Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015305.1 Kokia drynarioides strain JFW-HI SEQ_130350, 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: 751316
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 443 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:617469 original size:39 final size:39
Alignment explanation
Indices: 617273--617476 Score: 132
Period size: 39 Copynumber: 5.3 Consensus size: 39
617263 ACTATCAACT
*
617273 AATCTCTTACCCCGAGCCT-GGGGCAGATTGCAACCATCC
1 AATCTCTTACCCCGA-TCTAGGGGCAGATTGCAACCATCC
* * * * * * * *
617312 GATCTCTTACCCCGAGCTTGGGGCAGA-TCCTTATCAGCT
1 AATCTCTTACCCCGATCTAGGGGCAGATTGC-AACCATCC
* * * *
617351 AATCTCTTACCCCGAGTCTA-GGGCAAATTAC-GCCATTC
1 AATCTCTTACCCCGA-TCTAGGGGCAGATTGCAACCATCC
* * * * * *
617389 TATCTTTTACCCCGATCTTGGGACAGA-T-CATCATCAACC
1 AATCTCTTACCCCGATCTAGGGGCAGATTGCA--ACCATCC
*
617428 AATCTTTTACCCCGATCTAGGGGCAGATTGCAACCATCC
1 AATCTCTTACCCCGATCTAGGGGCAGATTGCAACCATCC
*
617467 AATATCTTAC
1 AATCTCTTAC
617477 TTAAAAAAAA
Statistics
Matches: 122, Mismatches: 33, Indels: 20
0.70 0.19 0.11
Matches are distributed among these distances:
36 1 0.01
37 4 0.03
38 24 0.20
39 86 0.70
40 5 0.04
41 2 0.02
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (39 bp):
AATCTCTTACCCCGATCTAGGGGCAGATTGCAACCATCC
Found at i:617988 original size:7 final size:7
Alignment explanation
Indices: 617976--618000 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
617966 AATTGAACCC
617976 AATTTTA
1 AATTTTA
617983 AATTTTA
1 AATTTTA
617990 AATTTTA
1 AATTTTA
617997 AATT
1 AATT
618001 ATTTTAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTTTA
Found at i:618024 original size:34 final size:33
Alignment explanation
Indices: 617984--618067 Score: 132
Period size: 34 Copynumber: 2.5 Consensus size: 33
617974 CCAATTTTAA
617984 ATTTTAAATTTTAAATTATTTTAAGTGTAAATTT
1 ATTTTAAA-TTTAAATTATTTTAAGTGTAAATTT
* *
618018 ATTTTAAATTTAAACTTATTTTGAGTTTAAATTT
1 ATTTTAAATTTAAA-TTATTTTAAGTGTAAATTT
618052 ATTTTAAATTTAAATT
1 ATTTTAAATTTAAATT
618068 TAAATTTAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
33 8 0.17
34 39 0.83
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.56
Consensus pattern (33 bp):
ATTTTAAATTTAAATTATTTTAAGTGTAAATTT
Found at i:618031 original size:6 final size:6
Alignment explanation
Indices: 617979--618076 Score: 62
Period size: 6 Copynumber: 16.8 Consensus size: 6
617969 TGAACCCAAT
* * * *
617979 TTTAAA TTTTAAA TTTTAAA -TT-AT TTTAAG TGTAAA TTT-AT TTTAAA
1 TTTAAA -TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * *
618026 TTTAAA CTT-AT TTTGAG TTTAAA TTT-AT TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
618072 TTTAA
1 TTTAA
618077 TTAAAAAAAA
Statistics
Matches: 71, Mismatches: 15, Indels: 11
0.73 0.15 0.11
Matches are distributed among these distances:
4 1 0.01
5 15 0.21
6 42 0.59
7 13 0.18
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:618078 original size:17 final size:17
Alignment explanation
Indices: 617984--618069 Score: 111
Period size: 17 Copynumber: 5.1 Consensus size: 17
617974 CCAATTTTAA
617984 ATTTTAAATTTTAAA-TT
1 ATTTTAAA-TTTAAATTT
* *
618001 ATTTTAAGTGTAAATTT
1 ATTTTAAATTTAAATTT
*
618018 ATTTTAAATTTAAACTT
1 ATTTTAAATTTAAATTT
* *
618035 ATTTTGAGTTTAAATTT
1 ATTTTAAATTTAAATTT
618052 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
618069 A
1 A
618070 AATTTAATTA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
16 5 0.09
17 53 0.91
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.56
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:619385 original size:96 final size:95
Alignment explanation
Indices: 619202--619392 Score: 330
Period size: 98 Copynumber: 2.0 Consensus size: 95
619192 TGCAAATCGG
*
619202 AGCTCTACTTTGAGAGCCCTTCAGAGAAAAATGAGGAAATGCTTTTTTTTTTTCTAAAACAGAAT
1 AGCTCTACTTTGAGAGCCCTTCAGAGAAAAATGAGGAAAAGCTTTTTTTTTTTCTAAAACAGAAT
619267 GAAAATGAATGCTTTCAAAAAAAAAAATTGA
66 GAAAATGAATGCTTTC-AAAAAAAAAATTGA
619298 AGCTCTACTTTGAGAGCCCTTCAGAGAAAAATGA-GAAAAGCTTTTATTTTTTTTTCTAAAACAG
1 AGCTCTACTTTGAGAGCCCTTCAGAGAAAAATGAGGAAAAGC--TT-TTTTTTTTTCTAAAACAG
619362 AATGAAAATGAATGCTTTCAAAAAAAAAATT
63 AATGAAAATGAATGCTTTCAAAAAAAAAATT
619393 CAGCTTAAAT
Statistics
Matches: 91, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
95 6 0.07
96 34 0.37
97 14 0.15
98 37 0.41
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.31
Consensus pattern (95 bp):
AGCTCTACTTTGAGAGCCCTTCAGAGAAAAATGAGGAAAAGCTTTTTTTTTTTCTAAAACAGAAT
GAAAATGAATGCTTTCAAAAAAAAAATTGA
Found at i:619965 original size:29 final size:29
Alignment explanation
Indices: 619823--620235 Score: 267
Period size: 29 Copynumber: 14.2 Consensus size: 29
619813 CTTAAAAACC
* *
619823 ACATTTTAACCCTTAAATTTCACAAAAATT
1 ACATTTTTACCCTTAAACTTC-CAAAAATT
*
619853 ACATTTTAACCCTTAAACATTTCC--AAATT
1 ACATTTTTACCCTTAAAC--TTCCAAAAATT
* * * *
619882 ACATTTTGACCCTCAAACTTTTCTAAAATT
1 ACATTTTTACCCTTAAAC-TTCCAAAAATT
* * *
619912 ACA-TTTTAACCTCAAAATTCTCAAAAATT
1 ACATTTTTACCCTTAAACTTC-CAAAAATT
** * *
619941 ACATTTTTGGCTTTGAACTTCCAAAAATT
1 ACATTTTTACCCTTAAACTTCCAAAAATT
*
619970 ACATTTTTACCCCTAAACTTCC-AAAATT
1 ACATTTTTACCCTTAAACTTCCAAAAATT
* * *
619998 CACGTTTTTACCCTTGATCTTCTCAAAAATT
1 -ACATTTTTACCCTTAAACTTC-CAAAAATT
* ** * *
620029 ACA--TTTGCCCCCAAACTTCTAAAAATC
1 ACATTTTTACCCTTAAACTTCCAAAAATT
*
620056 ACATTTTTACCTTTAAACTTCTCAAAAATT
1 ACATTTTTACCCTTAAACTTC-CAAAAATT
* ** *
620086 ACATTTTTTCCCTCGAACTT--AAAAATC
1 ACATTTTTACCCTTAAACTTCCAAAAATT
*
620113 ATATTTTTATCCC-TAAACTTCTCAAAAATT
1 ACATTTTTA-CCCTTAAACTTC-CAAAAATT
* * * * *
620143 A-AATTTT-GCCTCAAACTTTTCAAAAATC
1 ACATTTTTACCCTTAAAC-TTCCAAAAATT
** *
620171 ACATTTTTACCC-GGAACTTTCCTAAAATT
1 ACATTTTTACCCTTAAAC-TTCCAAAAATT
* *
620200 ACATTTTTACCCCTAAATTATCC-AAAATT
1 ACATTTTTACCCTTAAACT-TCCAAAAATT
620229 ACATTTT
1 ACATTTT
620236 AACCTCGAAC
Statistics
Matches: 298, Mismatches: 63, Indels: 45
0.73 0.16 0.11
Matches are distributed among these distances:
27 29 0.10
28 38 0.13
29 146 0.49
30 75 0.25
31 7 0.02
32 3 0.01
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (29 bp):
ACATTTTTACCCTTAAACTTCCAAAAATT
Found at i:620006 original size:58 final size:58
Alignment explanation
Indices: 619822--620240 Score: 268
Period size: 57 Copynumber: 7.2 Consensus size: 58
619812 TCTTAAAAAC
* * * * * * *
619822 CACATTTTAACCCTTAAATTTCACAAAAATTACATTTTAACCCTTAAACATTTCC-AAATT
1 CACATTTTTACCTTTGAACTTCTCAAAAATTACATTTTTACCC-CAAAC--TTCCAAAATT
* * ** * * * * *
619882 -ACATTTTGACCCTCAAACTTTTCTAAAATTACATTTTAACCTCAAAATTCTCAAAAATT
1 CACATTTTTACCTTTGAACTTCTCAAAAATTACATTTTTACCCCAAACTTC-C-AAAATT
**
619941 -ACATTTTTGGCTTTGAACTTC-CAAAAATTACATTTTTACCCCTAAACTTCCAAAATT
1 CACATTTTTACCTTTGAACTTCTCAAAAATTACATTTTTACCCC-AAACTTCCAAAATT
* * * ** * *
619998 CACGTTTTTACCCTTGATCTTCTCAAAAATTACA-TTTGCCCCCAAACTTCTAAAAAT
1 CACATTTTTACCTTTGAACTTCTCAAAAATTACATTTTTACCCCAAACTTCCAAAATT
* * * *
620055 CACATTTTTACCTTTAAACTTCTCAAAAATTACATTTTTTCCCTCGAACTT--AAAAAT
1 CACATTTTTACCTTTGAACTTCTCAAAAATTACATTTTTACCC-CAAACTTCCAAAATT
* * * * * * * *
620112 CATATTTTTATCC-CTAAACTTCTCAAAAATTA-AATTTTGCCTCAAACTTTTCAAAAAT
1 CACATTTTTA-CCTTTGAACTTCTCAAAAATTACATTTTTACCCCAAAC-TTCCAAAATT
** * *
620170 CACATTTTTACC-CGGAACTT-TCCTAAAATTACATTTTTACCCCTAAATTATCCAAAATT
1 CACATTTTTACCTTTGAACTTCT-CAAAAATTACATTTTTACCCC-AAACT-TCCAAAATT
*
620229 -ACATTTTAACCT
1 CACATTTTTACCT
620241 CGAACTCTCC
Statistics
Matches: 289, Mismatches: 53, Indels: 35
0.77 0.14 0.09
Matches are distributed among these distances:
55 4 0.01
56 13 0.04
57 98 0.34
58 87 0.30
59 87 0.30
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.38
Consensus pattern (58 bp):
CACATTTTTACCTTTGAACTTCTCAAAAATTACATTTTTACCCCAAACTTCCAAAATT
Found at i:620065 original size:57 final size:58
Alignment explanation
Indices: 619803--620182 Score: 317
Period size: 57 Copynumber: 6.5 Consensus size: 58
619793 CTCAAGAGGT
* * * * *
619803 CCTCAAAATTCTTAAAAACCACATTTTAACCCTTAAATTTCACAAAAATTACATTTTAAC
1 CCTCAAACTTC-TAAAAATCACATTTTTACCCTTAAACTTCTCAAAAATTACATTTT-AC
* ** * * * * * *
619863 CCTTAAACATT-TCCAAATTACATTTTGACCCTCAAACTTTTCTAAAATTACATTTTAA
1 CCTCAAAC-TTCTAAAAATCACATTTTTACCCTTAAACTTCTCAAAAATTACATTTTAC
* * ** * *
619921 CCTCAAAATTCTCAAAAATTACATTTTTGGCTTTGAACTTC-CAAAAATTACATTTTTAC
1 CCTCAAACTTCT-AAAAATCACATTTTTACCCTTAAACTTCTCAAAAATTACA-TTTTAC
* * * * * *
619980 CC-CTAAACTTCCAAAATTCACGTTTTTACCCTTGATCTTCTCAAAAATTACA-TTTGC
1 CCTC-AAACTTCTAAAAATCACATTTTTACCCTTAAACTTCTCAAAAATTACATTTTAC
* * *
620037 CCCCAAACTTCTAAAAATCACATTTTTACCTTTAAACTTCTCAAAAATTACATTTTTTC
1 CCTCAAACTTCTAAAAATCACATTTTTACCCTTAAACTTCTCAAAAATTACA-TTTTAC
* * * *
620096 CCTCGAAC-T-TAAAAATCATATTTTTATCCC-TAAACTTCTCAAAAATTAAATTTT-G
1 CCTCAAACTTCTAAAAATCACATTTTTA-CCCTTAAACTTCTCAAAAATTACATTTTAC
*
620151 CCTCAAACTTTTCAAAAATCACATTTTTACCC
1 CCTCAAACTTCT-AAAAATCACATTTTTACCC
620183 GGAACTTTCC
Statistics
Matches: 256, Mismatches: 51, Indels: 29
0.76 0.15 0.09
Matches are distributed among these distances:
55 7 0.03
56 5 0.02
57 89 0.35
58 59 0.23
59 88 0.34
60 6 0.02
61 2 0.01
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.37
Consensus pattern (58 bp):
CCTCAAACTTCTAAAAATCACATTTTTACCCTTAAACTTCTCAAAAATTACATTTTAC
Found at i:620383 original size:15 final size:15
Alignment explanation
Indices: 620356--620397 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
620346 TGATTCATGA
620356 TTCGTAT-TTTATTT
1 TTCGTATATTTATTT
*
620370 TTCTTATATTTA-TT
1 TTCGTATATTTATTT
620384 TTCGTATATTTATT
1 TTCGTATATTTATT
620398 CATTCATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.19, C:0.07, G:0.05, T:0.69
Consensus pattern (15 bp):
TTCGTATATTTATTT
Found at i:632093 original size:137 final size:137
Alignment explanation
Indices: 631847--632124 Score: 538
Period size: 137 Copynumber: 2.0 Consensus size: 137
631837 ATATATGGTA
*
631847 AATTGTAATCACAGTTGCGATCAAGCATGCTTCTTTTATCTTTTTACCTCATTCATTTGTTGTTT
1 AATTGTAATCACAGTTGCGATCAAGCATGCTTCTTTTATCTATTTACCTCATTCATTTGTTGTTT
*
631912 TCAATAAATTTTCTTTTGCACAAAAATTTTCTGCTTTTTGAATAACTTCTGCATAACTGGCTTGG
66 TCAATAAATTTTCTTTTGCACAAAAAATTTCTGCTTTTTGAATAACTTCTGCATAACTGGCTTGG
631977 TATGCAG
131 TATGCAG
631984 AATTGTAATCACAGTTGCGATCAAGCATGCTTCTTTTATCTATTTACCTCATTCATTTGTTGTTT
1 AATTGTAATCACAGTTGCGATCAAGCATGCTTCTTTTATCTATTTACCTCATTCATTTGTTGTTT
632049 TCAATAAATTTTCTTTTGCACAAAAAATTTCTGCTTTTTGAATAACTTCTGCATAACTGGCTTGG
66 TCAATAAATTTTCTTTTGCACAAAAAATTTCTGCTTTTTGAATAACTTCTGCATAACTGGCTTGG
632114 TATGCAG
131 TATGCAG
632121 AATT
1 AATT
632125 CAGATCTTGT
Statistics
Matches: 139, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
137 139 1.00
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.44
Consensus pattern (137 bp):
AATTGTAATCACAGTTGCGATCAAGCATGCTTCTTTTATCTATTTACCTCATTCATTTGTTGTTT
TCAATAAATTTTCTTTTGCACAAAAAATTTCTGCTTTTTGAATAACTTCTGCATAACTGGCTTGG
TATGCAG
Found at i:635092 original size:30 final size:30
Alignment explanation
Indices: 635056--635266 Score: 139
Period size: 30 Copynumber: 7.1 Consensus size: 30
635046 AAAATTTGGT
635056 GTTAAAATGTGATTTTTAAAAAGTTTAGGG
1 GTTAAAATGTGATTTTTAAAAAGTTTAGGG
* ** *
635086 GTTAAAATATG-GCTTTAGAAAGGTTTTA-GG
1 GTTAAAATGTGATTTTTA-AAAAG-TTTAGGG
* ** *
635116 G-TAAAATGTAATTTTTGGAAAGCTTGAGGG
1 GTTAAAATGTGATTTTTAAAAAG-TTTAGGG
*
635146 GTTAAAATGTGATTTTTTTAAAA-TTTA-GG
1 GTTAAAATGTGA-TTTTTAAAAAGTTTAGGG
* *
635175 GTAAAAAT-TGAATTTTTAGAAAGTTT-GAGG
1 GTTAAAATGTG-ATTTTTAAAAAGTTTAG-GG
* * * ** *
635205 GTAAAAATATAATTTTGGAAAAGTTTAGGA
1 GTTAAAATGTGATTTTTAAAAAGTTTAGGG
* * *
635235 GTAAAAATGTAATTTTTAGAAAGTTTAGGG
1 GTTAAAATGTGATTTTTAAAAAGTTTAGGG
635265 GT
1 GT
635267 CAATATAATT
Statistics
Matches: 139, Mismatches: 30, Indels: 24
0.72 0.16 0.12
Matches are distributed among these distances:
28 10 0.07
29 30 0.22
30 76 0.55
31 15 0.11
32 8 0.06
ACGTcount: A:0.37, C:0.01, G:0.24, T:0.38
Consensus pattern (30 bp):
GTTAAAATGTGATTTTTAAAAAGTTTAGGG
Found at i:635122 original size:59 final size:58
Alignment explanation
Indices: 635059--635352 Score: 208
Period size: 60 Copynumber: 5.0 Consensus size: 58
635049 ATTTGGTGTT
* * **
635059 AAAATGTGATTTTTAAAAAGTTTAGGGGTTAAAATATGGCTTTAGAAAGGTTTTAGGGT-
1 AAAATGTAATTTTTAGAAAGTTTAGGGGTTAAAATATGATTTTAGAAA-G-TTTAGGGTA
* * * ** *
635118 AAAATGTAATTTTTGGAAAGCTTGAGGGGTTAAAATGTGATTTTTTTAAAATTTAGGGTA
1 AAAATGTAATTTTTAGAAAG-TTTAGGGGTTAAAATATGA-TTTTAGAAAGTTTAGGGTA
* * *
635178 AAAAT-TGAATTTTTAGAAAGTTT-GAGGGTAAAAATATAATTTTGGAAAAGTTTAGGAGTA
1 AAAATGT-AATTTTTAGAAAGTTTAG-GGGTTAAAATATGATTTTAG-AAAGTTTAGG-GTA
* * *
635238 AAAATGTAATTTTTAGAAAGTTTAGGGG-T-CAATATAATTTTAGAGAAG-TTATGAGGTC
1 AAAATGTAATTTTTAGAAAGTTTAGGGGTTAAAATATGATTTTAGA-AAGTTTA-G-GGTA
* * * * * *
635296 AAAATTTAATTTTGGAGAAA--TTCGAGAGTCAAAATATGATTTCTAAAAAGTTTAGGG
1 AAAATGTAATTTT-TAGAAAGTTTAG-GGGTTAAAATATGATTT-TAGAAAGTTTAGGG
635353 ACCTATTAGT
Statistics
Matches: 187, Mismatches: 30, Indels: 36
0.74 0.12 0.14
Matches are distributed among these distances:
57 7 0.04
58 37 0.20
59 56 0.30
60 73 0.39
61 14 0.07
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.36
Consensus pattern (58 bp):
AAAATGTAATTTTTAGAAAGTTTAGGGGTTAAAATATGATTTTAGAAAGTTTAGGGTA
Found at i:635250 original size:89 final size:87
Alignment explanation
Indices: 635059--635311 Score: 221
Period size: 89 Copynumber: 2.8 Consensus size: 87
635049 ATTTGGTGTT
* * *
635059 AAAATGTGATTTTTA-AAAAGTTTAGGGGTTAAAAT-ATGGCTTTAGAAAGGTTTTAGGGTAAAA
1 AAAATGTAATTTTTAGAAAA-TTTAGGGGTAAAAATAAT---TTTAGAAA-GTTTGAGGGTAAAA
* * *
635122 TGTAATTTTTGG-AAAGCTTGAGGGGTT
61 TATAA-TTTTGGAAAAGCTTGAGGAGTA
* **
635149 AAAATGTGATTTTTTTAAAATTTA-GGGTAAAAATTGAATTTTTAGAAAGTTTGAGGGTAAAAAT
1 AAAATGTAATTTTTAGAAAATTTAGGGGTAAAAA-T-AA-TTTTAGAAAGTTTGAGGGT-AAAAT
*
635213 ATAATTTTGGAAAAG-TTTAGGAGTA
62 ATAATTTTGGAAAAGCTTGAGGAGTA
* * * *
635238 AAAATGTAATTTTTAGAAAGTTTAGGGGTCAATATAATTTTAGAGAAGTTATGA-GGTCAAAATT
1 AAAATGTAATTTTTAGAAAATTTAGGGGTAAAAATAATTTTAGA-AAGTT-TGAGGGT-AAAATA
635302 TAATTTTGGA
63 TAATTTTGGA
635312 GAAATTCGAG
Statistics
Matches: 138, Mismatches: 15, Indels: 22
0.79 0.09 0.13
Matches are distributed among these distances:
87 7 0.05
88 25 0.18
89 54 0.39
90 46 0.33
91 4 0.03
92 1 0.01
93 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.38
Consensus pattern (87 bp):
AAAATGTAATTTTTAGAAAATTTAGGGGTAAAAATAATTTTAGAAAGTTTGAGGGTAAAATATAA
TTTTGGAAAAGCTTGAGGAGTA
Found at i:635308 original size:30 final size:28
Alignment explanation
Indices: 635174--635348 Score: 99
Period size: 30 Copynumber: 5.9 Consensus size: 28
635164 TAAAATTTAG
635174 GGTAAAAAT-TGAATTTTTAGAAAGTTTGA
1 GGTAAAAATAT-AA-TTTTAGAAAGTTTGA
*
635203 GGGTAAAAATATAATTTTGGAAAAGTTT-A
1 -GGTAAAAATATAATTTTAG-AAAGTTTGA
* *
635232 GGAGTAAAAATGTAATTTTTAGAAAGTTTAGG
1 -G-GTAAAAATATAA-TTTTAGAAAGTTT-GA
*
635264 GGT--CAATATAATTTTAGAGAAGTTATGA
1 GGTAAAAATATAATTTTAGA-AAGTT-TGA
* * *
635292 GGTCAAAATTTAATTTTGGAGAAA-TTCGA
1 GGTAAAAATATAATTTT--AGAAAGTTTGA
* * *
635321 GAGTCAAAATATGATTTCTAAAAAGTTT
1 G-GTAAAAATATAATTT-TAGAAAGTTT
635349 AGGGACCTAT
Statistics
Matches: 116, Mismatches: 14, Indels: 30
0.73 0.09 0.19
Matches are distributed among these distances:
27 7 0.06
28 15 0.13
29 16 0.14
30 65 0.56
31 10 0.09
32 3 0.03
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (28 bp):
GGTAAAAATATAATTTTAGAAAGTTTGA
Found at i:635330 original size:88 final size:87
Alignment explanation
Indices: 635067--635352 Score: 201
Period size: 88 Copynumber: 3.2 Consensus size: 87
635057 TTAAAATGTG
* * * * *
635067 ATTTTTAAAAAGTTTAGGGGTTAAAAT-ATGGCTTTAGAAAGGTTTTAGGGT-AAAATGTAATTT
1 ATTTCTAAAAAGTTTAGGGGTCAATATAAT---TTTAGAAA-GTTTGAGGGTAAAAATATAA-TT
* * *
635130 TTGG-AAAGCTTGAGGGGTTAAAATGTGA
61 TTGGAAAAG-TTGAGGAGTAAAAATAT-A
* * * * *
635158 TTTTTTTAAAA-TTTA-GGGTAAAAATTGAATTTTTAGAAAGTTTGAGGGTAAAAATATAATTTT
1 ATTTCTAAAAAGTTTAGGGGTCAATA-T-AA-TTTTAGAAAGTTTGAGGGTAAAAATATAATTTT
* *
635221 GGAAAAGTTTAGGAGTAAAAATGTA
63 GGAAAAGTTGAGGAGTAAAAATATA
* * * *
635246 ATTTTTAGAAAGTTTAGGGGTCAATATAATTTTAGAGAAGTTATGA-GGTCAAAATTTAATTTTG
1 ATTTCTAAAAAGTTTAGGGGTCAATATAATTTTAGA-AAGTT-TGAGGGTAAAAATATAATTTTG
* *
635310 GAGAAA-TTCGA-GAGTCAAAATATG
64 GA-AAAGTT-GAGGAGTAAAAATATA
635334 ATTTCTAAAAAGTTTAGGG
1 ATTTCTAAAAAGTTTAGGG
635353 ACCTATTAGT
Statistics
Matches: 162, Mismatches: 21, Indels: 27
0.77 0.10 0.13
Matches are distributed among these distances:
87 7 0.04
88 63 0.39
89 49 0.30
90 32 0.20
91 9 0.06
92 1 0.01
93 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.37
Consensus pattern (87 bp):
ATTTCTAAAAAGTTTAGGGGTCAATATAATTTTAGAAAGTTTGAGGGTAAAAATATAATTTTGGA
AAAGTTGAGGAGTAAAAATATA
Found at i:636252 original size:19 final size:20
Alignment explanation
Indices: 636230--636272 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
636220 TTTGTGCACA
*
636230 TTTT-CTCTTTTTAAATCTG
1 TTTTCCTCTTTTTAAAACTG
*
636249 TTTTCCTTTTTTTAAAACTG
1 TTTTCCTCTTTTTAAAACTG
636269 TTTT
1 TTTT
636273 TTACGTGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.16, C:0.14, G:0.05, T:0.65
Consensus pattern (20 bp):
TTTTCCTCTTTTTAAAACTG
Found at i:636474 original size:10 final size:10
Alignment explanation
Indices: 636461--636508 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
636451 CAATTAATAA
636461 ATATATTAAT
1 ATATATTAAT
*
636471 ATATAATAAAT
1 ATAT-ATTAAT
* *
636482 AAATGTTAA-
1 ATATATTAAT
636491 ATATATTAAT
1 ATATATTAAT
636501 ATATATTA
1 ATATATTA
636509 GAAACGTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
9 7 0.23
10 15 0.50
11 8 0.27
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (10 bp):
ATATATTAAT
Found at i:637629 original size:39 final size:39
Alignment explanation
Indices: 637516--638112 Score: 334
Period size: 39 Copynumber: 15.4 Consensus size: 39
637506 TCCGCCTCTA
* *
637516 GCTCGGGGTAAGAGATTGGCTGATAGT-ATCTGCC-CAG
1 GCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCTCAG
* ** *
637553 GCTCGGGGTAATAGA-T--CAGATGGCTACAATCTGCCTCAG
1 GCTCGGGGTAAGAGATTGGTTGATGG-T--GATCTGCCTCAG
* * * *
637592 GCTCGAGGTAAGAGATTGGCTGATGATGATCTACCTCAG
1 GCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCTCAG
* * * * * ** *
637631 GCTCGGGGTAAAAGATCGGATGGTTGCAATCTACC-CTAG
1 GCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCTC-AG
* * *
637670 GCTTGGGGTAAGAGATTGGTTGATGGTGATCTGCCTTAA
1 GCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCTCAG
*
637709 GCTCGGGGTAAAAGATTGGTTGATGGTGATCTGCCTCAG
1 GCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCTCAG
* * *** * * *
637748 GCTCGGGGTAAAAGATCGAAAGGCT-ATAATCTGCC-CTAG
1 GCTCGGGGTAAGAGATTG-GTTGATGGTGATCTGCCTC-AG
* * *
637787 GCTCAGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAA
1 GCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCTCAG
* * * *
637826 GCTCGGGGTAAGAGATTGGCTGGTGGTGATCTGCCCCAA
1 GCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCTCAG
* * * * * * * * *
637865 GCTTGAGGTAAGAGATTGGCTG--GCTACAATTTACCCCAA
1 GCTCGGGGTAAGAGATTGGTTGATGGT--GATCTGCCTCAG
*
637904 GCTCAGGGTAAGAGATTGGTTGAT-GTGATCTGCC-CTAG
1 GCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCTC-AG
** *
637942 GCTCGGGGTAAGAGA-T--CAGATGGCTGCAATCTGCCCCAG
1 GCTCGGGGTAAGAGATTGGTTGATGG-TG--ATCTGCCTCAG
** * * * *
637981 GCTCGGGG-AAGAGATTGACTAATGATGATCTGTCTTAG
1 GCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCTCAG
* *
638019 GCTCGGGGTAAAAGA-TCG--GATGGCTGCAATCTGCC-CTAG
1 GCTCGGGGTAAGAGATTGGTTGATGG-TG--ATCTGCCTC-AG
* * * *
638058 GCTCGGGGTAAAAGATTGGCTAATGGTGATCTGCCTCAA
1 GCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCTCAG
**
638097 GCTTAGGGTAAGAGAT
1 GCTCGGGGTAAGAGAT
638113 CGGATGGTTG
Statistics
Matches: 434, Mismatches: 90, Indels: 70
0.73 0.15 0.12
Matches are distributed among these distances:
34 5 0.01
35 4 0.01
36 5 0.01
37 22 0.05
38 54 0.12
39 317 0.73
40 11 0.03
41 7 0.02
42 9 0.02
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.25
Consensus pattern (39 bp):
GCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCTCAG
Found at i:637661 original size:78 final size:78
Alignment explanation
Indices: 637516--638267 Score: 589
Period size: 78 Copynumber: 9.7 Consensus size: 78
637506 TCCGCCTCTA
* *
637516 GCTCGGGGTAAGAGATTGGCTGAT-A-GTATCTGCC-CAGGCTCGGGGTAATAGATCAGATGGCT
1 GCTCGGGGTAAGAGATTGGCTGATGATG-ATCTGCCTCAGGCTCGGGGTAAAAGATCGGATGGCT
* *
637578 ACAATCTGCCTCAG
65 GCAATCTGCCCCAG
* * *
637592 GCTCGAGGTAAGAGATTGGCTGATGATGATCTACCTCAGGCTCGGGGTAAAAGATCGGATGGTTG
1 GCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCTCAGGCTCGGGGTAAAAGATCGGATGGCTG
* *
637657 CAATCTACCCTAG
66 CAATCTGCCCCAG
* * * * * *
637670 GCTTGGGGTAAGAGATTGGTTGATGGTGATCTGCCTTAAGCTCGGGGTAAAAGATTGGTTGATGG
1 GCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCTCAGGCTCGGGGTAAAAGA-TCG--GATGG
*
637735 -TG--ATCTGCCTCAG
63 CTGCAATCTGCCCCAG
* * *** * * * * *
637748 GCTCGGGGTAAAAGATCGAAAGGCT-ATAATCTGCC-CTAGGCTCAGGGTAAGAGATTGGTTGAT
1 GCTCGGGGTAAGAGATTG-GCTGATGATGATCTGCCTC-AGGCTCGGGGTAAAAGA-TCG--GAT
*
637811 GG-TG--ATCTGCCCCAA
61 GGCTGCAATCTGCCCCAG
* * * * * * * * * *
637826 GCTCGGGGTAAGAGATTGGCTGGTGGTGATCTGCCCCAAGCTTGAGGTAAGAGATTGGCTGGCTA
1 GCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCTCAGGCTCGGGGTAAAAGATCGGATGGCTG
* * *
637891 CAATTTACCCCAA
66 CAATCTGCCCCAG
* * * *
637904 GCTCAGGGTAAGAGATTGGTTGATG-TGATCTGCC-CTAGGCTCGGGGTAAGAGATCAGATGGCT
1 GCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCTC-AGGCTCGGGGTAAAAGATCGGATGGCT
637967 GCAATCTGCCCCAG
65 GCAATCTGCCCCAG
* * * *
637981 GCTCGGGG-AAGAGATTGACTAATGATGATCTGTCTTAGGCTCGGGGTAAAAGATCGGATGGCTG
1 GCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCTCAGGCTCGGGGTAAAAGATCGGATGGCTG
*
638045 CAATCTGCCCTAG
66 CAATCTGCCCCAG
* * * * ** * *
638058 GCTCGGGGTAAAAGATTGGCTAATGGTGATCTGCCTCAAGCTTAGGGTAAGAGATCGGATGGTTG
1 GCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCTCAGGCTCGGGGTAAAAGATCGGATGGCTG
* * *
638123 TAATTTACCCCAG
66 CAATCTGCCCCAG
* ** * * ** * *
638136 GCTCGAGGTAAGAGATCAGATGGCT-ACAATTTGCCTCAGGCTCAGGGTAAAAGATCGGATGGCT
1 GCTCGGGGTAAGAGATTGGCT-GATGATGATCTGCCTCAGGCTCGGGGTAAAAGATCGGATGGCT
* * * *
638200 ACAATCTACCTCAA
65 GCAATCTGCCCCAG
* * * * * *
638214 GCTCGGGATAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCAGGTTAAAAGA
1 GCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCTCAGGCTCGGGGTAAAAGA
638268 ACCATGCCCC
Statistics
Matches: 536, Mismatches: 121, Indels: 36
0.77 0.17 0.05
Matches are distributed among these distances:
75 4 0.01
76 38 0.07
77 114 0.21
78 367 0.68
79 6 0.01
80 2 0.00
81 5 0.01
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.25
Consensus pattern (78 bp):
GCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCTCAGGCTCGGGGTAAAAGATCGGATGGCTG
CAATCTGCCCCAG
Found at i:637713 original size:117 final size:117
Alignment explanation
Indices: 637581--637957 Score: 477
Period size: 117 Copynumber: 3.2 Consensus size: 117
637571 GATGGCTACA
* * * * *
637581 ATCTGCCTCAGGCTCGAGGTAAGAGATTGGCTGATGATGATCTACCTCAGGCTCGGGGTAAAAGA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCTCAGGCTCGGGGTAAAAGA
* * **
637646 TCGGATGGTTGCAATCTACCCTAGGCTTGGGGTAAGAGATTGGTTGATGGTG
66 TCGGATGGCTACAATCTACCCTAGGCTCAGGGTAAGAGATTGGTTGATGGTG
** * *
637698 ATCTGCCTTAAGCTCGGGGTAAAAGATTGGTTGATGGTGATCTGCCTCAGGCTCGGGGTAAAAGA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCTCAGGCTCGGGGTAAAAGA
* * * *
637763 TCGAAAGGCTATAATCTGCCCTAGGCTCAGGGTAAGAGATTGGTTGATGGTG
66 TCGGATGGCTACAATCTACCCTAGGCTCAGGGTAAGAGATTGGTTGATGGTG
* * * * * *
637815 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGGTGGTGATCTGCCCCAAGCTTGAGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCTCAGGCTCGGGGTAAAAGA
* * * * *
637880 TTGGCTGGCTACAATTTACCCCAAGCTCAGGGTAAGAGATTGGTTGAT-GTG
66 TCGGATGGCTACAATCTACCCTAGGCTCAGGGTAAGAGATTGGTTGATGGTG
* *
637931 ATCTGCCCTAGGCTCGGGGTAAGAGAT
1 ATCTGCCCCAAGCTCGGGGTAAGAGAT
637958 CAGATGGCTG
Statistics
Matches: 224, Mismatches: 36, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
116 28 0.12
117 196 0.88
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.26
Consensus pattern (117 bp):
ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCTCAGGCTCGGGGTAAAAGA
TCGGATGGCTACAATCTACCCTAGGCTCAGGGTAAGAGATTGGTTGATGGTG
Found at i:638146 original size:39 final size:39
Alignment explanation
Indices: 638101--638229 Score: 136
Period size: 39 Copynumber: 3.3 Consensus size: 39
638091 CCTCAAGCTT
* **
638101 AGGGTAAGAGATCGGATGGTTGTAATTTACCCCAGGCTC
1 AGGGTAAGAGATCGGATGGCTACAATTTACCCCAGGCTC
* * *
638140 -GAGGTAAGAGATCAGATGGCTACAATTTGCCTCAGGCTC
1 AG-GGTAAGAGATCGGATGGCTACAATTTACCCCAGGCTC
* * * *
638179 AGGGTAAAAGATCGGATGGCTACAATCTACCTCAAGCTC
1 AGGGTAAGAGATCGGATGGCTACAATTTACCCCAGGCTC
638218 -GGGATAAGAGAT
1 AGGG-TAAGAGAT
638230 TGGCTGATGG
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
38 4 0.05
39 70 0.93
40 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.22
Consensus pattern (39 bp):
AGGGTAAGAGATCGGATGGCTACAATTTACCCCAGGCTC
Found at i:638158 original size:117 final size:117
Alignment explanation
Indices: 637548--638190 Score: 411
Period size: 117 Copynumber: 5.5 Consensus size: 117
637538 ATAGTATCTG
* * * * * *
637548 CCCAGGCTCGGGGTAATAGATCAGATGGCTACAATCTG-CCTCAGGCTCGAGGTAAGAGATTGGC
1 CCCAGGCTCGAGGTAAGAGATCTGATGGCTGCAATCTGCCCT-AGGCTCGGGGTAAAAGATTGGC
* * * * * *
637612 TGATGATGATCTACCTCAGGCTCGGGGTAAAAGATCGGATGGTTGCAATCTAC
65 TGATGGTGATCTGCCTCAGGCTTGGGGTAAGAGATCGGATGGCTGTAATCTAC
* * * * * *
637665 CCTAGGCTTGGGGTAAGAGATTGGTTGATGG-TG--ATCTGCCTTAAGCTCGGGGTAAAAGATTG
1 CCCAGGCTCGAGGTAAGAGA-T--CTGATGGCTGCAATCTGCCCTAGGCTCGGGGTAAAAGATTG
* * * * * * *
637727 GTTGATGGTGATCTGCCTCAGGCTCGGGGTAAAAGATCGAAAGGCTATAATCTGC
63 GCTGATGGTGATCTGCCTCAGGCTTGGGGTAAGAGATCGGATGGCTGTAATCTAC
* * * * *
637782 CCTAGGCTC-AGGGTAAGAGATTGGTTGATGG-TG--ATCTGCCCCAAGCTCGGGGTAAGAGATT
1 CCCAGGCTCGA-GGTAAGAGA-T--CTGATGGCTGCAATCTGCCCTAGGCTCGGGGTAAAAGATT
* * * * * * ** *
637843 GGCTGGTGGTGATCTGCCCCAAGCTTGAGGTAAGAGATTGGCTGGCTACAATTTAC
62 GGCTGATGGTGATCTGCCTCAGGCTTGGGGTAAGAGATCGGATGGCTGTAATCTAC
* * * * ** *
637899 CCCAAGCTC-AGGGTAAGAGAT-TGGTTGATGTGATCTGCCCTAGGCTCGGGGTAAGAGA-T--C
1 CCCAGGCTCGA-GGTAAGAGATCTGATGGCTGCAATCTGCCCTAGGCTCGGGGTAAAAGATTGGC
* * * * ** * **
637959 AGATGGCTGCAATCTGCCCCAGGCTCGGGG-AAGAGAT-TGACT-AATGATGATCTGT
65 TGATGG-TG--ATCTGCCTCAGGCTTGGGGTAAGAGATCGGA-TGGCTG-TAATCTAC
** * * *
638014 CTTAGGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCTAGGCTCGGGGTAAAAGATTGGCT
1 CCCAGGCTCGAGGTAAGAGATCTGATGGCTGCAATCTGCCCTAGGCTCGGGGTAAAAGATTGGCT
* * * * *
638079 AATGGTGATCTGCCTCAAGCTTAGGGTAAGAGATCGGATGGTTGTAATTTAC
66 GATGGTGATCTGCCTCAGGCTTGGGGTAAGAGATCGGATGGCTGTAATCTAC
* * * *
638131 CCCAGGCTCGAGGTAAGAGATCAGATGGCTACAATTTG-CCTCAGGCTCAGGGTAAAAGAT
1 CCCAGGCTCGAGGTAAGAGATCTGATGGCTGCAATCTGCCCT-AGGCTCGGGGTAAAAGAT
638191 CGGATGGCTA
Statistics
Matches: 412, Mismatches: 92, Indels: 44
0.75 0.17 0.08
Matches are distributed among these distances:
113 9 0.02
114 6 0.01
115 27 0.07
116 89 0.22
117 261 0.63
118 9 0.02
119 6 0.01
120 5 0.01
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.25
Consensus pattern (117 bp):
CCCAGGCTCGAGGTAAGAGATCTGATGGCTGCAATCTGCCCTAGGCTCGGGGTAAAAGATTGGCT
GATGGTGATCTGCCTCAGGCTTGGGGTAAGAGATCGGATGGCTGTAATCTAC
Found at i:638251 original size:117 final size:115
Alignment explanation
Indices: 637931--638267 Score: 304
Period size: 117 Copynumber: 2.9 Consensus size: 115
637921 GGTTGATGTG
* * * * *
637931 ATCTGCCCTAGGCTCGGGGTAAGAGATCAGATGGCTGCAATCTGCCCCAGGCTCGGGGAAGAGAT
1 ATCTGCCCTAGGCTCGGGGTAAAAGATCGGATGGCT-CAATCTGCCTCAAGCTCGGGTAAGAGAT
* * * * ** * * *
637996 TGACTAATGATGATCTGTCTTAGGCTCGGGGTAAAAGATCGGATGGCTGCA
65 TGGCTGATGGTGATCTGCCCCAGGCTCGAGGTAAAAGATCAGATGGCTACA
* * *
638047 ATCTGCCCTAGGCTCGGGGTAAAAGATTGGCTAATGG-T-GATCTGCCTCAAGCTTAGGGTAAGA
1 ATCTGCCCTAGGCTCGGGGTAAAAGATCGG---ATGGCTCAATCTGCCTCAAGC-TCGGGTAAGA
* * * * * * * *
638110 GATCGGATGGTTGTAATTTACCCCAGGCTCGAGGTAAGAGATCAGATGGCTACA
62 GATTGGCTGATGGTGATCTGCCCCAGGCTCGAGGTAAAAGATCAGATGGCTACA
* * *
638164 ATTTG-CCTCAGGCTCAGGGTAAAAGATCGGATGGCTACAATCTACCTCAAGCTCGGGATAAGAG
1 ATCTGCCCT-AGGCTCGGGGTAAAAGATCGGATGGCT-CAATCTGCCTCAAGCTCGGG-TAAGAG
*
638228 ATTGGCTGATGGTGATCTGCCCCAAGCTC-AGGTTAAAAGA
63 ATTGGCTGATGGTGATCTGCCCCAGGCTCGAGG-TAAAAGA
638268 ACCATGCCCC
Statistics
Matches: 171, Mismatches: 40, Indels: 19
0.74 0.17 0.08
Matches are distributed among these distances:
114 4 0.02
115 1 0.01
116 48 0.28
117 113 0.66
118 1 0.01
119 4 0.02
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.23
Consensus pattern (115 bp):
ATCTGCCCTAGGCTCGGGGTAAAAGATCGGATGGCTCAATCTGCCTCAAGCTCGGGTAAGAGATT
GGCTGATGGTGATCTGCCCCAGGCTCGAGGTAAAAGATCAGATGGCTACA
Found at i:644964 original size:3 final size:3
Alignment explanation
Indices: 644956--645006 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
644946 TACAAAAATC
*
644956 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA AAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
645004 GAA
1 GAA
645007 AAAAAAAACA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:645191 original size:29 final size:30
Alignment explanation
Indices: 645143--645283 Score: 144
Period size: 29 Copynumber: 4.7 Consensus size: 30
645133 TTGGGGGGTT
*
645143 AAAATGTGATTTTTAGAAAGTTTAAAGGTA
1 AAAATGTAATTTTTAGAAAGTTTAAAGGTA
* * * *
645173 AAAATGTAA-TATTAAAAAGTTTAAGGGTT
1 AAAATGTAATTTTTAGAAAGTTTAAAGGTA
* * *
645202 ATAATATAATTTTTTAGAAAGTTT-AGGGTA
1 AAAATGTAA-TTTTTAGAAAGTTTAAAGGTA
* * *
645232 AAAATGTAATTTTTGGAAAGTTTTAAGGTC
1 AAAATGTAATTTTTAGAAAGTTTAAAGGTA
645262 AAAATGT-ATTTTTAGAGAAGTT
1 AAAATGTAATTTTTAGA-AAGTT
645284 ACGGGGTCGA
Statistics
Matches: 91, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
29 44 0.48
30 36 0.40
31 11 0.12
ACGTcount: A:0.42, C:0.01, G:0.18, T:0.39
Consensus pattern (30 bp):
AAAATGTAATTTTTAGAAAGTTTAAAGGTA
Found at i:645252 original size:60 final size:60
Alignment explanation
Indices: 645103--645347 Score: 182
Period size: 60 Copynumber: 4.1 Consensus size: 60
645093 TCATGAAGGT
* * *** * *
645103 TTTAGGGTCAAAATATAATTTTTGGAAAGCTTGGGGGGTTAAAATGTGATTTTTAGAAAG
1 TTTAGGGTAAAAATGTAATTTTTGGAAAGCTTTAAGGGTTAAAATATAATTTTTAGAAAG
* * ** *
645163 TTTAAAGGTAAAAATGTAA-TATTAAAAAG-TTTAAGGGTTATAATATAATTTTTTAGAAAG
1 TTT-AGGGTAAAAATGTAATTTTTGGAAAGCTTTAAGGGTTAAAATATAA-TTTTTAGAAAG
* * *
645223 TTTAGGGTAAAAATGTAATTTTTGGAAAGTTTTAA-GGTCAAAATGT-ATTTTTAGAGAAG
1 TTTAGGGTAAAAATGTAATTTTTGGAAAGCTTTAAGGGTTAAAATATAATTTTTAGA-AAG
** * * * *
645282 -TTACGGGGTCGAAATGT-ACTTTTGGAGAAG-TTTGA-GGTTAAAATATGATTTTTGGAAAG
1 TTTA--GGGTAAAAATGTAATTTTTGGA-AAGCTTTAAGGGTTAAAATATAATTTTTAGAAAG
*
645341 TTCAGGG
1 TTTAGGG
645348 ACCTATTAGG
Statistics
Matches: 148, Mismatches: 27, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
58 14 0.09
59 55 0.37
60 62 0.42
61 17 0.11
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (60 bp):
TTTAGGGTAAAAATGTAATTTTTGGAAAGCTTTAAGGGTTAAAATATAATTTTTAGAAAG
Found at i:646489 original size:10 final size:10
Alignment explanation
Indices: 646476--646523 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
646466 CAATTAATAA
646476 ATATATTAAT
1 ATATATTAAT
*
646486 ATATAATAAAT
1 ATAT-ATTAAT
* *
646497 AAATGTTAA-
1 ATATATTAAT
646506 ATATATTAAT
1 ATATATTAAT
646516 ATATATTA
1 ATATATTA
646524 TAAACATTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
9 7 0.23
10 15 0.50
11 8 0.27
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (10 bp):
ATATATTAAT
Found at i:647973 original size:16 final size:16
Alignment explanation
Indices: 647952--647984 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
647942 TGTTAATCCT
647952 CCTCTAGTGTCTTTAG
1 CCTCTAGTGTCTTTAG
647968 CCTCTAGTGTCTTTAG
1 CCTCTAGTGTCTTTAG
647984 C
1 C
647985 AACAATATTA
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:0.12, C:0.27, G:0.18, T:0.42
Consensus pattern (16 bp):
CCTCTAGTGTCTTTAG
Found at i:651665 original size:27 final size:25
Alignment explanation
Indices: 651628--651677 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
651618 CTAGCTGGTT
*
651628 AAAATCAAAAAAATTATTAAAAAATCA
1 AAAAT-AAAAAAAAT-TTAAAAAATCA
*
651655 AAAATAAAAAATATTTAAAAAAT
1 AAAATAAAAAAAATTTAAAAAAT
651678 TATAAAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 9 0.43
26 7 0.33
27 5 0.24
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (25 bp):
AAAATAAAAAAAATTTAAAAAATCA
Found at i:652726 original size:30 final size:31
Alignment explanation
Indices: 652692--652756 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
652682 AATTTTCAAC
652692 TCAATCACTCAAC-TT-TAAAAAAATAACAAA
1 TCAATCACT-AACGTTATAAAAAAATAACAAA
* * *
652722 TCAATCACTAACGTTATCAAAAAGTGACAAA
1 TCAATCACTAACGTTATAAAAAAATAACAAA
652753 TCAA
1 TCAA
652757 CCACCCACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 3 0.10
30 11 0.37
31 16 0.53
ACGTcount: A:0.52, C:0.20, G:0.05, T:0.23
Consensus pattern (31 bp):
TCAATCACTAACGTTATAAAAAAATAACAAA
Found at i:660579 original size:14 final size:14
Alignment explanation
Indices: 660556--660609 Score: 85
Period size: 14 Copynumber: 4.0 Consensus size: 14
660546 AAAAACACAC
660556 AAAG-AACCAGAAA
1 AAAGAAACCAGAAA
660569 AAAGAAACCAGAAA
1 AAAGAAACCAGAAA
*
660583 GAA-AAACCAGAAA
1 AAAGAAACCAGAAA
660596 AAAGAAACCAGAAA
1 AAAGAAACCAGAAA
660610 GAAACGTGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
13 16 0.43
14 21 0.57
ACGTcount: A:0.70, C:0.15, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAGAAACCAGAAA
Found at i:660592 original size:27 final size:27
Alignment explanation
Indices: 660560--660613 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
660550 ACACACAAAG
660560 AACCAGAAAAAAGAAACCAGAAAGAAA
1 AACCAGAAAAAAGAAACCAGAAAGAAA
660587 AACCAGAAAAAAGAAACCAGAAAGAAA
1 AACCAGAAAAAAGAAACCAGAAAGAAA
660614 CGTGCTAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.70, C:0.15, G:0.15, T:0.00
Consensus pattern (27 bp):
AACCAGAAAAAAGAAACCAGAAAGAAA
Found at i:661089 original size:15 final size:16
Alignment explanation
Indices: 661069--661098 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
661059 AATTATTTAA
661069 ATAAATT-ATAAAATT
1 ATAAATTAATAAAATT
661084 ATAAATTAATAAAAT
1 ATAAATTAATAAAAT
661099 AATGAAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATAAATTAATAAAATT
Found at i:666353 original size:22 final size:19
Alignment explanation
Indices: 666324--666366 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 19
666314 CCTTATAATC
*
666324 ATTTAAGCTTAATTTCTATCA
1 ATTTAAGCCTAA-TTC-ATCA
666345 ATTTCAAGCCTAATTCATCA
1 ATTT-AAGCCTAATTCATCA
666365 AT
1 AT
666367 ATCTCAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 7 0.35
22 7 0.35
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.42
Consensus pattern (19 bp):
ATTTAAGCCTAATTCATCA
Found at i:680125 original size:11 final size:12
Alignment explanation
Indices: 680109--680161 Score: 54
Period size: 12 Copynumber: 4.1 Consensus size: 12
680099 ATATATTCAT
680109 TATTTTA-AATA
1 TATTTTATAATA
680120 TATTTTATAATA
1 TATTTTATAATA
680132 TATCTATCTTATATATA
1 TA--T-T-TTATA-ATA
680149 TATTTTATAATA
1 TATTTTATAATA
680161 T
1 T
680162 GTTTATTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
11 7 0.19
12 10 0.28
13 5 0.14
14 2 0.06
15 2 0.06
16 5 0.14
17 5 0.14
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.57
Consensus pattern (12 bp):
TATTTTATAATA
Found at i:680161 original size:16 final size:16
Alignment explanation
Indices: 680117--680171 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
680107 ATTATTTTAA
680117 ATATATTTTATAATAT
1 ATATATTTTATAATAT
* *
680133 ATCTA-TCT-T-ATAT
1 ATATATTTTATAATAT
680146 ATATATTTTATAATAT
1 ATATATTTTATAATAT
* *
680162 GTTTATTTTA
1 ATATATTTTA
680172 AGTCAGTTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
13 8 0.27
14 3 0.10
15 3 0.10
16 16 0.53
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (16 bp):
ATATATTTTATAATAT
Found at i:684524 original size:27 final size:27
Alignment explanation
Indices: 684486--684574 Score: 97
Period size: 27 Copynumber: 3.3 Consensus size: 27
684476 ACTCTGAATG
* *
684486 ATATTCATGGCCTGACCAACCCGTATT
1 ATATCCATGGCCTGACCAACCCGTATA
** *
684513 ATATCCATGGCCAAACCAACCCGTATG
1 ATATCCATGGCCTGACCAACCCGTATA
* * * *
684540 ATATCCATCGTCTGACCACCCCGGATA
1 ATATCCATGGCCTGACCAACCCGTATA
684567 ATATCCAT
1 ATATCCAT
684575 CACTTGACCA
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.29, C:0.33, G:0.13, T:0.25
Consensus pattern (27 bp):
ATATCCATGGCCTGACCAACCCGTATA
Found at i:684649 original size:18 final size:18
Alignment explanation
Indices: 684628--684668 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
684618 GTTTGGCTCA
684628 TGCTCGGGCTTCG-GATCG
1 TGCTCGGGC-TCGAGATCG
684646 TGCTCGGGCTCGAGATCG
1 TGCTCGGGCTCGAGATCG
*
684664 AGCTC
1 TGCTC
684669 ATGCTCAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.10, C:0.29, G:0.37, T:0.24
Consensus pattern (18 bp):
TGCTCGGGCTCGAGATCG
Found at i:696278 original size:149 final size:149
Alignment explanation
Indices: 696076--696362 Score: 468
Period size: 149 Copynumber: 1.9 Consensus size: 149
696066 CACACCTCAC
696076 TTCTTCATCTTCATCTTATTCCCTTTTGATTTCAATATCTTTAGTTACAAATCTATCTCAAAGCT
1 TTCTTCATCTTCATCTTATTCCCTTTTGATTTCAATATCTTTAGTTACAAATCTATCTCAAAGCT
* * * * *
696141 TGAATCTTTGAAACTCATTAACCTAAAAAAACTTAAAAGGAATAAGCTATTGGATTCAAAGATAT
66 TGAATCTTTGAAACCCATTAACCCAAAAAAACTTAAAAGGAAGAAGATATTGGAATCAAAGATAT
*
696206 TGAATCTTCACACACACTA
131 TAAATCTTCACACACACTA
* *
696225 TTCTTCATCTTCATCTTCTTCCCTTTTGA-TTCTAATATCTTTAGTTACAAATCTGTCTCAAAGC
1 TTCTTCATCTTCATCTTATTCCCTTTTGATTTC-AATATCTTTAGTTACAAATCTATCTCAAAGC
* *
696289 TTGAATCTTTGAAACCCATTAACCCAAAAAAACTTAACAGGAAGAAGATATTGGAATCAAATATA
65 TTGAATCTTTGAAACCCATTAACCCAAAAAAACTTAAAAGGAAGAAGATATTGGAATCAAAGATA
696354 TTAAATCTT
130 TTAAATCTT
696363 TGGGTTAATG
Statistics
Matches: 127, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
148 3 0.02
149 124 0.98
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (149 bp):
TTCTTCATCTTCATCTTATTCCCTTTTGATTTCAATATCTTTAGTTACAAATCTATCTCAAAGCT
TGAATCTTTGAAACCCATTAACCCAAAAAAACTTAAAAGGAAGAAGATATTGGAATCAAAGATAT
TAAATCTTCACACACACTA
Found at i:707750 original size:29 final size:28
Alignment explanation
Indices: 707697--707751 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
707687 CAAATCAAAT
* *
707697 AAATTATTAAAATTCATAAGAATTTTAA
1 AAATTATTAAAAATCATAAAAATTTTAA
707725 AAATATATTAAAAAT-ATAAAATATTTT
1 AAAT-TATTAAAAATCATAAAA-ATTTT
707752 TCAACTGGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 9 0.39
29 14 0.61
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (28 bp):
AAATTATTAAAAATCATAAAAATTTTAA
Found at i:715475 original size:22 final size:22
Alignment explanation
Indices: 715450--715491 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
715440 ATCTCCATTG
* *
715450 ATGAAATTTTAGAATCTTTTGA
1 ATGAAATATTAAAATCTTTTGA
715472 ATGAAATATTAAAATCTTTT
1 ATGAAATATTAAAATCTTTT
715492 CATACTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (22 bp):
ATGAAATATTAAAATCTTTTGA
Found at i:715881 original size:117 final size:118
Alignment explanation
Indices: 715740--715951 Score: 381
Period size: 117 Copynumber: 1.8 Consensus size: 118
715730 AAATAGAAAA
*
715740 TAAATTAACACATGCAACCCAACAAGCAAATGCATCTAAAATAGTAACAAAATTAACAGTAAAAC
1 TAAATTAACACATGCAACCCAACAAGCAAATGCATCTAAAATAGTAACAAAATTAACAATAAAAC
715805 AAGAGTTAAAAAATATTCAAGCAATAATAATATATATATATATAATATATACT
66 AAGAGTTAAAAAATATTCAAGCAATAATAATATATATATATATAATATATACT
** *
715858 TAAA-TAACACATGCAACTTAACAAGCAAATGCATCTAAAATAGTAACAAAATTAATAATAAAAC
1 TAAATTAACACATGCAACCCAACAAGCAAATGCATCTAAAATAGTAACAAAATTAACAATAAAAC
715922 AAGAGTTAAAAAATATTCAAGCAATAATAA
66 AAGAGTTAAAAAATATTCAAGCAATAATAA
715952 CAAAATAATA
Statistics
Matches: 90, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
117 86 0.96
118 4 0.04
ACGTcount: A:0.56, C:0.13, G:0.07, T:0.24
Consensus pattern (118 bp):
TAAATTAACACATGCAACCCAACAAGCAAATGCATCTAAAATAGTAACAAAATTAACAATAAAAC
AAGAGTTAAAAAATATTCAAGCAATAATAATATATATATATATAATATATACT
Found at i:731247 original size:46 final size:46
Alignment explanation
Indices: 731168--731309 Score: 203
Period size: 46 Copynumber: 3.1 Consensus size: 46
731158 ACTACTAATT
* * ** *
731168 TGTAATATTAGTTATGCACTAGGACGATGTTGTAGTTATCATGTGG
1 TGTAATACTAGTTATGCACTTGGAAAATATTGTAGTTATCATGTGG
731214 TGTAATACTAGTTATGCACTTGGAAAATATTGTAGTTATCATGTGG
1 TGTAATACTAGTTATGCACTTGGAAAATATTGTAGTTATCATGTGG
* * * *
731260 CGTACTACTAGTTATGCACTTGAAAAATATTATAGTTATCATGTGG
1 TGTAATACTAGTTATGCACTTGGAAAATATTGTAGTTATCATGTGG
731306 TGTA
1 TGTA
731310 CTATTAATTT
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 86 1.00
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.39
Consensus pattern (46 bp):
TGTAATACTAGTTATGCACTTGGAAAATATTGTAGTTATCATGTGG
Found at i:731713 original size:13 final size:15
Alignment explanation
Indices: 731684--731721 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
731674 TCAGAAAAGT
731684 AATTCATTTTCCAAA
1 AATTCATTTTCCAAA
731699 AATT-ATTTT-CAAA
1 AATTCATTTTCCAAA
*
731712 AAATCATTTT
1 AATTCATTTT
731722 TAATCAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 7 0.33
14 10 0.48
15 4 0.19
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTCATTTTCCAAA
Found at i:731803 original size:16 final size:14
Alignment explanation
Indices: 731779--731823 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
731769 TTTAAATGGA
731779 TTCT-ATTTTTATTT
1 TTCTCATTTTT-TTT
*
731793 TTCTCCTTTTTTTT
1 TTCTCATTTTTTTT
731807 TTCTCATTTTCTTTT
1 TTCTCATTTT-TTTT
731822 TT
1 TT
731824 TCTTCTCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.78
Consensus pattern (14 bp):
TTCTCATTTTTTTT
Found at i:731823 original size:21 final size:21
Alignment explanation
Indices: 731796--731843 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
731786 TTTATTTTTC
731796 TCCTTTTTTT-TT-TCTCATT
1 TCCTTTTTTTCTTCTCTCATT
* *
731815 TTCTTTTTTTCTTCTCTCCTT
1 TCCTTTTTTTCTTCTCTCATT
731836 TCCTTTTT
1 TCCTTTTT
731844 CAACATGTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.38
20 2 0.08
21 13 0.54
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (21 bp):
TCCTTTTTTTCTTCTCTCATT
Found at i:732346 original size:19 final size:18
Alignment explanation
Indices: 732307--732350 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 18
732297 TTTTCCTTAA
732307 TTTTTTATATTTAGTTTTT
1 TTTTTTATATTTA-TTTTT
732326 TTTTTTATATTT-TTTGATT
1 TTTTTTATATTTATTT--TT
732345 TTTTTT
1 TTTTTT
732351 TTCTAGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.13
19 20 0.87
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.82
Consensus pattern (18 bp):
TTTTTTATATTTATTTTT
Found at i:732346 original size:21 final size:21
Alignment explanation
Indices: 732322--732361 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
732312 TATATTTAGT
*
732322 TTTTTTTTTTATATTTTTTGA
1 TTTTTTTTTTATAGTTTTTGA
*
732343 TTTTTTTTTTCTAGTTTTT
1 TTTTTTTTTTATAGTTTTT
732362 ATCTGCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.03, G:0.05, T:0.82
Consensus pattern (21 bp):
TTTTTTTTTTATAGTTTTTGA
Found at i:743563 original size:30 final size:29
Alignment explanation
Indices: 743513--743592 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 29
743503 TTTTGATAAA
**
743513 ATTAAGAAAA-AATATCATTTTTATTTGAAT
1 ATTAAGAAAATAA-ATCATTTTT-TTCAAAT
*
743543 ATTAAGAAAATAAATTATTTTTTTCAAAT
1 ATTAAGAAAATAAATCATTTTTTTCAAAT
*
743572 -TTAAAAAAATAAATCGATTTT
1 ATTAAGAAAATAAATC-ATTTT
743593 AGATACATGC
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
28 13 0.30
29 10 0.23
30 18 0.42
31 2 0.05
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (29 bp):
ATTAAGAAAATAAATCATTTTTTTCAAAT
Found at i:743575 original size:28 final size:28
Alignment explanation
Indices: 743496--743585 Score: 78
Period size: 28 Copynumber: 3.1 Consensus size: 28
743486 TTATTTTGTC
*
743496 AAATTATTTTTGA-TAAAATTAAGAAAA-
1 AAATTATTTTT-ATTAAATTTAAGAAAAT
* *
743523 AATATCATTTTTATTTGAATATTAAGAAAAT
1 AA-ATTATTTTTA-TTAAAT-TTAAGAAAAT
*
743554 AAATTATTTTT-TTCAAATTTAAAAAAAT
1 AAATTATTTTTATT-AAATTTAAGAAAAT
743582 AAAT
1 AAAT
743586 CGATTTTAGA
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
27 3 0.06
28 23 0.45
29 6 0.12
30 17 0.33
31 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.42
Consensus pattern (28 bp):
AAATTATTTTTATTAAATTTAAGAAAAT
Found at i:746596 original size:2 final size:2
Alignment explanation
Indices: 746585--746619 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
746575 AAACCTAAAC
746585 AT AT -T 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
746620 TGAAATTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:750498 original size:22 final size:23
Alignment explanation
Indices: 750473--750524 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
750463 AATATTAATA
*
750473 TTTTTTTT-TAATTTGA-CAATT
1 TTTTTTTTCTAACTTGATCAATT
*
750494 TTTTTTTTCTAACTTGATTCTATT
1 TTTTTTTTCTAACTTGA-TCAATT
750518 TTTTTTT
1 TTTTTTT
750525 CGTAAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 8 0.31
22 7 0.27
24 11 0.42
ACGTcount: A:0.17, C:0.08, G:0.04, T:0.71
Consensus pattern (23 bp):
TTTTTTTTCTAACTTGATCAATT
Found at i:750994 original size:26 final size:26
Alignment explanation
Indices: 750948--750997 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
750938 AATTTTCTCT
*
750948 TTTTTTATAATTTTATATTTTAAACA
1 TTTTTAATAATTTTATATTTTAAACA
*
750974 TTTTTAAT-ATTTTCATTTTTTAAA
1 TTTTTAATAATTTT-ATATTTTAAA
750998 AGGCTAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (26 bp):
TTTTTAATAATTTTATATTTTAAACA
Done.