Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168015.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_27, 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: 15675301
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 118000 characters in sequence are not A, C, G, or T
File 79 of 93
Found at i:11896326 original size:5 final size:5
Alignment explanation
Indices: 11896316--11896361 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
11896306 TATAATTTAA
* *
11896316 AATAT AATAT AATAT AATAT AATAAT AAAAT AAAAT AA-AT AA-AT AA
1 AATAT AATAT AATAT AATAT AAT-AT AATAT AATAT AATAT AATAT AA
11896362 ATATTTTATG
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
4 8 0.21
5 27 0.69
6 4 0.10
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (5 bp):
AATAT
Found at i:11896362 original size:13 final size:14
Alignment explanation
Indices: 11896313--11896358 Score: 58
Period size: 13 Copynumber: 3.3 Consensus size: 14
11896303 CATTATAATT
11896313 TAAAATATAATATAA
1 TAAAATATAATA-AA
*
11896328 TATAATATAAT-AA
1 TAAAATATAATAAA
*
11896341 TAAAATAAAATAAA
1 TAAAATATAATAAA
11896355 TAAA
1 TAAA
11896359 TAAATATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 11 0.41
14 6 0.22
15 10 0.37
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
TAAAATATAATAAA
Found at i:11898235 original size:35 final size:35
Alignment explanation
Indices: 11898167--11898244 Score: 88
Period size: 35 Copynumber: 2.2 Consensus size: 35
11898157 GAAAATCGAG
* * *
11898167 ATAAATT-TTTACTTGATTTAATTTTATAATATTT
1 ATAAATTATTTAATTGATTTAATATTAAAATATTT
11898201 ATAAATTATTTAATTAGATTT-ATATTAAAATATTT
1 ATAAATTATTTAATT-GATTTAATATTAAAATATTT
*
11898236 TTAATATTA
1 ATAA-ATTA
11898245 AATTTGATCT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
34 7 0.19
35 21 0.57
36 9 0.24
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (35 bp):
ATAAATTATTTAATTGATTTAATATTAAAATATTT
Found at i:11899649 original size:17 final size:16
Alignment explanation
Indices: 11899612--11899646 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
11899602 ATAAAAATAA
11899612 TTTAAAAAATTTAAAT
1 TTTAAAAAATTTAAAT
11899628 TTTAAAAAATTTAAAT
1 TTTAAAAAATTTAAAT
11899644 TTT
1 TTT
11899647 TAATAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTAAAAAATTTAAAT
Found at i:11906161 original size:52 final size:52
Alignment explanation
Indices: 11906091--11906247 Score: 210
Period size: 52 Copynumber: 3.0 Consensus size: 52
11906081 TATAACTATA
* * *
11906091 CAAACTTGCCCATTAAGAATCTCTCTCTTCTTAGAATTCTTCTCTTATAAGT
1 CAAACTTGCCTATTAAGAATCTCTCTCTTCTTAGAATTCTTCTTTTGTAAGT
* * *
11906143 CAAACTTGCTTATTAAGAATCTCTTTCCTT-TTAGAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATCTCTCT-CTTCTTAGAATTCTTCTTTTGTAAGT
* *
11906195 CAAACTTACCTATTAAGAAT-TCTCTTTCTCTTAGAATTCTTCTTTTGTAAGT
1 CAAACTTGCCTATTAAGAATCTCTCTCT-TCTTAGAATTCTTCTTTTGTAAGT
11906247 C
1 C
11906248 TTCTTGTCCA
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
50 1 0.01
51 5 0.05
52 82 0.90
53 3 0.03
ACGTcount: A:0.26, C:0.22, G:0.08, T:0.44
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCTCTCTCTTCTTAGAATTCTTCTTTTGTAAGT
Found at i:11906333 original size:47 final size:47
Alignment explanation
Indices: 11906259--11906350 Score: 157
Period size: 47 Copynumber: 2.0 Consensus size: 47
11906249 TCTTGTCCAT
*
11906259 CAAGTAATATCTGACAAATCTCAAACAAATCTCAAACAAATCTCTAA
1 CAAGCAATATCTGACAAATCTCAAACAAATCTCAAACAAATCTCTAA
* *
11906306 CAAGCAATATCTGACAAATCTTAAACAAATCTCTAACAAATCTCT
1 CAAGCAATATCTGACAAATCTCAAACAAATCTCAAACAAATCTCT
11906351 TATGAGATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.47, C:0.24, G:0.04, T:0.25
Consensus pattern (47 bp):
CAAGCAATATCTGACAAATCTCAAACAAATCTCAAACAAATCTCTAA
Found at i:11906350 original size:11 final size:11
Alignment explanation
Indices: 11906272--11906350 Score: 79
Period size: 11 Copynumber: 6.9 Consensus size: 11
11906262 GTAATATCTG
*
11906272 ACAAATCTCAA
1 ACAAATCTCTA
*
11906283 ACAAATCTCAA
1 ACAAATCTCTA
11906294 ACAAATCTCTA
1 ACAAATCTCTA
* *
11906305 ACAAGCAATATCTG
1 AC-A--AATCTCTA
11906319 ACAAATCT-TAA
1 ACAAATCTCT-A
11906330 ACAAATCTCTA
1 ACAAATCTCTA
11906341 ACAAATCTCT
1 ACAAATCTCT
11906351 TATGAGATTT
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
10 1 0.02
11 46 0.79
12 2 0.03
13 1 0.02
14 8 0.14
ACGTcount: A:0.48, C:0.25, G:0.03, T:0.24
Consensus pattern (11 bp):
ACAAATCTCTA
Found at i:11907280 original size:52 final size:51
Alignment explanation
Indices: 11907194--11907338 Score: 157
Period size: 52 Copynumber: 2.8 Consensus size: 51
11907184 TATAACCATA
* * * * *
11907194 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTGCCTATTAAGAAT-TCTTTTCTCTTAGAATTCTTCTCCTGCAAGT
* *
11907246 CAAACTTGCCTATTAAGAATTCATTTTCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATTC-TTTTCTCTTAGAATTCTTCTCCTGCAAGT
* * *
11907298 CAAATTTACTTATTAAGAATATTCTTTT-TCTTAGAATTCTT
1 CAAACTTGCCTATTAAG-A-ATTCTTTTCTCTTAGAATTCTT
11907339 TTTTTGTAAG
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
51 1 0.01
52 69 0.87
53 5 0.06
54 4 0.05
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.43
Consensus pattern (51 bp):
CAAACTTGCCTATTAAGAATTCTTTTCTCTTAGAATTCTTCTCCTGCAAGT
Found at i:11909706 original size:2 final size:2
Alignment explanation
Indices: 11909699--11909727 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11909689 AAATGTGCAA
11909699 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
11909728 TGTTTCTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:11920918 original size:2 final size:2
Alignment explanation
Indices: 11920911--11920949 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
11920901 TTAAAGACAA
*
11920911 AT AT AT AT TT 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 AT AT AT A
11920950 AAACTAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:11923517 original size:38 final size:38
Alignment explanation
Indices: 11923461--11923543 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 38
11923451 TTATAATCTA
* * *
11923461 AGCTTAAACATAAAATATAAGAA-TC-GATCAAGCTTTG
1 AGCTCAAACATAAAATATAA-AACTCAAATCAAACTTTG
11923498 AGACTCAAACATAAAATATAAAACTCAAATCAAACTTTG
1 AG-CTCAAACATAAAATATAAAACTCAAATCAAACTTTG
11923537 AGCTCAA
1 AGCTCAA
11923544 GTTTTCGAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
37 4 0.10
38 24 0.60
39 12 0.30
ACGTcount: A:0.49, C:0.17, G:0.10, T:0.24
Consensus pattern (38 bp):
AGCTCAAACATAAAATATAAAACTCAAATCAAACTTTG
Found at i:11924402 original size:46 final size:47
Alignment explanation
Indices: 11924331--11924420 Score: 155
Period size: 46 Copynumber: 1.9 Consensus size: 47
11924321 TTCTAAGGCA
*
11924331 AAAACGAAAAGACTGAGATTGCACAAAG-TCAACTTTCATGTAGCAT
1 AAAACGAAAAGACTGAGATTCCACAAAGTTCAACTTTCATGTAGCAT
*
11924377 AAAACGAAAAGACTGAGATTCCACAAAGTTTAACTTTCATGTAG
1 AAAACGAAAAGACTGAGATTCCACAAAGTTCAACTTTCATGTAG
11924421 TATACTGCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
46 27 0.66
47 14 0.34
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (47 bp):
AAAACGAAAAGACTGAGATTCCACAAAGTTCAACTTTCATGTAGCAT
Found at i:11932304 original size:108 final size:106
Alignment explanation
Indices: 11932139--11932351 Score: 349
Period size: 108 Copynumber: 2.0 Consensus size: 106
11932129 AAGAAGCAAA
* *
11932139 CCATCCATAATAATTTAAATCAAGGTGAATTAAAGCGTCATCTCAAGCCGCACCATAAACTGAAT
1 CCATCCAAAATAATTTAAATCAAGGTGAATTAAAGCATCATCTCAAGCCGCACCATAAACTGAAT
11932204 GCAGAAACATGAGATAAAACCACAATAACTTGTAAAGTTAG
66 GCAGAAACATGAGATAAAACCACAATAACTTGTAAAGTTAG
11932245 CCATCCAAAATAATTTTAAATCAAGGTGAATTTAAAGCATCATCTCAAG--GCACGACATAAACT
1 CCATCCAAAATAA-TTTAAATCAAGGTGAA-TTAAAGCATCATCTCAAGCCGCAC--CATAAACT
*
11932308 GAATGCAGAAGCATGAGATAAAACCACAATAACTTGTAAAGTTA
62 GAATGCAGAAACATGAGATAAAACCACAATAACTTGTAAAGTTA
11932352 ACAATGTGGG
Statistics
Matches: 100, Mismatches: 3, Indels: 6
0.92 0.03 0.06
Matches are distributed among these distances:
106 16 0.16
107 16 0.16
108 68 0.68
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.23
Consensus pattern (106 bp):
CCATCCAAAATAATTTAAATCAAGGTGAATTAAAGCATCATCTCAAGCCGCACCATAAACTGAAT
GCAGAAACATGAGATAAAACCACAATAACTTGTAAAGTTAG
Found at i:11933450 original size:15 final size:15
Alignment explanation
Indices: 11933430--11933459 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11933420 TTACCTCCAT
11933430 CAAGGCTCATAAGAG
1 CAAGGCTCATAAGAG
*
11933445 CAAGGCTGATAAGAG
1 CAAGGCTCATAAGAG
11933460 AACAAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.17, G:0.30, T:0.13
Consensus pattern (15 bp):
CAAGGCTCATAAGAG
Found at i:11935868 original size:6 final size:6
Alignment explanation
Indices: 11935859--11935904 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
11935849 ATTATTTAAT
*
11935859 TTTATA TTTATATA TTTATA TTTAT- TTAAT- TTTATA TTTATA TTTA
1 TTTATA -TT-TATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTA
11935905 AAAAATTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
5 8 0.23
6 19 0.54
7 4 0.11
8 4 0.11
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTATA
Found at i:11935869 original size:16 final size:16
Alignment explanation
Indices: 11935850--11935899 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
11935840 TTTTTAATTA
11935850 TTATTTAATTTTATAT
1 TTATTTAATTTTATAT
*
11935866 TTATAT-A-TTTATAT
1 TTATTTAATTTTATAT
11935880 TTATTTAATTTTATAT
1 TTATTTAATTTTATAT
11935896 TTAT
1 TTAT
11935900 ATTTAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 12 0.40
15 2 0.07
16 16 0.53
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTTAATTTTATAT
Found at i:11935874 original size:8 final size:7
Alignment explanation
Indices: 11935853--11935924 Score: 51
Period size: 7 Copynumber: 10.3 Consensus size: 7
11935843 TTAATTATTA
11935853 TTTA-AT
1 TTTATAT
11935859 TTTATA-
1 TTTATAT
11935865 TTTATAT
1 TTTATAT
11935872 ATTTATAT
1 -TTTATAT
*
11935880 TTATTTAAT
1 TT-TAT-AT
11935889 TTTATA-
1 TTTATAT
11935895 TTTATAT
1 TTTATAT
* * *
11935902 TTAAAAA
1 TTTATAT
*
11935909 ATTATAT
1 TTTATAT
11935916 TTTATAT
1 TTTATAT
11935923 TT
1 TT
11935925 AAAAAATAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 11
0.70 0.14 0.15
Matches are distributed among these distances:
6 16 0.32
7 19 0.38
8 11 0.22
9 4 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTATAT
Found at i:11935911 original size:22 final size:22
Alignment explanation
Indices: 11935864--11935931 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 22
11935854 TTAATTTTAT
***
11935864 ATTTATATATTTATATTTATTTA
1 ATTT-TATATTTATATTTAAAAA
11935887 ATTTTATATTTATATTTAAAAA
1 ATTTTATATTTATATTTAAAAA
*
11935909 ATTATAT-TTTATATTTAAAAA
1 ATTTTATATTTATATTTAAAAA
11935930 AT
1 AT
11935932 AATATTTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 16 0.39
22 21 0.51
23 4 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTTATATTTATATTTAAAAA
Found at i:11935921 original size:21 final size:22
Alignment explanation
Indices: 11935866--11935941 Score: 93
Period size: 21 Copynumber: 3.5 Consensus size: 22
11935856 AATTTTATAT
***
11935866 TTATATATTTATATTTATTTAA
1 TTATATATTTATATTTAAAAAA
*
11935888 TTTTATATTTATATTTAAAAAA
1 TTATATATTTATATTTAAAAAA
11935910 TTATAT-TTTATATTTAAAAAA
1 TTATATATTTATATTTAAAAAA
*
11935931 TAATAT-TTTAT
1 TTATATATTTAT
11935942 TAATTTTGGA
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
21 25 0.52
22 23 0.48
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTATATATTTATATTTAAAAAA
Found at i:11937698 original size:16 final size:16
Alignment explanation
Indices: 11937677--11937709 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
11937667 AACATAATTT
11937677 TTTTATTTTTTAAGGA
1 TTTTATTTTTTAAGGA
11937693 TTTTATTTTTTAAGGA
1 TTTTATTTTTTAAGGA
11937709 T
1 T
11937710 ATTGATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (16 bp):
TTTTATTTTTTAAGGA
Found at i:11939380 original size:21 final size:21
Alignment explanation
Indices: 11939337--11939380 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
11939327 TATTGAAAAT
*
11939337 ATTTATTATTAAATTTATCAA
1 ATTTATTATTAAATTTATAAA
*
11939358 ATTTATTATT-TATTTATTAAA
1 ATTTATTATTAAATTTA-TAAA
11939379 AT
1 AT
11939381 AGTAATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTATTATTAAATTTATAAA
Found at i:11939503 original size:17 final size:15
Alignment explanation
Indices: 11939463--11939507 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 15
11939453 AAATAGTCAT
11939463 ATTATTAAAATATTA
1 ATTATTAAAATATTA
*
11939478 TTATATTAAACATTATTA
1 AT-TATTAAA-A-TATTA
11939496 ATTATTAAAATA
1 ATTATTAAAATA
11939508 ATACAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 3 0.12
16 8 0.32
17 8 0.32
18 6 0.24
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTATTAAAATATTA
Found at i:11943362 original size:27 final size:27
Alignment explanation
Indices: 11943306--11943362 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
11943296 AAAGATAGCA
** * *
11943306 AATTAATTATTTCAAATAATAATAATT
1 AATTAATTATTAAAAATAATAAAAAAT
11943333 AATTAATTATTAAAAATAATAAAAAAT
1 AATTAATTATTAAAAATAATAAAAAAT
11943360 AAT
1 AAT
11943363 GGATATCCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (27 bp):
AATTAATTATTAAAAATAATAAAAAAT
Found at i:11947719 original size:39 final size:39
Alignment explanation
Indices: 11947650--11947736 Score: 111
Period size: 39 Copynumber: 2.2 Consensus size: 39
11947640 GTTCTTCGGT
* * * *
11947650 TGTTGCTGCAGCGGGAGTGTCAATGTAAGCGTGTTTTCA
1 TGTTGCTGCAGCGGAAGTGCCAATGCAAGCGTATTTTCA
* * *
11947689 TGTTGCTGCGGCGGAAGTGCCAGTGCAAGCGTATTTTCG
1 TGTTGCTGCAGCGGAAGTGCCAATGCAAGCGTATTTTCA
11947728 TGTTGCTGC
1 TGTTGCTGC
11947737 TGTTCTTCTG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.15, C:0.18, G:0.34, T:0.32
Consensus pattern (39 bp):
TGTTGCTGCAGCGGAAGTGCCAATGCAAGCGTATTTTCA
Found at i:11958041 original size:8 final size:7
Alignment explanation
Indices: 11958026--11958072 Score: 51
Period size: 7 Copynumber: 6.4 Consensus size: 7
11958016 TAATTAATTA
11958026 ATTTTAT
1 ATTTTAT
11958033 ATTTATAT
1 ATTT-TAT
11958041 ATTTATAT
1 ATTT-TAT
11958049 ATATTTA-
1 AT-TTTAT
*
11958056 ATTTAAT
1 ATTTTAT
11958063 ATTTTAT
1 ATTTTAT
11958070 ATT
1 ATT
11958073 AAAAAATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
6 3 0.09
7 15 0.43
8 15 0.43
9 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
ATTTTAT
Found at i:11960355 original size:2 final size:2
Alignment explanation
Indices: 11960348--11960384 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11960338 TAGTGAAAAT
11960348 TA TA TA TA TA 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 TA TA TA TA TA T
11960385 GAAGCATGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11961363 original size:2 final size:2
Alignment explanation
Indices: 11961356--11961398 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
11961346 AGTTGATGAC
*
11961356 AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT A- AT 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
11961396 AT A
1 AT A
11961399 AGTTTGTTGC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11974572 original size:2 final size:2
Alignment explanation
Indices: 11974565--11974617 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
11974555 TTAACTAGGT
11974565 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
11974607 AG AG AG AG AG A
1 AG AG AG AG AG A
11974618 ACTAACTTTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11986903 original size:2 final size:2
Alignment explanation
Indices: 11986898--11986934 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11986888 AACGGAAGTC
11986898 TA TA TA TA TA 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 TA TA TA TA TA T
11986935 TTTAAATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11989566 original size:9 final size:9
Alignment explanation
Indices: 11989552--11989581 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
11989542 TACAAATTAA
11989552 TTTTTAATT
1 TTTTTAATT
11989561 TTTTTAA-T
1 TTTTTAATT
11989569 TTTTTAATT
1 TTTTTAATT
11989578 TTTT
1 TTTT
11989582 CTCAGCCCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTAATT
Found at i:11989569 original size:16 final size:17
Alignment explanation
Indices: 11989548--11989581 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
11989538 CAATTACAAA
11989548 TTAA-TTTTTAATTTTT
1 TTAATTTTTTAATTTTT
11989564 TTAATTTTTTAATTTTT
1 TTAATTTTTTAATTTTT
11989581 T
1 T
11989582 CTCAGCCCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTAATTTTTTAATTTTT
Found at i:11989571 original size:8 final size:8
Alignment explanation
Indices: 11989548--11989581 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
11989538 CAATTACAAA
11989548 TTAA-TTT
1 TTAATTTT
11989555 TTAATTTTT
1 TTAA-TTTT
11989564 TTAATTTT
1 TTAATTTT
11989572 TTAATTTT
1 TTAATTTT
11989580 TT
1 TT
11989582 CTCAGCCCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 4 0.16
8 14 0.56
9 7 0.28
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTAATTTT
Found at i:11990494 original size:14 final size:14
Alignment explanation
Indices: 11990475--11990516 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
11990465 AATATATTAC
*
11990475 AATAAATTCATAAT
1 AATAAATTAATAAT
11990489 AATAAA-TAATAAT
1 AATAAATTAATAAT
11990502 CAAT-AATTAATAAT
1 -AATAAATTAATAAT
11990516 A
1 A
11990517 CAAAAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 9 0.36
14 16 0.64
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (14 bp):
AATAAATTAATAAT
Found at i:11999257 original size:2 final size:2
Alignment explanation
Indices: 11999252--11999277 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11999242 TCTGGTCTGC
11999252 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
11999278 CCATGTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12000942 original size:25 final size:25
Alignment explanation
Indices: 12000896--12000943 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
12000886 TTTCAAGAGC
*
12000896 ATTTTTTATTTTTCTTGGAATTTAG
1 ATTTTTTATTTTTCTTGAAATTTAG
*
12000921 ATTTTTTTTTCTTTCTT-AAATTT
1 ATTTTTTATT-TTTCTTGAAATTT
12000944 TGAAATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (25 bp):
ATTTTTTATTTTTCTTGAAATTTAG
Found at i:12003632 original size:2 final size:2
Alignment explanation
Indices: 12003625--12003649 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12003615 TTTAAAATAA
12003625 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 A
12003650 AATTGTGGCC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12007022 original size:29 final size:30
Alignment explanation
Indices: 12006980--12007064 Score: 77
Period size: 29 Copynumber: 2.9 Consensus size: 30
12006970 TAAAATTATA
12006980 ATAAAA-TA-TTTAATATAATATTTAAATT
1 ATAAAATTATTTTAATATAATATTTAAATT
* * * * *
12007008 TTAAAATT-TTTTAATGTTATATATGAATT
1 ATAAAATTATTTTAATATAATATTTAAATT
*
12007037 ATAAATTTATTAATTAATATAATATTTA
1 ATAAAATTATT--TTAATATAATATTTA
12007065 TTTTAATATA
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
28 5 0.12
29 23 0.56
30 2 0.05
32 11 0.27
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (30 bp):
ATAAAATTATTTTAATATAATATTTAAATT
Found at i:12007072 original size:17 final size:18
Alignment explanation
Indices: 12007036--12007076 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
12007026 ATATATGAAT
12007036 TATAA-ATTTATTAATTAA
1 TATAATATTTATT-ATTAA
12007054 TATAATATTTATT-TTAA
1 TATAATATTTATTATTAA
12007071 TATAAT
1 TATAAT
12007077 TAATTTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.45
18 5 0.23
19 7 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TATAATATTTATTATTAA
Found at i:12007082 original size:19 final size:19
Alignment explanation
Indices: 12007040--12007083 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
12007030 ATGAATTATA
12007040 AATTTATTAATTAATATAAT
1 AATTTATT-ATTAATATAAT
12007060 -ATTTATT-TTAATATAATT
1 AATTTATTATTAATATAA-T
12007078 AATTTA
1 AATTTA
12007084 AAATAATGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 9 0.41
18 1 0.05
19 12 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AATTTATTATTAATATAAT
Found at i:12008625 original size:12 final size:11
Alignment explanation
Indices: 12008599--12008637 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
12008589 TATTACATTG
*
12008599 TTATTTAATATT
1 TTATTT-ATTTT
12008611 TTATTTATTTAT
1 TTATTTATTT-T
12008623 TTATTTATTTT
1 TTATTTATTTT
12008634 TTAT
1 TTAT
12008638 GTGAATCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 8 0.32
12 17 0.68
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTATTTATTTT
Found at i:12008688 original size:3 final size:3
Alignment explanation
Indices: 12008680--12008704 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12008670 ATTTGAGTGG
12008680 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
12008705 TTCATGTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:12012982 original size:21 final size:20
Alignment explanation
Indices: 12012927--12013011 Score: 68
Period size: 21 Copynumber: 4.2 Consensus size: 20
12012917 TTTTAACGTG
*
12012927 ATAAA-TATAATAATATAAAA
1 ATAAATTATAATAAT-TAATA
* *
12012947 ATAATATATCTTAATAATTTATA
1 ATAA-AT-T-ATAATAATTAATA
*
12012970 ATAAATTTATAATAATAAATA
1 ATAAA-TTATAATAATTAATA
12012991 AT-AATTA-AATAATTAATA
1 ATAAATTATAATAATTAATA
12013009 ATA
1 ATA
12013012 TCAAAAAAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
18 12 0.23
19 3 0.06
20 6 0.12
21 13 0.25
22 2 0.04
23 9 0.17
24 7 0.13
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (20 bp):
ATAAATTATAATAATTAATA
Found at i:12012990 original size:18 final size:18
Alignment explanation
Indices: 12012927--12013011 Score: 59
Period size: 18 Copynumber: 4.6 Consensus size: 18
12012917 TTTTAACGTG
12012927 ATAAAT-ATAA-TAATATA
1 ATAAATAATAATTAA-ATA
*
12012944 A-AAATAATATATCTTAATA
1 ATAAATAATA-AT-TAAATA
**
12012963 ATTTATAATAAATTTATAATA
1 ATAAATAAT-AA-TTA-AATA
12012984 ATAAATAATAATTAAATA
1 ATAAATAATAATTAAATA
*
12013002 ATTAATAATA
1 ATAAATAATA
12013012 TCAAAAAAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 15
0.71 0.09 0.20
Matches are distributed among these distances:
16 4 0.08
17 4 0.08
18 14 0.26
19 7 0.13
20 11 0.21
21 13 0.25
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAAATAATAATTAAATA
Found at i:12013155 original size:11 final size:11
Alignment explanation
Indices: 12013128--12013183 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
12013118 AAAAATTTTT
12013128 TAATTAAAATTAA
1 TAATT-AAA-TAA
12013141 -AATTAAATAA
1 TAATTAAATAA
*
12013151 TAATTAAAAAA
1 TAATTAAATAA
*
12013162 TAATTAAAAAA
1 TAATTAAATAA
* *
12013173 TTATCAAATAA
1 TAATTAAATAA
12013184 ACGATTCAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
10 3 0.08
11 31 0.82
12 4 0.11
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (11 bp):
TAATTAAATAA
Found at i:12013643 original size:14 final size:16
Alignment explanation
Indices: 12013620--12013658 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
12013610 AAAAAACTTA
*
12013620 TAAATGTTAAAA-T-T
1 TAAATTTTAAAATTAT
12013634 TAAATTTTAAAATTAT
1 TAAATTTTAAAATTAT
12013650 TAAATTTTA
1 TAAATTTTA
12013659 TCTCTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.50
15 1 0.05
16 10 0.45
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (16 bp):
TAAATTTTAAAATTAT
Found at i:12013688 original size:13 final size:13
Alignment explanation
Indices: 12013670--12013694 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12013660 CTCTTAAAAA
12013670 TAATTAAATTAAT
1 TAATTAAATTAAT
12013683 TAATTAAATTAA
1 TAATTAAATTAA
12013695 CTTATGAGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TAATTAAATTAAT
Found at i:12015007 original size:39 final size:39
Alignment explanation
Indices: 12014964--12015041 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
12014954 TTGTGGACGG
12014964 ATATATTTTGTGTTTAAAATTATTTAAATTTAATATTTT
1 ATATATTTTGTGTTTAAAATTATTTAAATTTAATATTTT
*
12015003 ATATATTTTGTGTTTAGAATTATTTAAATTTAATATTTT
1 ATATATTTTGTGTTTAAAATTATTTAAATTTAATATTTT
12015042 GAGTTTAGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (39 bp):
ATATATTTTGTGTTTAAAATTATTTAAATTTAATATTTT
Found at i:12015040 original size:30 final size:33
Alignment explanation
Indices: 12014991--12015055 Score: 91
Period size: 30 Copynumber: 2.1 Consensus size: 33
12014981 AATTATTTAA
*
12014991 ATTTAATATTTTATATATTTTGTGTTTAGAATT
1 ATTTAATATTTTATATATTTTGAGTTTAGAATT
*
12015024 ATTTAA-A-TTTA-ATATTTTGAGTTTAGATTT
1 ATTTAATATTTTATATATTTTGAGTTTAGAATT
12015054 AT
1 AT
12015056 ATTTACAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 19 0.63
31 4 0.13
32 1 0.03
33 6 0.20
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.58
Consensus pattern (33 bp):
ATTTAATATTTTATATATTTTGAGTTTAGAATT
Found at i:12015631 original size:83 final size:84
Alignment explanation
Indices: 12015475--12015719 Score: 244
Period size: 83 Copynumber: 2.9 Consensus size: 84
12015465 ATATTTATAG
* * * * ** * * * *
12015475 TTAAATTAAAATCAAAGCCCGTTGCCTACACGTTTAGCCTTGACAAAAGAATTAATATTTATAA-
1 TTAAATCAAAATAAAAGCTCGTGGCCTACACACTTCGCATTGACAAAAAAATTAATTTTTATAAT
* *
12015539 CATTGATTTTGCCGATACA
66 CTTTGATTTTGCCAATACA
* * *
12015558 TTGAATCAAAACT-AAAGCTCGTGGCCTACACACTTCGCTTTGATAAAAAAA-TAATTTTTATAA
1 TTAAATCAAAA-TAAAAGCTCGTGGCCTACACACTTCGCATTGACAAAAAAATTAATTTTTATAA
* **
12015621 TCTTTAATTTTGTTAATACA
65 TCTTTGATTTTGCCAATACA
* *
12015641 TTAAATTAAAATAAAAGCTCGTGGCTTACACACTTCGCATTGACAAAAAAATTAATATTTAATTA
1 TTAAATCAAAATAAAAGCTCGTGGCCTACACACTTCGCATTGACAAAAAAATT-A-ATTT--TTA
12015706 TAATCTTTGATTTT
62 TAATCTTTGATTTT
12015720 ATCTACACGT
Statistics
Matches: 132, Mismatches: 22, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
82 12 0.09
83 97 0.73
84 2 0.02
85 1 0.01
86 4 0.03
88 16 0.12
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (84 bp):
TTAAATCAAAATAAAAGCTCGTGGCCTACACACTTCGCATTGACAAAAAAATTAATTTTTATAAT
CTTTGATTTTGCCAATACA
Found at i:12018029 original size:53 final size:55
Alignment explanation
Indices: 12017947--12018054 Score: 175
Period size: 53 Copynumber: 2.0 Consensus size: 55
12017937 TCCGTTGATG
* *
12017947 CTGATTGAGAACATGACCACCCGAGGTACTATTTCCATTGATACTGATTGAAAAC
1 CTGATTGAGAACATGACCACCCGAGGTACTATGTCCATTGATACTGACTGAAAAC
*
12018002 CTGATTGA-AA-ATGACCACCTGAGGTACTATGTCCATTGATACTGACTGAAAAC
1 CTGATTGAGAACATGACCACCCGAGGTACTATGTCCATTGATACTGACTGAAAAC
12018055 ATGACCACCT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
53 40 0.80
54 2 0.04
55 8 0.16
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (55 bp):
CTGATTGAGAACATGACCACCCGAGGTACTATGTCCATTGATACTGACTGAAAAC
Found at i:12026431 original size:2 final size:2
Alignment explanation
Indices: 12026424--12026451 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12026414 TTAGTTATCA
12026424 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
12026452 GAACTTAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12028409 original size:34 final size:33
Alignment explanation
Indices: 12028330--12028411 Score: 83
Period size: 34 Copynumber: 2.4 Consensus size: 33
12028320 GAAACATCCG
* **
12028330 AAAATAAATTTTTTGAATTTCTTAATGGTTTTCA
1 AAAATAAA-TTTTTGAAGTTCTTAAAAGTTTTCA
* **
12028364 AACATCCATTTTTGAAAGTTCTTAAAAGTTTTCA
1 AAAATAAATTTTTG-AAGTTCTTAAAAGTTTTCA
*
12028398 AAAATAGATTTTTG
1 AAAATAAATTTTTG
12028412 GTACATTGAA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
33 6 0.16
34 32 0.84
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.45
Consensus pattern (33 bp):
AAAATAAATTTTTGAAGTTCTTAAAAGTTTTCA
Found at i:12028824 original size:33 final size:34
Alignment explanation
Indices: 12028787--12028881 Score: 128
Period size: 30 Copynumber: 2.9 Consensus size: 34
12028777 TGCTTTCTGT
* *
12028787 TACATTG-AAACGTTTTCAAAATTGAATTTTTGG
1 TACATTGAAAAAGTTTTCAAAAATGAATTTTTGG
12028820 TACATTGAAAAAGTTTTCAAAAATGAATTTTT-G
1 TACATTGAAAAAGTTTTCAAAAATGAATTTTTGG
*
12028853 ---ATTGAAAAAGTTTTCGAAAATGAATTTTT
1 TACATTGAAAAAGTTTTCAAAAATGAATTTTT
12028882 AGCAACTTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
30 28 0.48
33 8 0.14
34 22 0.38
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.41
Consensus pattern (34 bp):
TACATTGAAAAAGTTTTCAAAAATGAATTTTTGG
Found at i:12030641 original size:20 final size:20
Alignment explanation
Indices: 12030596--12030642 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
12030586 CACTGTTTAA
*
12030596 AATTTTTGGCGTATTTTTCT
1 AATTTTTGACGTATTTTTCT
*
12030616 AGTTTTTGACGTA-TTTTCT
1 AATTTTTGACGTATTTTTCT
12030635 CAATTTTT
1 -AATTTTT
12030643 AATAGAACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.17, C:0.11, G:0.13, T:0.60
Consensus pattern (20 bp):
AATTTTTGACGTATTTTTCT
Found at i:12031153 original size:24 final size:24
Alignment explanation
Indices: 12031126--12031171 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
12031116 TTAATTATCC
12031126 AATGATGAAATTTATA-AAAATTTT
1 AATGAT-AAATTTATATAAAATTTT
* *
12031150 AATGGTAAATTTCTATAAAATT
1 AATGATAAATTTATATAAAATT
12031172 CTTAGGTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (24 bp):
AATGATAAATTTATATAAAATTTT
Found at i:12031687 original size:52 final size:51
Alignment explanation
Indices: 12031630--12031796 Score: 187
Period size: 52 Copynumber: 3.2 Consensus size: 51
12031620 CTTTCCAAAA
*
12031630 AAAAAAGAAA-ATTTCTAAATGGGCCCAAATGGTGAAAATTTTAGAAATTTC
1 AAAAAAGAAAGATTTCTAAAT-GGCCCAAATGGTGAAAAATTTAGAAATTTC
* * ***
12031681 GAAAAAA-AAATATTTCTAAATTGACCCAAATGGTGAAAAATTTAGAAATAAAAA
1 -AAAAAAGAAAGATTTCTAAA-TGGCCCAAATGGTGAAAAATTTAGAAAT--TTC
*
12031735 AATAATAAAAAAGATTTCTAAATGGCCCAAATGGTGAAAAATTTAGAAA-TTC
1 AA-AA-AAGAAAGATTTCTAAATGGCCCAAATGGTGAAAAATTTAGAAATTTC
12031787 AAAAAAGAAA
1 AAAAAAGAAA
12031797 AATATTTTTA
Statistics
Matches: 97, Mismatches: 11, Indels: 16
0.78 0.09 0.13
Matches are distributed among these distances:
50 5 0.05
51 5 0.05
52 42 0.43
53 3 0.03
54 2 0.02
55 28 0.29
56 12 0.12
ACGTcount: A:0.54, C:0.08, G:0.13, T:0.25
Consensus pattern (51 bp):
AAAAAAGAAAGATTTCTAAATGGCCCAAATGGTGAAAAATTTAGAAATTTC
Found at i:12037999 original size:12 final size:12
Alignment explanation
Indices: 12037982--12038009 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
12037972 CACTTTCAAT
12037982 GTAAGATTCCAA
1 GTAAGATTCCAA
12037994 GTAAGATTCCAA
1 GTAAGATTCCAA
12038006 GTAA
1 GTAA
12038010 TGGATATCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (12 bp):
GTAAGATTCCAA
Found at i:12043520 original size:83 final size:83
Alignment explanation
Indices: 12043379--12043550 Score: 249
Period size: 83 Copynumber: 2.1 Consensus size: 83
12043369 ATGATTGTCA
* * *
12043379 AGGAGCATTTTATTTTTAAAAGTTGTGGTTGCCTCTGTTTAGAGGAGCAATTTATTTTCCAACGT
1 AGGAGCAATTTATTTTTAAAAGTTGTGGTTGCCTCTGTTTAGAGGAGCAATTTATTTTCAAAAGT
*
12043444 TATGGTGCCTCTGTTTAG
66 GATGGTGCCTCTGTTTAG
* *
12043462 AGGAGCAATTTATTTTTCAAAA-TTGTGG-TGCCTTTGTTTAGATGAGCAATTTATTTTTCAAAA
1 AGGAGCAATTTATTTTT-AAAAGTTGTGGTTGCCTCTGTTTAGAGGAGCAATTTA-TTTTCAAAA
*
12043525 GTGGTGGTGCCTCTGTTTAG
64 GTGATGGTGCCTCTGTTTAG
12043545 AGGAGC
1 AGGAGC
12043551 TTTTTTCAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
82 23 0.29
83 53 0.66
84 4 0.05
ACGTcount: A:0.23, C:0.12, G:0.24, T:0.41
Consensus pattern (83 bp):
AGGAGCAATTTATTTTTAAAAGTTGTGGTTGCCTCTGTTTAGAGGAGCAATTTATTTTCAAAAGT
GATGGTGCCTCTGTTTAG
Found at i:12043545 original size:42 final size:42
Alignment explanation
Indices: 12043379--12043586 Score: 254
Period size: 41 Copynumber: 5.1 Consensus size: 42
12043369 ATGATTGTCA
*
12043379 AGGAGCATTTTATTTTT-AAAAGTTGTGGTTGCCTCTGTTTAG
1 AGGAGCAATTTATTTTTCAAAAGTTGTGG-TGCCTCTGTTTAG
* * *
12043421 AGGAGCAATTTA-TTTTCCAACGTTATGGTGCCTCTGTTTAG
1 AGGAGCAATTTATTTTTCAAAAGTTGTGGTGCCTCTGTTTAG
*
12043462 AGGAGCAATTTATTTTTCAAAA-TTGTGGTGCCTTTGTTTAG
1 AGGAGCAATTTATTTTTCAAAAGTTGTGGTGCCTCTGTTTAG
* *
12043503 ATGAGCAATTTATTTTTCAAAAGTGGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTATTTTTCAAAAGTTGTGGTGCCTCTGTTTAG
* * *
12043545 AGGAGC----T-TTTTTC-AAAGTTGTTGAGCCTCTATTTAG
1 AGGAGCAATTTATTTTTCAAAAGTTGTGGTGCCTCTGTTTAG
12043581 AGGAGC
1 AGGAGC
12043587 TTTGTTTACT
Statistics
Matches: 147, Mismatches: 16, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
36 25 0.17
37 6 0.04
38 1 0.01
41 67 0.46
42 48 0.33
ACGTcount: A:0.23, C:0.12, G:0.24, T:0.41
Consensus pattern (42 bp):
AGGAGCAATTTATTTTTCAAAAGTTGTGGTGCCTCTGTTTAG
Found at i:12044124 original size:20 final size:20
Alignment explanation
Indices: 12044086--12044124 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12044076 TTAAAATTTT
* *
12044086 CAGCATATTTTTCCTGTTTC
1 CAGCATATTTTCCCAGTTTC
12044106 CAGCATATTTTCCCAGTTT
1 CAGCATATTTTCCCAGTTT
12044125 TCAATAGAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.26, G:0.10, T:0.46
Consensus pattern (20 bp):
CAGCATATTTTCCCAGTTTC
Found at i:12044473 original size:13 final size:13
Alignment explanation
Indices: 12044457--12044494 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
12044447 TTTTTTTATT
12044457 TTTATTTTATTTA
1 TTTATTTTATTTA
* *
12044470 TTTATTTTATGTG
1 TTTATTTTATTTA
12044483 TTTATTTT-TTTA
1 TTTATTTTATTTA
12044495 GTATTTTTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 2 0.10
13 19 0.90
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.76
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:12046095 original size:19 final size:17
Alignment explanation
Indices: 12046071--12046110 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 17
12046061 AAATCACAAC
12046071 TTATCATTTTATTATTATT
1 TTATCATTTTA-T-TTATT
12046090 TTATCATTTTATTTATT
1 TTATCATTTTATTTATT
12046107 TTAT
1 TTAT
12046111 TAGAAAGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.43
18 1 0.05
19 11 0.52
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (17 bp):
TTATCATTTTATTTATT
Found at i:12048059 original size:9 final size:9
Alignment explanation
Indices: 12048047--12048089 Score: 68
Period size: 9 Copynumber: 4.6 Consensus size: 9
12048037 TAAAACTCCA
12048047 AAAAATTTT
1 AAAAATTTT
12048056 AAAAAATTTT
1 -AAAAATTTT
12048066 AAAAATTTT
1 AAAAATTTT
12048075 AAAAATTCTT
1 AAAAATT-TT
12048085 AAAAA
1 AAAAA
12048090 ATTCAAAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
9 16 0.50
10 16 0.50
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (9 bp):
AAAAATTTT
Found at i:12048059 original size:10 final size:10
Alignment explanation
Indices: 12048046--12048150 Score: 99
Period size: 10 Copynumber: 10.4 Consensus size: 10
12048036 ATAAAACTCC
12048046 AAAAAATTTT
1 AAAAAATTTT
12048056 AAAAAATTTT
1 AAAAAATTTT
12048066 -AAAAATTTT
1 AAAAAATTTT
12048075 -AAAAATTCTT
1 AAAAAATT-TT
*
12048085 AAAAAA-TTC
1 AAAAAATTTT
*
12048094 AAAACAATTCT
1 AAAA-AATTTT
12048105 AAAAAATTTT
1 AAAAAATTTT
* * *
12048115 GAAAACTTCTA
1 AAAAAATT-TT
*
12048126 AACAAAATTTA
1 AA-AAAATTTT
12048137 AAAAAATTTT
1 AAAAAATTTT
12048147 AAAA
1 AAAA
12048151 TTTATAACAA
Statistics
Matches: 79, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
9 21 0.27
10 37 0.47
11 16 0.20
12 5 0.06
ACGTcount: A:0.59, C:0.07, G:0.01, T:0.33
Consensus pattern (10 bp):
AAAAAATTTT
Found at i:12048172 original size:30 final size:32
Alignment explanation
Indices: 12048105--12048172 Score: 97
Period size: 30 Copynumber: 2.2 Consensus size: 32
12048095 AAACAATTCT
*
12048105 AAAAAATTTTGAAAACTTCTAAACAAAATTTA
1 AAAAAATTTTGAAAACTTCTAAACAAAAATTA
12048137 AAAAAATTTT-AAAA-TT-TATAACAAAAATTA
1 AAAAAATTTTGAAAACTTCTA-AACAAAAATTA
12048167 AAAAAA
1 AAAAAA
12048173 AAACGAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
29 2 0.06
30 18 0.53
31 4 0.12
32 10 0.29
ACGTcount: A:0.63, C:0.06, G:0.01, T:0.29
Consensus pattern (32 bp):
AAAAAATTTTGAAAACTTCTAAACAAAAATTA
Found at i:12048172 original size:31 final size:32
Alignment explanation
Indices: 12048105--12048173 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
12048095 AAACAATTCT
*
12048105 AAAAAATTTTGAAAACTTCTAAACAAAATTTA
1 AAAAAATTTTGAAAACTTCTAAACAAAATTAA
12048137 AAAAAATTTT-AAAA-TT-TATAACAAAAATTAA
1 AAAAAATTTTGAAAACTTCTA-AAC-AAAATTAA
12048168 AAAAAA
1 AAAAAA
12048174 AACGAAATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
29 2 0.06
30 5 0.15
31 17 0.50
32 10 0.29
ACGTcount: A:0.64, C:0.06, G:0.01, T:0.29
Consensus pattern (32 bp):
AAAAAATTTTGAAAACTTCTAAACAAAATTAA
Found at i:12048255 original size:21 final size:20
Alignment explanation
Indices: 12048214--12048259 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
12048204 TGATAATTTT
*
12048214 AAAATTTCAAAAATTCAAAA
1 AAAATTTCAAAAAATCAAAA
* *
12048234 AAAATTATTAAAAAATCCAAA
1 AAAATT-TCAAAAAATCAAAA
12048255 AAAAT
1 AAAAT
12048260 AAAAATTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAATTTCAAAAAATCAAAA
Found at i:12048284 original size:27 final size:28
Alignment explanation
Indices: 12048251--12048314 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
12048241 TTAAAAAATC
12048251 CAAAAAAATAAAAATTT-TGAAAATTTT
1 CAAAAAAATAAAAATTTCTGAAAATTTT
* * *
12048278 -AATAAAAATTAAATTTTCTTAAAATTTT
1 CAA-AAAAATAAAAATTTCTGAAAATTTT
12048306 CAAAAAAAT
1 CAAAAAAAT
12048315 CATAAAAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 2 0.06
27 12 0.39
28 15 0.48
29 2 0.06
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.36
Consensus pattern (28 bp):
CAAAAAAATAAAAATTTCTGAAAATTTT
Found at i:12048870 original size:29 final size:29
Alignment explanation
Indices: 12048838--12048920 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 29
12048828 TAAAAAAATT
12048838 TTTAGAATTTTTTAAAATTTTTTAGAATG
1 TTTAGAATTTTTTAAAATTTTTTAGAATG
* * *** *
12048867 TTTATAATTTTTAAAAAAAATTTAGAATT
1 TTTAGAATTTTTTAAAATTTTTTAGAATG
* * *
12048896 TTTTGAAAATTTTTAAACTTTTTTA
1 TTTAG-AATTTTTTAAAATTTTTTA
12048921 TTTTTTTTAT
Statistics
Matches: 39, Mismatches: 14, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
29 26 0.67
30 13 0.33
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (29 bp):
TTTAGAATTTTTTAAAATTTTTTAGAATG
Found at i:12048910 original size:20 final size:19
Alignment explanation
Indices: 12048793--12048997 Score: 114
Period size: 20 Copynumber: 10.6 Consensus size: 19
12048783 TTAAGTTTCC
*
12048793 TTAATTTTTTTAAAAATTT
1 TTAAATTTTTTAAAAATTT
* *
12048812 TT--ATTTTTT-TAAGTTT
1 TTAAATTTTTTAAAAATTT
* * * *
12048828 TAAAAAAATTTTTAGAATTTT
1 T--TAAATTTTTTAAAAATTT
* *
12048849 TTAAAATTTTTT-AGAATGT
1 TT-AAATTTTTTAAAAATTT
* **
12048868 TTATAATTTTTAAAAAAAAT
1 TTA-AATTTTTTAAAAATTT
*
12048888 TTAGAATTTTTTGAAAATTT
1 TTA-AATTTTTTAAAAATTT
***
12048908 TTAAACTTTTTT-ATTTTTT
1 TTAAA-TTTTTTAAAAATTT
*
12048927 TTATAATTTTTTAAAAAATT
1 TTA-AATTTTTTAAAAATTT
* **
12048947 CTAAATTTCGTAAAAATTT
1 TTAAATTTTTTAAAAATTT
12048966 TTAGAATTTTTTAAAAATTT
1 TTA-AATTTTTTAAAAATTT
12048986 TTAAAATTTTTT
1 TT-AAATTTTTT
12048998 TTAAAACTTC
Statistics
Matches: 137, Mismatches: 36, Indels: 25
0.69 0.18 0.13
Matches are distributed among these distances:
16 6 0.04
17 6 0.04
18 1 0.01
19 44 0.32
20 73 0.53
21 7 0.05
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (19 bp):
TTAAATTTTTTAAAAATTT
Found at i:12048927 original size:78 final size:78
Alignment explanation
Indices: 12048845--12048997 Score: 193
Period size: 78 Copynumber: 2.0 Consensus size: 78
12048835 ATTTTTAGAA
* ** * *
12048845 TTTTTTAAAATTTTTTAGAATGTT-TATAATTT-TTAAAAAAAATTTAGAATTTTTTGAAAATTT
1 TTTTTTAAAATTTTTTAAAAAATTCTA-AATTTCGT-AAAAAAATTTAGAATTTTTTAAAAATTT
*
12048908 TTAAACTTTTTTATT
64 TTAAAATTTTTTATT
* **
12048923 TTTTTTATAATTTTTTAAAAAATTCTAAATTTCGTAAAAATTTTTAGAATTTTTTAAAAATTTTT
1 TTTTTTAAAATTTTTTAAAAAATTCTAAATTTCGTAAAAAAATTTAGAATTTTTTAAAAATTTTT
12048988 AAAATTTTTT
66 AAAATTTTTT
12048998 TTAAAACTTC
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
78 61 0.95
79 3 0.05
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (78 bp):
TTTTTTAAAATTTTTTAAAAAATTCTAAATTTCGTAAAAAAATTTAGAATTTTTTAAAAATTTTT
AAAATTTTTTATT
Found at i:12050022 original size:2 final size:2
Alignment explanation
Indices: 12050015--12050045 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12050005 TTCATCTATG
12050015 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 A
12050046 CTTTGGCAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12051860 original size:32 final size:32
Alignment explanation
Indices: 12051824--12051885 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
12051814 ACATCAAGAT
12051824 ATATATCTAGCTATGTATTGAAAGTGATTGTA
1 ATATATCTAGCTATGTATTGAAAGTGATTGTA
*
12051856 ATATATCTTGCTATGTATTGAAAGTGATTG
1 ATATATCTAGCTATGTATTGAAAGTGATTG
12051886 CAAGATCGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.42
Consensus pattern (32 bp):
ATATATCTAGCTATGTATTGAAAGTGATTGTA
Found at i:12054656 original size:29 final size:30
Alignment explanation
Indices: 12054609--12054667 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 30
12054599 CAAAGAAATC
12054609 TACAACAATAGATAGGTGAGACAAGTTTCACA
1 TACAACAATAG--AGGTGAGACAAGTTTCACA
12054641 TACAACAATAG-GGTGAGACAAGTTTCA
1 TACAACAATAGAGGTGAGACAAGTTTCA
12054668 TAGCAAATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 16 0.59
32 11 0.41
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.22
Consensus pattern (30 bp):
TACAACAATAGAGGTGAGACAAGTTTCACA
Found at i:12055730 original size:22 final size:22
Alignment explanation
Indices: 12055705--12055753 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
12055695 TGAAAAAATA
12055705 TGTTC-ATGAAATATTTTTGAAG
1 TGTTCAATGAAA-ATTTTTGAAG
*
12055727 TGTTCATATGAAAATTTTTTAAG
1 TGTTCA-ATGAAAATTTTTGAAG
12055750 TGTT
1 TGTT
12055754 TAAAAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 5 0.21
23 13 0.54
24 6 0.25
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.49
Consensus pattern (22 bp):
TGTTCAATGAAAATTTTTGAAG
Found at i:12062688 original size:29 final size:28
Alignment explanation
Indices: 12062646--12062728 Score: 69
Period size: 29 Copynumber: 2.9 Consensus size: 28
12062636 AATAAATATG
* * *
12062646 AATAAAATGAATATAAATAAATAGACACG
1 AATAATATAAATATAAATAAATA-ACACA
* ** *
12062675 ACTAATATAAATATATACGAATTAACACA
1 AATAATATAAATATA-AATAAATAACACA
*
12062704 AATAATATAAATATATATAAA-AACA
1 AATAATATAAATATAAATAAATAACA
12062729 TGATTAAAAT
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
27 4 0.10
28 2 0.05
29 30 0.73
30 5 0.12
ACGTcount: A:0.61, C:0.08, G:0.05, T:0.25
Consensus pattern (28 bp):
AATAATATAAATATAAATAAATAACACA
Found at i:12062836 original size:25 final size:25
Alignment explanation
Indices: 12062778--12062837 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 25
12062768 ACAACTTAAT
* *
12062778 AAATTTAACATATTAATAATATAAAA
1 AAATTT-ACATATTAAAAAAATAAAA
*
12062804 AAGTATTTATATATTAAAAAAATAAAA
1 AA--ATTTACATATTAAAAAAATAAAA
12062831 AAATTTA
1 AAATTTA
12062838 ATACTCATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
25 5 0.17
26 2 0.07
27 18 0.62
28 4 0.14
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (25 bp):
AAATTTACATATTAAAAAAATAAAA
Found at i:12063181 original size:18 final size:18
Alignment explanation
Indices: 12063160--12063194 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12063150 TAAATATAAA
*
12063160 AAATATGTTAAATGTATT
1 AAATATATTAAATGTATT
12063178 AAATATATTAAATGTAT
1 AAATATATTAAATGTAT
12063195 ACTCATATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (18 bp):
AAATATATTAAATGTATT
Found at i:12066881 original size:3 final size:3
Alignment explanation
Indices: 12066867--12066921 Score: 74
Period size: 3 Copynumber: 18.3 Consensus size: 3
12066857 CTACTCTGTT
* * *
12066867 TGA TGA TAA TGA TGA TGA TGA TGA TGA TGA TGA TGA CGA CGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
*
12066915 TAA TGA T
1 TGA TGA T
12066922 TATGGGGATG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.36, C:0.04, G:0.29, T:0.31
Consensus pattern (3 bp):
TGA
Found at i:12071350 original size:165 final size:165
Alignment explanation
Indices: 12071078--12071403 Score: 634
Period size: 165 Copynumber: 2.0 Consensus size: 165
12071068 AACTAAAATA
12071078 ACTGTTAGAAAAATGCTATCTTGGTATCTCTGTATTTTGGGAACTTATCAATACACAATGTTTAG
1 ACTGTTAGAAAAATGCTATCTTGGTATCTCTGTATTTTGGGAACTTATCAATACACAATGTTTAG
*
12071143 ATATTCAGCAAATGTTTTATGAAAAATTCATGTGTGTGGAGGTCCATCATAATAACCCTTTGAAT
66 ATATTCAGCAAATGTTTTATGAAAAATTCATGTGTGTGGAGGTCCACCATAATAACCCTTTGAAT
*
12071208 TTATCCATTAAGCGTTGCTTTTTGGAGGAATACTT
131 TTATCCATTAAGCCTTGCTTTTTGGAGGAATACTT
12071243 ACTGTTAGAAAAATGCTATCTTGGTATCTCTGTATTTTGGGAACTTATCAATACACAATGTTTAG
1 ACTGTTAGAAAAATGCTATCTTGGTATCTCTGTATTTTGGGAACTTATCAATACACAATGTTTAG
12071308 ATATTCAGCAAATGTTTTATGAAAAATTCATGTGTGTGGAGGTCCACCATAATAACCCTTTGAAT
66 ATATTCAGCAAATGTTTTATGAAAAATTCATGTGTGTGGAGGTCCACCATAATAACCCTTTGAAT
12071373 TTATCCATTAAGCCTTGCTTTTTGGAGGAAT
131 TTATCCATTAAGCCTTGCTTTTTGGAGGAAT
12071404 GCTTTGAGTT
Statistics
Matches: 159, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
165 159 1.00
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.38
Consensus pattern (165 bp):
ACTGTTAGAAAAATGCTATCTTGGTATCTCTGTATTTTGGGAACTTATCAATACACAATGTTTAG
ATATTCAGCAAATGTTTTATGAAAAATTCATGTGTGTGGAGGTCCACCATAATAACCCTTTGAAT
TTATCCATTAAGCCTTGCTTTTTGGAGGAATACTT
Found at i:12078107 original size:16 final size:15
Alignment explanation
Indices: 12078069--12078107 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
12078059 TTTTAATTGT
12078069 TTTAAATTTAAAATA
1 TTTAAATTTAAAATA
* *
12078084 TTTTAATTTAAATTCA
1 TTTAAATTTAAAAT-A
12078100 TTTAAATT
1 TTTAAATT
12078108 GAATTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTAAATTTAAAATA
Found at i:12079504 original size:21 final size:21
Alignment explanation
Indices: 12079478--12079520 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
12079468 CTAACCGCTT
12079478 TTTATTTGATAATTTAAAATA
1 TTTATTTGATAATTTAAAATA
12079499 TTTATTTGATAATTTAAAATA
1 TTTATTTGATAATTTAAAATA
12079520 T
1 T
12079521 AATACGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (21 bp):
TTTATTTGATAATTTAAAATA
Found at i:12079543 original size:13 final size:13
Alignment explanation
Indices: 12079514--12079563 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
12079504 TTGATAATTT
**
12079514 AAAATATAATACG
1 AAAATATAATATA
12079527 AAAATATAATATA
1 AAAATATAATATA
*
12079540 AAAATAATATAAATA
1 AAAAT-ATA-ATATA
12079555 AAAATATAA
1 AAAATATAA
12079564 AAGTAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
13 17 0.53
14 6 0.19
15 9 0.28
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (13 bp):
AAAATATAATATA
Found at i:12079550 original size:16 final size:15
Alignment explanation
Indices: 12079529--12079560 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12079519 ATAATACGAA
12079529 AATATAATATAAAAAT
1 AATATAA-ATAAAAAT
12079545 AATATAAATAAAAAT
1 AATATAAATAAAAAT
12079560 A
1 A
12079561 TAAAAGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AATATAAATAAAAAT
Found at i:12079613 original size:21 final size:19
Alignment explanation
Indices: 12079583--12079623 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
12079573 AATTTAAATT
12079583 TTTAAAAAAATTATAAATAAA
1 TTTAAAAAAATTA-AAA-AAA
*
12079604 TTTAATAAAATTAAAAAAA
1 TTTAAAAAAATTAAAAAAA
12079623 T
1 T
12079624 ATATTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 3 0.16
21 12 0.63
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
TTTAAAAAAATTAAAAAAA
Found at i:12092327 original size:18 final size:18
Alignment explanation
Indices: 12092304--12092340 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
12092294 CATAATAATT
*
12092304 TTATTCTTTTCCATTTTA
1 TTATTCTTTTCCAATTTA
12092322 TTATTCTTTTCCAATTTA
1 TTATTCTTTTCCAATTTA
12092340 T
1 T
12092341 CTTTTGCTTC
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:0.19, C:0.16, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATTCTTTTCCAATTTA
Found at i:12098328 original size:21 final size:20
Alignment explanation
Indices: 12098280--12098328 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
12098270 TTATAATTTT
* *
12098280 TTATACATAAAAAGATGTAAT
1 TTATA-ATAAAAAAATGTAAA
12098301 TTAATAATAAAAAAACTGTAAA
1 TT-ATAATAAAAAAA-TGTAAA
12098323 TTATAA
1 TTATAA
12098329 ATTTATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (20 bp):
TTATAATAAAAAAATGTAAA
Found at i:12106376 original size:28 final size:29
Alignment explanation
Indices: 12106343--12106402 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
12106333 ATTCTTTGAT
*
12106343 TTTAAA-AAATTTAAT-CTCTCTAATATTA
1 TTTAAAGAAATTTAATCCT-TATAATATTA
*
12106371 TTTAAAGAAATTTAGTCCTTATAATATTA
1 TTTAAAGAAATTTAATCCTTATAATATTA
12106400 TTT
1 TTT
12106403 TTTAAGAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 6 0.21
29 20 0.71
30 2 0.07
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.48
Consensus pattern (29 bp):
TTTAAAGAAATTTAATCCTTATAATATTA
Found at i:12106537 original size:29 final size:29
Alignment explanation
Indices: 12106443--12106537 Score: 102
Period size: 29 Copynumber: 3.2 Consensus size: 29
12106433 AAGTTCTTTA
* *
12106443 AAAAATAATATTAT-AGAGATTAATTTTTT
1 AAAAATAATATTATAAG-GATTAAATTCTT
**
12106472 AAAAAAATAATATTATAAAAATTAAATTCTT
1 --AAAAATAATATTATAAGGATTAAATTCTT
**
12106503 TTAAATAATATTATAAGGATTAAATTCTT
1 AAAAATAATATTATAAGGATTAAATTCTT
12106532 AAAAAT
1 AAAAAT
12106538 TGAAAAGTAG
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
29 29 0.55
31 23 0.43
32 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (29 bp):
AAAAATAATATTATAAGGATTAAATTCTT
Found at i:12108450 original size:17 final size:16
Alignment explanation
Indices: 12108402--12108453 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
12108392 AATTTTTTAT
12108402 TATAATTTTTATAATT-
1 TATAATTTTTAT-ATTA
* *
12108418 TAAAATTTTAAT-TTA
1 TATAATTTTTATATTA
12108433 TACTAATTTTTATATTA
1 TA-TAATTTTTATATTA
12108450 TATA
1 TATA
12108454 TAGATAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
14 2 0.07
15 2 0.07
16 20 0.69
17 5 0.17
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
TATAATTTTTATATTA
Found at i:12108825 original size:16 final size:17
Alignment explanation
Indices: 12108801--12108840 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
12108791 ATCATAAATA
*
12108801 TATATTTAATAATTATT
1 TATATTTAAAAATTATT
*
12108818 TA-ATTTAAAAATTTTT
1 TATATTTAAAAATTATT
12108834 TATATTT
1 TATATTT
12108841 TTAAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATATTTAAAAATTATT
Found at i:12108918 original size:22 final size:22
Alignment explanation
Indices: 12108893--12108935 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
12108883 AAAGAAGTCA
*
12108893 GTATAATTTTAAATTTAGATAT
1 GTATAATTTTAAATTGAGATAT
12108915 GTATAATTTTAAATTGAGATA
1 GTATAATTTTAAATTGAGATA
12108936 AAATATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.47
Consensus pattern (22 bp):
GTATAATTTTAAATTGAGATAT
Found at i:12112599 original size:2 final size:2
Alignment explanation
Indices: 12112592--12112618 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12112582 CTATAACGCT
12112592 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
12112619 TTCTCTATCT
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:12116054 original size:18 final size:18
Alignment explanation
Indices: 12116031--12116066 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
12116021 TCCTGATCTG
12116031 TATACAGTTTTATGTCTC
1 TATACAGTTTTATGTCTC
*
12116049 TATACATTTTTATGTCTC
1 TATACAGTTTTATGTCTC
12116067 AGGGCCCAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.17, G:0.08, T:0.53
Consensus pattern (18 bp):
TATACAGTTTTATGTCTC
Found at i:12121650 original size:13 final size:13
Alignment explanation
Indices: 12121632--12121656 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12121622 CTTCCATAGC
12121632 TGAAAAAGAAACG
1 TGAAAAAGAAACG
12121645 TGAAAAAGAAAC
1 TGAAAAAGAAAC
12121657 CGAAGATTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.08, G:0.20, T:0.08
Consensus pattern (13 bp):
TGAAAAAGAAACG
Found at i:12123375 original size:32 final size:33
Alignment explanation
Indices: 12123334--12123402 Score: 122
Period size: 32 Copynumber: 2.1 Consensus size: 33
12123324 AAGAAAACCG
12123334 AAATATGAACAAAAAAAAAA-TTACAACTATTA
1 AAATATGAACAAAAAAAAAATTTACAACTATTA
*
12123366 AAATATGAACAAAAAAAAAATTTACTACTATTA
1 AAATATGAACAAAAAAAAAATTTACAACTATTA
12123399 AAAT
1 AAAT
12123403 TTTAATTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 20 0.57
33 15 0.43
ACGTcount: A:0.64, C:0.09, G:0.03, T:0.25
Consensus pattern (33 bp):
AAATATGAACAAAAAAAAAATTTACAACTATTA
Found at i:12123683 original size:16 final size:17
Alignment explanation
Indices: 12123662--12123702 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
12123652 AAATATTAAT
12123662 TTTTTAATT-TAAAATA
1 TTTTTAATTATAAAATA
12123678 TTTTT-ATTATAAAATA
1 TTTTTAATTATAAAATA
12123694 TTATTTAAT
1 TT-TTTAAT
12123703 ATTATTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 3 0.14
16 14 0.64
17 3 0.14
18 2 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTTAATTATAAAATA
Found at i:12125802 original size:38 final size:38
Alignment explanation
Indices: 12125751--12125862 Score: 194
Period size: 38 Copynumber: 3.0 Consensus size: 38
12125741 GATTAAGTGC
*
12125751 AACTCCTTCTTAAATGATCAAAAATGATAAATAAACTT
1 AACTCCTTCTTAAATTATCAAAAATGATAAATAAACTT
12125789 AACTCCTTCTTAAATTATCAAAAATGATAAATAAACTT
1 AACTCCTTCTTAAATTATCAAAAATGATAAATAAACTT
12125827 AACT-C--CTTAAATTATCAAAAATGATAAATAAACTT
1 AACTCCTTCTTAAATTATCAAAAATGATAAATAAACTT
12125862 A
1 A
12125863 CTCTAAAATG
Statistics
Matches: 73, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
35 31 0.42
37 1 0.01
38 41 0.56
ACGTcount: A:0.49, C:0.15, G:0.04, T:0.32
Consensus pattern (38 bp):
AACTCCTTCTTAAATTATCAAAAATGATAAATAAACTT
Found at i:12133656 original size:13 final size:13
Alignment explanation
Indices: 12133633--12133679 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
12133623 TAATTAACTG
*
12133633 TAAATAAAAAAAT
1 TAAATATAAAAAT
*
12133646 TTAATATAAAAAT
1 TAAATATAAAAAT
*
12133659 AAAAATATAAAAAT
1 -TAAATATAAAAAT
12133673 TAAATAT
1 TAAATAT
12133680 TTATTAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
TAAATATAAAAAT
Found at i:12134472 original size:18 final size:19
Alignment explanation
Indices: 12134427--12134472 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
12134417 ATATAATTTA
12134427 TTAATTAAAATAATAAAAAT
1 TTAATT-AAATAATAAAAAT
* *
12134447 ATATTTAAAT-ATAAAAAT
1 TTAATTAAATAATAAAAAT
12134465 TTAATTAA
1 TTAATTAA
12134473 GCTCGTGAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 14 0.64
19 4 0.18
20 4 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAATTAAATAATAAAAAT
Found at i:12134525 original size:137 final size:137
Alignment explanation
Indices: 12134286--12134546 Score: 373
Period size: 137 Copynumber: 1.9 Consensus size: 137
12134276 TTCGAAATAT
*
12134286 TTTATTAATTAAAATAATAAAAATATATTTAAATATAAAAATTTAACTAGACTCGTGAGCTACTC
1 TTTATTAATTAAAATAATAAAAATATATTTAAATATAAAAATTTAACTAGACTCGTGAACTACTC
* * * *
12134351 GAATCAAGTATAAAAATGCTCAAATTCGACTCAATCGATGAATCAAACTATTCGAACTCGAATTC
66 GAATCAAGTATAAAAATACTCAAATTCAACTCAATCGATAAATCAAACTACTCGAACTCGAATTC
12134416 AATATAA
131 AATATAA
* *
12134423 TTTATTAATTAAAATAATAAAAATATATTTAAATATAAAAATTTAATTA-AGCTCGTGAACTATT
1 TTTATTAATTAAAATAATAAAAATATATTTAAATATAAAAATTTAACTAGA-CTCGTGAACTACT
* * * ** *
12134487 TGAAT-AAGATATAAAAATACTCAAATTTAATTTGATCGATAAATCAAATTACTCGAACTC
65 CGAATCAAG-TATAAAAATACTCAAATTCAACTCAATCGATAAATCAAACTACTCGAACTC
12134547 AAGCTCGATT
Statistics
Matches: 109, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
136 4 0.04
137 105 0.96
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (137 bp):
TTTATTAATTAAAATAATAAAAATATATTTAAATATAAAAATTTAACTAGACTCGTGAACTACTC
GAATCAAGTATAAAAATACTCAAATTCAACTCAATCGATAAATCAAACTACTCGAACTCGAATTC
AATATAA
Found at i:12134842 original size:26 final size:27
Alignment explanation
Indices: 12134805--12134874 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 27
12134795 AAAAGAATTT
12134805 ATTAAAATAAATTTTATTAA-TAAAAA
1 ATTAAAATAAATTTTATTAATTAAAAA
*
12134831 ATT-AAATCAAA-TTTATTTAATTAAAAT
1 ATTAAAAT-AAATTTTA-TTAATTAAAAA
12134858 ATTAAAATAAATTTTAT
1 ATTAAAATAAATTTTAT
12134875 CTATTTATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
25 8 0.21
26 10 0.26
27 12 0.32
28 8 0.21
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (27 bp):
ATTAAAATAAATTTTATTAATTAAAAA
Found at i:12140199 original size:67 final size:67
Alignment explanation
Indices: 12140091--12140225 Score: 245
Period size: 67 Copynumber: 2.0 Consensus size: 67
12140081 ACTTTAGAGC
12140091 TGGTTGGACTAGTAGTCCTAGATATTTTACAATCCGTGGTTGAATCAGATTATGAGTGCTGCCAG
1 TGGTTGGACTAGTAGTCCTAGATATTTTACAATCCGTGGTTGAATCAGATTATGAGTGCTGCCAG
12140156 AA
66 AA
*
12140158 TGGTTGGACTAGTAGTTCC-AGATATTTTATAATCCGTGGTTGAATCAGATTATGAGTGCTGCCA
1 TGGTTGGACTAGTAG-TCCTAGATATTTTACAATCCGTGGTTGAATCAGATTATGAGTGCTGCCA
12140222 GAA
65 GAA
12140225 T
1 T
12140226 CAATCAACAC
Statistics
Matches: 66, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
67 63 0.95
68 3 0.05
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (67 bp):
TGGTTGGACTAGTAGTCCTAGATATTTTACAATCCGTGGTTGAATCAGATTATGAGTGCTGCCAG
AA
Found at i:12141265 original size:21 final size:20
Alignment explanation
Indices: 12141241--12141279 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
12141231 AAGTCAAATT
*
12141241 TCTTTTTTATTATTTTTCTTC
1 TCTTATTTATT-TTTTTCTTC
12141262 TCTTATTTATTTTTTTCT
1 TCTTATTTATTTTTTTCT
12141280 AACAATTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (20 bp):
TCTTATTTATTTTTTTCTTC
Found at i:12144561 original size:125 final size:125
Alignment explanation
Indices: 12144339--12144588 Score: 362
Period size: 125 Copynumber: 2.0 Consensus size: 125
12144329 CAATATTTTG
* * *
12144339 AGCATATAAATGATATGCAAAATGAAAAGTTTGTACATATTAACTTGAAATGATCGTATTAGAGA
1 AGCATATAAATGATATACAAAATAAAAAGTTTGTACATATTAACTTGAAATGATCATATTAGAGA
* *
12144404 TTCAATCTCAAGTGAGGGTAATTGTCATAAATGAAAATTGAATTCCAAAATATTTGGTTA
66 TTCAATCTCAAGTGAGGGTAATTCTCATAAATGAAAATTGAATTCCAAAATATTTAGTTA
* * * *
12144464 AGCATATAAATTATATACAAAATAAAAAGTTTAG-ACATATTAGCTTGAAGTGATTATATTAGAG
1 AGCATATAAATGATATACAAAATAAAAAGTTT-GTACATATTAACTTGAAATGATCATATTAGAG
*
12144528 ATTCAATCTCAAGT-AGGGGTAATTACT-ATAAATGAAAATTGTATTCCAAAATATTTAGTTA
65 ATTCAATCTCAAGTGA-GGGTAATT-CTCATAAATGAAAATTGAATTCCAAAATATTTAGTTA
12144589 GTAGTACTAC
Statistics
Matches: 112, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
124 1 0.01
125 109 0.97
126 2 0.02
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.34
Consensus pattern (125 bp):
AGCATATAAATGATATACAAAATAAAAAGTTTGTACATATTAACTTGAAATGATCATATTAGAGA
TTCAATCTCAAGTGAGGGTAATTCTCATAAATGAAAATTGAATTCCAAAATATTTAGTTA
Found at i:12149395 original size:34 final size:33
Alignment explanation
Indices: 12149356--12149457 Score: 136
Period size: 34 Copynumber: 3.0 Consensus size: 33
12149346 TTCTAGAGTT
12149356 TATAATTTTTTGAAAATAAATTTTTAAAAAATCA
1 TATAATTTTTTGAAAAT-AATTTTTAAAAAATCA
* *
12149390 TATAATTTTTTAAAAATGAATTTCTT-AAAAATTA
1 TATAATTTTTTGAAAAT-AATTT-TTAAAAAATCA
12149424 TA-AATTTTTTGAAAATAATTTTTCAAAAAATCA
1 TATAATTTTTTGAAAATAATTTTT-AAAAAATCA
12149457 T
1 T
12149458 CCATTTTGGG
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
31 2 0.03
32 5 0.08
33 21 0.35
34 30 0.50
35 2 0.03
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (33 bp):
TATAATTTTTTGAAAATAATTTTTAAAAAATCA
Found at i:12150031 original size:21 final size:21
Alignment explanation
Indices: 12150005--12150045 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12149995 AAAATTGTTA
12150005 TTTTTTATATTTTAAAATTAT
1 TTTTTTATATTTTAAAATTAT
* *
12150026 TTTTTTATTTTTTAATATTA
1 TTTTTTATATTTTAAAATTA
12150046 AAAATCATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTTTATATTTTAAAATTAT
Found at i:12151860 original size:22 final size:22
Alignment explanation
Indices: 12151835--12151876 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
12151825 TAAATTTTTT
*
12151835 ATTTTTATAT-TATTTTAATAAA
1 ATTTTTA-ATGTATTTAAATAAA
12151857 ATTTTTAATGTATTTAAATA
1 ATTTTTAATGTATTTAAATA
12151877 GATATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
ATTTTTAATGTATTTAAATAAA
Found at i:12152028 original size:24 final size:22
Alignment explanation
Indices: 12151990--12152056 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 22
12151980 TTTTGATTCG
* *
12151990 AAATTTAATTCAAATTTAATATAT
1 AAATTTAATT-AAATTAAATA-AA
12152014 AAATTTAATCTAAATTAAATAAA
1 AAATTTAAT-TAAATTAAATAAA
* *
12152037 AAAATTAATATAAATAAAAT
1 AAATTTAAT-TAAATTAAAT
12152057 GAATCAAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
23 18 0.49
24 18 0.49
25 1 0.03
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (22 bp):
AAATTTAATTAAATTAAATAAA
Found at i:12152331 original size:2 final size:2
Alignment explanation
Indices: 12152324--12152359 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
12152314 GTTAGCATGC
12152324 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12152360 TTGGGAGTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12158106 original size:30 final size:30
Alignment explanation
Indices: 12158071--12158130 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
12158061 TAGTAATATT
12158071 TTAT-TTTAAAT-AAATTATTATATTTTTA
1 TTATATTTAAATAAAATTATTATATTTTTA
* *
12158099 TTATATTTAAATAAAATTTTTATTTTTTTA
1 TTATATTTAAATAAAATTATTATATTTTTA
12158129 TT
1 TT
12158131 TGTGTTAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 4 0.14
29 7 0.25
30 17 0.61
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (30 bp):
TTATATTTAAATAAAATTATTATATTTTTA
Found at i:12158130 original size:25 final size:27
Alignment explanation
Indices: 12158069--12158131 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 27
12158059 TATAGTAATA
12158069 TTTTATTTTAAATAAATTATTATATTTT
1 TTTTA-TTTAAATAAATTATTATATTTT
12158097 TATTATATTTAAATAAAATT-TT-TA-TTT
1 T-TT-TATTTAAAT-AAATTATTATATTTT
12158124 TTTTATTT
1 TTTTATTT
12158132 GTGTTAAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
25 5 0.16
26 2 0.06
27 4 0.12
28 3 0.09
29 11 0.34
30 7 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTTATTTAAATAAATTATTATATTTT
Found at i:12158233 original size:30 final size:30
Alignment explanation
Indices: 12158177--12158242 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
12158167 TGTTAAAATT
* * *
12158177 TTATTTAATTACAAATTAAAGATTAAAGAC
1 TTATTTAAATACAAATTAAAGATTAAAAAA
*
12158207 TTATTTAAATATAAATTAAA-ATTTAAAAAA
1 TTATTTAAATACAAATTAAAGA-TTAAAAAA
12158237 TTATTT
1 TTATTT
12158243 GGGTGTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 1 0.03
30 30 0.97
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (30 bp):
TTATTTAAATACAAATTAAAGATTAAAAAA
Found at i:12172024 original size:25 final size:23
Alignment explanation
Indices: 12171996--12172067 Score: 72
Period size: 25 Copynumber: 3.0 Consensus size: 23
12171986 TGTCTCATTT
*
12171996 TTTTTAAATGTCTCAAAATTATATA
1 TTTTTAAAT-T-TTAAAATTATATA
* *
12172021 TTTTTTAATATTTAAAATTTTTATA
1 TTTTTAAAT-TTTAAAA-TTATATA
*
12172046 TTTTTATATTTTAAAATTATAT
1 TTTTTAAATTTTAAAATTATAT
12172068 TTTATGATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
23 5 0.13
24 12 0.31
25 22 0.56
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (23 bp):
TTTTTAAATTTTAAAATTATATA
Found at i:12172037 original size:24 final size:25
Alignment explanation
Indices: 12172010--12172067 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
12172000 TAAATGTCTC
12172010 AAAATTATATAT-TTTTTA-ATATTT
1 AAAATTATATATATTTTTATAT-TTT
*
12172034 AAAATT-TTTATATTTTTATATTTT
1 AAAATTATATATATTTTTATATTTT
12172058 AAAATTATAT
1 AAAATTATAT
12172068 TTTATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
23 4 0.14
24 21 0.72
25 4 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
AAAATTATATATATTTTTATATTTT
Found at i:12172845 original size:13 final size:15
Alignment explanation
Indices: 12172815--12172847 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12172805 AAAATCTAAA
*
12172815 TTTTGTTATATGATT
1 TTTTCTTATATGATT
12172830 TTTTCTTATAT-ATT
1 TTTTCTTATATGATT
12172844 TTTT
1 TTTT
12172848 AAATTTATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.18, C:0.03, G:0.06, T:0.73
Consensus pattern (15 bp):
TTTTCTTATATGATT
Found at i:12173126 original size:17 final size:17
Alignment explanation
Indices: 12173093--12173125 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12173083 AACCAAAAAA
12173093 AAAAAAACAAAAGTTTT
1 AAAAAAACAAAAGTTTT
*
12173110 AAAAACACAAAA-TTTT
1 AAAAAAACAAAAGTTTT
12173126 TCATGATGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.64, C:0.09, G:0.03, T:0.24
Consensus pattern (17 bp):
AAAAAAACAAAAGTTTT
Found at i:12177056 original size:3 final size:3
Alignment explanation
Indices: 12177048--12177085 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
12177038 CATATTTCCT
12177048 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
12177086 GTGTTCCTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:12181214 original size:29 final size:30
Alignment explanation
Indices: 12181179--12181249 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
12181169 CTAAGAAAAA
*
12181179 TTAAAATTCAAATAA-CAAATTAAAAATTT
1 TTAAAATTCAAAAAATCAAATTAAAAATTT
* *
12181208 TTAAAATT-AAAAAATCACATTAAATATTT
1 TTAAAATTCAAAAAATCAAATTAAAAATTT
12181237 TATAATAATTCAA
1 T-TAA-AATTCAA
12181250 GAACCGAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 5 0.14
29 21 0.60
30 3 0.09
31 4 0.11
32 2 0.06
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (30 bp):
TTAAAATTCAAAAAATCAAATTAAAAATTT
Found at i:12198197 original size:2 final size:2
Alignment explanation
Indices: 12198190--12198235 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
12198180 GTATTCACAT
*
12198190 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GG
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
12198232 GA GA
1 GA GA
12198236 AGTGAAAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Done.