCCA
1 CATTATCGACATGAAAGGATGCCA
1020735 CTCATGGTAT
Statistics
Matches: 174, Mismatches: 33, Indels: 1
0.84 0.16 0.00
Matches are distributed among these distances:
45 5 0.03
46 169 0.97
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.24
Consensus pattern (46 bp):
CATTATCGACATGAAAGGATGCCATAAATGAAAATGCATAATGGTG
Found at i:1025267 original size:8 final size:8
Alignment explanation
Indices: 1025254--1025305 Score: 104
Period size: 8 Copynumber: 6.5 Consensus size: 8
1025244 GGGTGTTTAA
1025254 GAAAAGGG
1 GAAAAGGG
1025262 GAAAAGGG
1 GAAAAGGG
1025270 GAAAAGGG
1 GAAAAGGG
1025278 GAAAAGGG
1 GAAAAGGG
1025286 GAAAAGGG
1 GAAAAGGG
1025294 GAAAAGGG
1 GAAAAGGG
1025302 GAAA
1 GAAA
1025306 GTGAAAAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 44 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (8 bp):
GAAAAGGG
Found at i:1026471 original size:49 final size:48
Alignment explanation
Indices: 1026417--1026572 Score: 208
Period size: 49 Copynumber: 3.2 Consensus size: 48
1026407 ATTGCTCTAA
1026417 AATGCAAGTTAAATGCCTAACAGTGCATTTTTGGCAGAAAGGTGCCACT
1 AATGCAAGTTAAATGCCTAAC-GTGCATTTTTGGCAGAAAGGTGCCACT
* * * * * *
1026466 AATGCAAGTTAGATGACAAATGGTGCATTTATGGCAGAAAGGTGCCATT
1 AATGCAAGTTAAATGCCTAA-CGTGCATTTTTGGCAGAAAGGTGCCACT
*
1026515 AATGCAAGTTAAATGCCTAACGATGCA-TTTTGGCATAAAGGTGCCACT
1 AATGCAAGTTAAATGCCTAACG-TGCATTTTTGGCAGAAAGGTGCCACT
1026563 -ATGCAAGTTA
1 AATGCAAGTTA
1026573 TATGATAAAC
Statistics
Matches: 92, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
47 10 0.11
48 19 0.21
49 63 0.68
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (48 bp):
AATGCAAGTTAAATGCCTAACGTGCATTTTTGGCAGAAAGGTGCCACT
Found at i:1026638 original size:46 final size:46
Alignment explanation
Indices: 1026585--1026673 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
1026575 TGATAAACAA
* *
1026585 TGCATTATCAGTATGAAAGGATGTCATAAATGAAAATGCATAACGG
1 TGCATTATCAGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
* *
1026631 TGCATTATCGGCATGAAATGATGCCATAAATGAAAATGCATAA
1 TGCATTATCAGCATGAAAGGATGCCATAAATGAAAATGCATAA
1026674 TGGTAGGATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (46 bp):
TGCATTATCAGCATGAAAGGATGCCATAAATGAAAATGCATAACGG
Found at i:1026665 original size:17 final size:16
Alignment explanation
Indices: 1026643--1026703 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 16
1026633 CATTATCGGC
1026643 ATGAAATGATGCCATAA
1 ATGAAA-GATGCCATAA
1026660 ATGAAA-ATG-CAT-A
1 ATGAAAGATGCCATAA
* *
1026673 ATGGTAGGATGCCATAA
1 AT-GAAAGATGCCATAA
1026690 ATGAAA-ATG-CATAA
1 ATGAAAGATGCCATAA
1026704 CGGTGCATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 11
0.71 0.08 0.22
Matches are distributed among these distances:
13 3 0.08
14 10 0.28
15 9 0.25
16 5 0.14
17 9 0.25
ACGTcount: A:0.48, C:0.10, G:0.20, T:0.23
Consensus pattern (16 bp):
ATGAAAGATGCCATAA
Found at i:1026689 original size:76 final size:76
Alignment explanation
Indices: 1026602--1026749 Score: 260
Period size: 76 Copynumber: 1.9 Consensus size: 76
1026592 TCAGTATGAA
* * *
1026602 AGGATGTCATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAATGATGCCATAAATGAAAA
1 AGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGATGCCATAAATGAAAA
1026667 TGCATAATGGT
66 TGCATAATGGT
*
1026678 AGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGTATAAAAGGATGCCATAAATGAAAA
1 AGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGATGCCATAAATGAAAA
1026743 TGCATAA
66 TGCATAA
1026750 CAGTGCATAA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 68 1.00
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.24
Consensus pattern (76 bp):
AGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGATGCCATAAATGAAAA
TGCATAATGGT
Found at i:1026729 original size:46 final size:46
Alignment explanation
Indices: 1026678--1026805 Score: 175
Period size: 46 Copynumber: 2.8 Consensus size: 46
1026668 GCATAATGGT
* *
1026678 AGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGTATAAA
1 AGGATGCCATAAATGAAAATGCATAACGGTGCATTATAGGCATAAA
* * *
1026724 AGGATGCCATAAATGAAAATGCATAACAGTGCATAATAGGCATGAA
1 AGGATGCCATAAATGAAAATGCATAACGGTGCATTATAGGCATAAA
* * * *
1026770 AGGATGCCACAAATGAAAATACATAATGGTGTATTA
1 AGGATGCCATAAATGAAAATGCATAACGGTGCATTA
1026806 ACAAATGAAA
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.23
Consensus pattern (46 bp):
AGGATGCCATAAATGAAAATGCATAACGGTGCATTATAGGCATAAA
Found at i:1026810 original size:28 final size:28
Alignment explanation
Indices: 1026778--1026831 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
1026768 AAAGGATGCC
1026778 ACAAATGAAAATACATAATGGTGTATTA
1 ACAAATGAAAATACATAATGGTGTATTA
1026806 ACAAATGAAAATACATAATGGTGTAT
1 ACAAATGAAAATACATAATGGTGTAT
1026832 AAAAGATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (28 bp):
ACAAATGAAAATACATAATGGTGTATTA
Found at i:1027374 original size:25 final size:25
Alignment explanation
Indices: 1027328--1027378 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
1027318 TTTCAACGAA
*
1027328 TTTTTTATTTTTGTAATAAAATATTT
1 TTTTTTAATTTTGTAATAAAAT-TTT
1027354 TTTTTTAATTTTG-AA-ACAAATTTT
1 TTTTTTAATTTTGTAATA-AAATTTT
1027378 T
1 T
1027379 ATGGGTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 5 0.22
25 6 0.26
26 12 0.52
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTAATTTTGTAATAAAATTTT
Found at i:1029552 original size:55 final size:55
Alignment explanation
Indices: 1029463--1029910 Score: 568
Period size: 55 Copynumber: 8.2 Consensus size: 55
1029453 CTATGTGTAC
* * *
1029463 TATCAGCACTATGTGTGCAAAACCAC-AGAATTCATAATATGTTTATGAACAACTG
1 TATCGGCACTAAGTGTGCAAAACCACGA-AATTCATAATATGTTTATGAACAACCG
* * *
1029518 TATCGGCACTAAGTGTGCAAAACCACGAAATTCATAATATATTTATAAACTACCG
1 TATCGGCACTAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACAACCG
* * * **
1029573 TATCGGCACTAAGTGTGGAAAACCACAAAATTTATAATATGTTTATGAA-AGATTG
1 TATCGGCACTAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACA-ACCG
* * *
1029628 TATCGGCACTAAGTATGTAAAACCAC-AGAATTCATAATATGCTTATGAACAACCG
1 TATCGGCACTAAGTGTGCAAAACCACGA-AATTCATAATATGTTTATGAACAACCG
* * *
1029683 TATCAGCACTAAGTGTGCAAAACCACGGAATTCAT--T-TGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACAACCG
* * * *
1029735 TATCGACACTAAGTATGAAAAACCACGGAATTCATAATATGTTTATGAACAACCG
1 TATCGGCACTAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACAACCG
* * * *
1029790 TATCAGCACTAAGTGTACAAAACCATGAAATTCATAATATGTTTATGAACTA-CG
1 TATCGGCACTAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACAACCG
*
1029844 ATATCGACACTAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACAACCG
1 -TATCGGCACTAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACAACCG
*
1029900 TATCGACACTA
1 TATCGGCACTA
1029911 CGTATGCACC
Statistics
Matches: 339, Mismatches: 44, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
52 45 0.13
53 1 0.00
54 4 0.01
55 285 0.84
56 4 0.01
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.27
Consensus pattern (55 bp):
TATCGGCACTAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACAACCG
Found at i:1029857 original size:217 final size:219
Alignment explanation
Indices: 1029463--1029903 Score: 611
Period size: 217 Copynumber: 2.0 Consensus size: 219
1029453 CTATGTGTAC
* * *
1029463 TATCAGCACTATGTGTGCAAAACCACAGAATTCATAATATGTTTATGAACAACTGTATCGGCACT
1 TATCAGCACTAAGTGTGCAAAACCACAGAATTCAT-ATATGTTTATGAACAACCGTATCGACACT
* * * * **
1029528 AAGTGTGCAAAACCACGAAATTCATAATATATTTATAAACTACCGTATCGGCACTAAGTGTGGAA
65 AAGTATGAAAAACCACGAAATTCATAATATATTTATAAACAACCGTATCAGCACTAAGTGTACAA
* * * *
1029593 AACCACAAAATTTATAATATGTTTATGAAAGATTGTATCGGCACTAAGTATGTAAAACCAC-AGA
130 AACCACAAAATTCATAATATGTTTATGAAAGATCGTATCGACACTAAGTATGCAAAACCACGA-A
1029657 ATTCATAATATGCTTATGAACAACCG
194 ATTCATAATATGCTTATGAACAACCG
* *
1029683 TATCAGCACTAAGTGTGCAAAACCACGGAATTCAT-T-TGTTTATGAACGACCGTATCGACACTA
1 TATCAGCACTAAGTGTGCAAAACCACAGAATTCATATATGTTTATGAACAACCGTATCGACACTA
* * *
1029746 AGTATGAAAAACCACGGAATTCATAATATGTTTATGAACAACCGTATCAGCACTAAGTGTACAAA
66 AGTATGAAAAACCACGAAATTCATAATATATTTATAAACAACCGTATCAGCACTAAGTGTACAAA
** ** *
1029811 ACCATGAAATTCATAATATGTTTATGAACTA-CGATATCGACACTAAGTGTGCAAAACCACGAAA
131 ACCACAAAATTCATAATATGTTTATGAAAGATCG-TATCGACACTAAGTATGCAAAACCACGAAA
*
1029875 TTCATAATATGTTTATGAACAACCG
195 TTCATAATATGCTTATGAACAACCG
1029900 TATC
1 TATC
1029904 GACACTACGT
Statistics
Matches: 195, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
216 1 0.01
217 159 0.82
218 2 0.01
220 33 0.17
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (219 bp):
TATCAGCACTAAGTGTGCAAAACCACAGAATTCATATATGTTTATGAACAACCGTATCGACACTA
AGTATGAAAAACCACGAAATTCATAATATATTTATAAACAACCGTATCAGCACTAAGTGTACAAA
ACCACAAAATTCATAATATGTTTATGAAAGATCGTATCGACACTAAGTATGCAAAACCACGAAAT
TCATAATATGCTTATGAACAACCG
Found at i:1031957 original size:12 final size:12
Alignment explanation
Indices: 1031940--1031965 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1031930 TTGTTGTTCT
1031940 TGCTCCTCGGGC
1 TGCTCCTCGGGC
1031952 TGCTCCTCGGGC
1 TGCTCCTCGGGC
1031964 TG
1 TG
1031966 TTCAGGCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.38, G:0.35, T:0.27
Consensus pattern (12 bp):
TGCTCCTCGGGC
Found at i:1033623 original size:20 final size:19
Alignment explanation
Indices: 1033600--1033636 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1033590 AGAACCCCAG
*
1033600 GGGGGTATCGATTCCCCTA
1 GGGGGAATCGATTCCCCTA
*
1033619 GGGGGAATCGGTTCCCCT
1 GGGGGAATCGATTCCCCT
1033637 TCAAAGGGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.14, C:0.27, G:0.35, T:0.24
Consensus pattern (19 bp):
GGGGGAATCGATTCCCCTA
Found at i:1037549 original size:22 final size:21
Alignment explanation
Indices: 1037507--1037546 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1037497 GAGTTTATTT
*
1037507 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1037528 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1037547 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1039579 original size:22 final size:22
Alignment explanation
Indices: 1039525--1039580 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
1039515 AAACCATTCA
*
1039525 GGGGGAATCGATACCCCATTGG
1 GGGGGAATCGGTACCCCATTGG
1039547 GGGGGAATCGGTACCCCATTGG
1 GGGGGAATCGGTACCCCATTGG
1039569 GGGGGAATCGGT
1 GGGGGAATCGGT
1039581 TCCCTCTGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.20, C:0.20, G:0.43, T:0.18
Consensus pattern (22 bp):
GGGGGAATCGGTACCCCATTGG
Found at i:1047406 original size:55 final size:55
Alignment explanation
Indices: 1047317--1047652 Score: 473
Period size: 55 Copynumber: 6.1 Consensus size: 55
1047307 GTGTATTATA
* * *
1047317 GACACTAAGTGTGCAAAACCACAAAATTCGTAATATGTTTATGAACAACCGAATC
1 GACACTAAGTGTGCAAAACCACAGAATTCATAATATGTTTATGAACAACCGTATC
*
1047372 AACACTAAGTGTGCAAAACCACAGAATTCATAATATGTTTATGAACAACCGTATC
1 GACACTAAGTGTGCAAAACCACAGAATTCATAATATGTTTATGAACAACCGTATC
* * **
1047427 GACACTAAGTGTACAAAACCAC-GAAATTCATAATATGTTTACGAACAATAGTATC
1 GACACTAAGTGTGCAAAACCACAG-AATTCATAATATGTTTATGAACAACCGTATC
* *
1047482 GACACTAAGCGTGCAAAACCACAGAATTTAT-ATATGTTTATGAACAACCGTATC
1 GACACTAAGTGTGCAAAACCACAGAATTCATAATATGTTTATGAACAACCGTATC
* * *
1047536 -AGCACTAAGTGTGCAAAACCATAGAATTCATAATATGTTTATGAACGACCGTATT
1 GA-CACTAAGTGTGCAAAACCACAGAATTCATAATATGTTTATGAACAACCGTATC
* * *
1047591 GGCACTAACTGTGCAAAACCAC-GAAATTCATAATATGTTTATGAACGACCGTATC
1 GACACTAAGTGTGCAAAACCACAG-AATTCATAATATGTTTATGAACAACCGTATC
1047646 GACACTA
1 GACACTA
1047653 GGTGAACACC
Statistics
Matches: 250, Mismatches: 25, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
53 1 0.00
54 48 0.19
55 200 0.80
56 1 0.00
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.26
Consensus pattern (55 bp):
GACACTAAGTGTGCAAAACCACAGAATTCATAATATGTTTATGAACAACCGTATC
Found at i:1047548 original size:164 final size:164
Alignment explanation
Indices: 1047317--1047652 Score: 521
Period size: 164 Copynumber: 2.0 Consensus size: 164
1047307 GTGTATTATA
*
1047317 GACACTAAGTGTGCAAAACCACAAAATTCGTAATATGTTTATGAACAACCGAATCAACACTAAGT
1 GACACTAAGCGTGCAAAACCACAAAATTC-TAATATGTTTATGAACAACCGAATCAACACTAAGT
*
1047382 GTGCAAAACCACAGAATTCATAATATGTTTATGAACAACCGTATCGACACTAAGTGTACAAAACC
65 GTGCAAAACCACAGAATTCATAATATGTTTATGAACAACCGTATCGACACTAACTGTACAAAACC
*
1047447 ACGAAATTCATAATATGTTTACGAACAATAGTATC
130 ACGAAATTCATAATATGTTTACGAACAACAGTATC
* * *
1047482 GACACTAAGCGTGCAAAACCACAGAATT-TATATATGTTTATGAACAACCGTATCAGCACTAAGT
1 GACACTAAGCGTGCAAAACCACAAAATTCTA-ATATGTTTATGAACAACCGAATCAACACTAAGT
* * * * *
1047546 GTGCAAAACCATAGAATTCATAATATGTTTATGAACGACCGTATTGGCACTAACTGTGCAAAACC
65 GTGCAAAACCACAGAATTCATAATATGTTTATGAACAACCGTATCGACACTAACTGTACAAAACC
* * *
1047611 ACGAAATTCATAATATGTTTATGAACGACCGTATC
130 ACGAAATTCATAATATGTTTACGAACAACAGTATC
1047646 GACACTA
1 GACACTA
1047653 GGTGAACACC
Statistics
Matches: 156, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
163 2 0.01
164 128 0.82
165 26 0.17
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.26
Consensus pattern (164 bp):
GACACTAAGCGTGCAAAACCACAAAATTCTAATATGTTTATGAACAACCGAATCAACACTAAGTG
TGCAAAACCACAGAATTCATAATATGTTTATGAACAACCGTATCGACACTAACTGTACAAAACCA
CGAAATTCATAATATGTTTACGAACAACAGTATC
Found at i:1047678 original size:109 final size:109
Alignment explanation
Indices: 1047340--1047678 Score: 388
Period size: 109 Copynumber: 3.1 Consensus size: 109
1047330 CAAAACCACA
* * * *
1047340 AAATTCGTAATATGTTTATGAACAACCGAATCAACACTAAGTGTGCAAAACCACAGAATTCATAA
1 AAATTCATAATATGTTTATGAACAACCGTATCGACACTAACTGTGCAAAACCACAGAATTCATAA
* * *
1047405 TATGTTTATGAACAACCGTATCGACACTAAGTGTACAAAACC-ACG
66 TATGTTTATGAACAACCGTATCGACACTAGGTG-A-ACAACCAAAG
* ** *
1047450 AAATTCATAATATGTTTACGAACAATAGTATCGACACTAAGC-GTGCAAAACCACAGAATTTAT-
1 AAATTCATAATATGTTTATGAACAACCGTATCGACACTAA-CTGTGCAAAACCACAGAATTCATA
*
1047513 ATATGTTTATGAACAACCGTATC-AGCACTAAGTGTGCAA-AACCATAG
65 ATATGTTTATGAACAACCGTATCGA-CACT-AG-GTG-AACAACCAAAG
* * *
1047560 -AATTCATAATATGTTTATGAACGACCGTATTGGCACTAACTGTGCAAAACCAC-GAAATTCATA
1 AAATTCATAATATGTTTATGAACAACCGTATCGACACTAACTGTGCAAAACCACAG-AATTCATA
* *
1047623 ATATGTTTATGAACGACCGTATCGACACTAGGTGAACACCTCAAAG
65 ATATGTTTATGAACAACCGTATCGACACTAGGTGAACAAC-CAAAG
1047669 AAATT-ATAAT
1 AAATTCATAAT
1047679 GATTTGAAAA
Statistics
Matches: 195, Mismatches: 22, Indels: 25
0.81 0.09 0.10
Matches are distributed among these distances:
107 2 0.01
108 8 0.04
109 93 0.48
110 87 0.45
111 5 0.03
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.26
Consensus pattern (109 bp):
AAATTCATAATATGTTTATGAACAACCGTATCGACACTAACTGTGCAAAACCACAGAATTCATAA
TATGTTTATGAACAACCGTATCGACACTAGGTGAACAACCAAAG
Found at i:1050830 original size:36 final size:36
Alignment explanation
Indices: 1050783--1050887 Score: 183
Period size: 36 Copynumber: 2.9 Consensus size: 36
1050773 ATAGGGTTTG
*
1050783 AATACAAGGCACTATCAAAGCTCCAACCATCTTTCA
1 AATACAAGGCACTATCAAAGCTCAAACCATCTTTCA
* *
1050819 AATACAAGGCACTATCAGAGCTCGAACCATCTTTCA
1 AATACAAGGCACTATCAAAGCTCAAACCATCTTTCA
1050855 AATACAAGGCACTATCAAAGCTCAAACCATCTT
1 AATACAAGGCACTATCAAAGCTCAAACCATCTT
1050888 CAACAATATG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 65 1.00
ACGTcount: A:0.39, C:0.29, G:0.10, T:0.22
Consensus pattern (36 bp):
AATACAAGGCACTATCAAAGCTCAAACCATCTTTCA
Done.