Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000686.1 Hibiscus syriacus cultivar Beakdansim tig00001340_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1443669
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:217420 original size:13 final size:13
Alignment explanation
Indices: 217398--217459 Score: 56
Period size: 13 Copynumber: 4.6 Consensus size: 13
217388 TTTTTTTTCC
217398 TTTATCTTATTTA-
1 TTTAT-TTATTTAT
217411 TTTATTTTATTTAT
1 TTTA-TTTATTTAT
**
217425 TTTATTT-TTCCCT
1 TTTATTTATT-TAT
217438 TTTACTTTATTTAT
1 TTTA-TTTATTTAT
217452 TTTATTTA
1 TTTATTTA
217460 CCTTGTTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
12 2 0.05
13 23 0.57
14 13 0.32
15 2 0.05
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTATTTATTTAT
Found at i:219599 original size:102 final size:100
Alignment explanation
Indices: 219164--219601 Score: 395
Period size: 102 Copynumber: 4.3 Consensus size: 100
219154 CAAAGATGCA
* * * * * * * *
219164 ACCTATAATGTTAGACTTATAAACCTATTTTGTCTAAATGTTCCATACTA-AAAATGGTTTCAAA
1 ACCTATAATGTTATACTTATAAACATGTTTTGTCTTATTTTTTCATAATATAAAA-GGTTTCAAA
* * *
219228 AATATAA-TATTAACGGTTGACAATTAAAAAAATGCAC-
65 CATATAACT-TAAAC-GTTGATAATT-AAAAAATGCACT
219265 ATCCTATAATGTTATACTTATAAACATGTTTTGTCTTATTTTTTCATAATATAAAAGGTTTCAAA
1 A-CCTATAATGTTATACTTATAAACATGTTTTGTCTTATTTTTTCATAATATAAAAGGTTTCAAA
* *
219330 CATATAACTTAAACGGTTGAAAATTAAAAAATGCGCT
65 CATATAACTTAAAC-GTTGATAATTAAAAAATGCACT
* * * * * * * * *
219367 ACCTAAAAGGTTAGACTTATCAACCTGCTTTGTCGTATTGTTGT-ATAATA-AAAACGGTTTGAA
1 ACCTATAATGTTATACTTATAAACATGTTTTGTCTTATT-TTTTCATAATATAAAA-GGTTTCAA
* * ** *
219430 ACAAATAATCTTAATA-ATTTCTAATTAAAAGAATGCACA
64 ACATATAA-CTTAA-ACGTTGATAATTAAAA-AATGCACT
* * *
219469 ACCTACAATGGTATACTTATAAACATGTTTTGTCTTACTTTTTTCATAATATAAAAGATTTCAAA
1 ACCTATAATGTTATACTTATAAACATGTTTTGTCTTA-TTTTTTCATAATATAAAAGGTTTCAAA
* * * *
219534 CATATAACGTAAACGTTGGATAAGTAAAAAAGGCTCT
65 CATATAACTTAAACGTT-GATAATTAAAAAATGCACT
219571 ACCTATAATGTTATACTTATGAAA-ATGTTTT
1 ACCTATAATGTTATACTTAT-AAACATGTTTT
219602 TCCTTAGTTT
Statistics
Matches: 272, Mismatches: 50, Indels: 29
0.77 0.14 0.08
Matches are distributed among these distances:
100 4 0.01
101 73 0.27
102 153 0.56
103 38 0.14
104 4 0.01
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (100 bp):
ACCTATAATGTTATACTTATAAACATGTTTTGTCTTATTTTTTCATAATATAAAAGGTTTCAAAC
ATATAACTTAAACGTTGATAATTAAAAAATGCACT
Found at i:219713 original size:21 final size:21
Alignment explanation
Indices: 219689--219734 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
219679 TATTTTCCAT
*
219689 TTCATTTTGAGTTTTTGTTT-A
1 TTCATTTTGAATTTTT-TTTAA
219710 TTCATTTTGAATTTTTTTTAA
1 TTCATTTTGAATTTTTTTTAA
219731 TTCA
1 TTCA
219735 CTCGTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.20, C:0.07, G:0.09, T:0.65
Consensus pattern (21 bp):
TTCATTTTGAATTTTTTTTAA
Found at i:224045 original size:20 final size:20
Alignment explanation
Indices: 224008--224048 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
223998 TTTTGTTTTA
*
224008 ATTATGTTTTAGATTCATTT
1 ATTATGTTTGAGATTCATTT
224028 ATTATGTTTGA-ATATCATTT
1 ATTATGTTTGAGAT-TCATTT
224048 A
1 A
224049 CATGCCATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.56
Consensus pattern (20 bp):
ATTATGTTTGAGATTCATTT
Found at i:224994 original size:19 final size:20
Alignment explanation
Indices: 224970--225012 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
224960 CAAGAGCATG
*
224970 TATTTTCATT-AAATTCATA
1 TATTTTCATTAAAAATCATA
224989 TATTTTCATTAAAAATCATA
1 TATTTTCATTAAAAATCATA
225009 TATT
1 TATT
225013 GTCAAAAGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTTTCATTAAAAATCATA
Found at i:229145 original size:19 final size:20
Alignment explanation
Indices: 229121--229167 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
229111 CAAGAGAAAT
*
229121 TATTTTCATT-AAAGTCATA
1 TATTTTCATTAAAAATCATA
229140 TATTTTCATTAAAAATCATA
1 TATTTTCATTAAAAATCATA
229160 TATTTTCA
1 TATTTTCA
229168 AAGGGATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (20 bp):
TATTTTCATTAAAAATCATA
Found at i:233571 original size:2 final size:2
Alignment explanation
Indices: 233564--233588 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
233554 TAATCCTTTA
233564 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
233589 CTCGTATTTT
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:235282 original size:47 final size:48
Alignment explanation
Indices: 235212--235303 Score: 134
Period size: 47 Copynumber: 1.9 Consensus size: 48
235202 TTTAATTCGC
* *
235212 TTTCTGAATAAATGCATGCGAACTAGAGATCATTAGGTTAGGTTTATT
1 TTTCTGAATAAATGCATGCGAACTAGAGAGCATGAGGTTAGGTTTATT
*
235260 TTTCTTGAAT-AAT-CATGCGAACTAGATAGCATGAGGTTAGGTTT
1 TTTC-TGAATAAATGCATGCGAACTAGAGAGCATGAGGTTAGGTTT
235304 TTTATGTTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
47 28 0.70
48 7 0.17
49 5 0.12
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (48 bp):
TTTCTGAATAAATGCATGCGAACTAGAGAGCATGAGGTTAGGTTTATT
Found at i:249890 original size:20 final size:20
Alignment explanation
Indices: 249852--249889 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
249842 AAAATACAGT
249852 GAAGGGATCGATCCGTTTTG
1 GAAGGGATCGATCCGTTTTG
*
249872 GAAGGGGTCGATCC-TTTT
1 GAAGGGATCGATCCGTTTT
249890 TCACGGGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
GAAGGGATCGATCCGTTTTG
Found at i:255459 original size:55 final size:57
Alignment explanation
Indices: 255376--255481 Score: 180
Period size: 55 Copynumber: 1.9 Consensus size: 57
255366 ATGGCACTAA
*
255376 GTGTGCAAAAACTTAAGAAATTCATACTAAGTGTATGAATTTATGTATGGGCACTTT
1 GTGTGCAAAAACTTAAGAAATTCATACTAAGTGTATGAATTTACGTATGGGCACTTT
*
255433 GTGTGC-AAAAC-TAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
1 GTGTGCAAAAACTTAAGAAATTCATACTAAGTGTATGAATTTACGTATGGG
255482 AAATATATGT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
55 36 0.77
56 5 0.11
57 6 0.13
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (57 bp):
GTGTGCAAAAACTTAAGAAATTCATACTAAGTGTATGAATTTACGTATGGGCACTTT
Found at i:255892 original size:81 final size:81
Alignment explanation
Indices: 255765--256128 Score: 525
Period size: 81 Copynumber: 4.5 Consensus size: 81
255755 GAGGCCTAAT
255765 TGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAA
1 TGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAA
*
255830 AGAATAGTGGCCTAGC
66 AGAATAATGGCCTAGC
* * * *
255846 TGTGCATTTGGTAGAAAGGTTTCAATTATGCCACTTAGATGAACGGTTAAATACTGTTGAGTAAA
1 TGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAA
*
255911 AGAATAATGGCCTAGT
66 AGAATAATGGCCTAGC
* * * *
255927 TGTTCATTTGGAAGAAAGGTGTCAATTATGCCAATTAGATGAAC-GTTAAATATCGTTGAGTAAA
1 TGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAA
*
255991 AGAATAATGGCCTAGT
66 AGAATAATGGCCTAGC
* ** * * *
256007 TGTGCATTTGGCAAAAATATGTCAATTATGCCAGTTATATGAACAGTTAAATATCGTTGAGTAAA
1 TGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAA
*
256072 AG-ATAAATGACCTAGC
66 AGAAT-AATGGCCTAGC
* *
256088 TGTGCAATTGGCAGAAAGGTGTCAATTATGCTAGTTAGATG
1 TGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATG
256129 CTTTGTTGTT
Statistics
Matches: 254, Mismatches: 27, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
80 73 0.29
81 181 0.71
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (81 bp):
TGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAA
AGAATAATGGCCTAGC
Found at i:256035 original size:161 final size:162
Alignment explanation
Indices: 255757--256128 Score: 534
Period size: 161 Copynumber: 2.3 Consensus size: 162
255747 GTGCCTTTGA
*
255757 GGCCTAATTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
1 GGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
* * * * *
255822 TGAGTAAAAGAATAGTGGCCTAGCTGTGCATTTGGTAGAAAGGTTTCAATTATGCCACTTAGATG
66 TGAGTAAAAGAATAATGGCCTAGCTGTGCATTTGGCAAAAAGATGTCAATTATGCCACTTAGATG
*
255887 AACGGTTAAATA-CTGTTGAGTAAAAGA-ATAAT
131 AACAGTTAAATATC-GTTGAGTAAAAGATA-AAT
* * * *
255919 GGCCTAGTTGTTCATTTGGAAGAAAGGTGTCAATTATGCCAATTAGATGAAC-GTTAAATATCGT
1 GGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
* * * *
255983 TGAGTAAAAGAATAATGGCCTAGTTGTGCATTTGGCAAAAATATGTCAATTATGCCAGTTATATG
66 TGAGTAAAAGAATAATGGCCTAGCTGTGCATTTGGCAAAAAGATGTCAATTATGCCACTTAGATG
256048 AACAGTTAAATATCGTTGAGTAAAAGATAAAT
131 AACAGTTAAATATCGTTGAGTAAAAGATAAAT
* * * *
256080 GACCTAGCTGTGCAATTGGCAGAAAGGTGTCAATTATGCTAGTTAGATG
1 GGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATG
256129 CTTTGTTGTT
Statistics
Matches: 186, Mismatches: 22, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
161 136 0.73
162 50 0.27
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (162 bp):
GGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
TGAGTAAAAGAATAATGGCCTAGCTGTGCATTTGGCAAAAAGATGTCAATTATGCCACTTAGATG
AACAGTTAAATATCGTTGAGTAAAAGATAAAT
Found at i:257899 original size:16 final size:16
Alignment explanation
Indices: 257878--257910 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
257868 AATGTTAGAA
*
257878 ATCGAAACAAGTGATT
1 ATCGAAACAAATGATT
257894 ATCGAAACAAATGATT
1 ATCGAAACAAATGATT
257910 A
1 A
257911 CCTACAGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.24
Consensus pattern (16 bp):
ATCGAAACAAATGATT
Found at i:259901 original size:28 final size:27
Alignment explanation
Indices: 259865--259930 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 27
259855 AATTTATTCG
*
259865 TTTTCATTTTTTTTTGGATTT-TTTTCTA
1 TTTTTATTTTTTTTT-GATTTGTTTT-TA
259893 TTTTTATTTATTTTTTGATTTGTTTTTA
1 TTTTTATTT-TTTTTTGATTTGTTTTTA
259921 -TTTTATTTTT
1 TTTTTATTTTT
259931 GATGAAAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
26 2 0.06
27 8 0.23
28 15 0.43
29 10 0.29
ACGTcount: A:0.12, C:0.03, G:0.06, T:0.79
Consensus pattern (27 bp):
TTTTTATTTTTTTTTGATTTGTTTTTA
Found at i:260010 original size:20 final size:20
Alignment explanation
Indices: 259968--260010 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
259958 AATTGAAATT
* *
259968 AAAATTGAAACAAAACTGAA
1 AAAATTGAAAAAAAACCGAA
259988 AAAATTGAAAAAGAAACCGAA
1 AAAATTGAAAAA-AAACCGAA
260009 AA
1 AA
260011 TGATTAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.67, C:0.09, G:0.12, T:0.12
Consensus pattern (20 bp):
AAAATTGAAAAAAAACCGAA
Found at i:266799 original size:13 final size:14
Alignment explanation
Indices: 266767--266803 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
266757 AATGTCTTTA
266767 TTCAATA-AATATG
1 TTCAATACAATATG
*
266780 TTAAATACAATATG
1 TTCAATACAATATG
266794 -TCAATACAAT
1 TTCAATACAAT
266804 CATCATATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (14 bp):
TTCAATACAATATG
Found at i:267770 original size:19 final size:19
Alignment explanation
Indices: 267746--267784 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
267736 TGTCCAAAAA
267746 TAGCAGCGACAAAAGCTAT
1 TAGCAGCGACAAAAGCTAT
267765 TAGCAGCGACAAAAGCTAT
1 TAGCAGCGACAAAAGCTAT
267784 T
1 T
267785 CCCAACTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.18
Consensus pattern (19 bp):
TAGCAGCGACAAAAGCTAT
Found at i:270254 original size:24 final size:24
Alignment explanation
Indices: 270222--270268 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
270212 GTCATCCACC
270222 ACATTCTCTTTCCCTGGATGATAT
1 ACATTCTCTTTCCCTGGATGATAT
270246 ACATTCTCTTTCCCTGGATGATA
1 ACATTCTCTTTCCCTGGATGATA
270269 CTCGATTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.21, C:0.26, G:0.13, T:0.40
Consensus pattern (24 bp):
ACATTCTCTTTCCCTGGATGATAT
Found at i:275792 original size:17 final size:17
Alignment explanation
Indices: 275770--275809 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
275760 CAATGACTGA
275770 GGATTAATTAGGTGATT
1 GGATTAATTAGGTGATT
275787 GGATTAATTAGGTGATT
1 GGATTAATTAGGTGATT
275804 GGATTA
1 GGATTA
275810 CTTTGGAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.30, T:0.40
Consensus pattern (17 bp):
GGATTAATTAGGTGATT
Found at i:280880 original size:19 final size:19
Alignment explanation
Indices: 280856--280893 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
280846 GATTTTAGTG
280856 AGCAAAATATAGAGTTAAA
1 AGCAAAATATAGAGTTAAA
280875 AGCAAAATATAGAGTTAAA
1 AGCAAAATATAGAGTTAAA
280894 TTAATGAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.58, C:0.05, G:0.16, T:0.21
Consensus pattern (19 bp):
AGCAAAATATAGAGTTAAA
Found at i:285354 original size:19 final size:19
Alignment explanation
Indices: 285330--285366 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
285320 ATTAAAAAGT
285330 CATTTAATTAGTTATAAGG
1 CATTTAATTAGTTATAAGG
285349 CATTTAATTAGTTATAAG
1 CATTTAATTAGTTATAAG
285367 AAAATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43
Consensus pattern (19 bp):
CATTTAATTAGTTATAAGG
Found at i:290145 original size:18 final size:19
Alignment explanation
Indices: 290107--290141 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
290097 AAGGAAGAAT
290107 AAATGATAATAAATATAAG
1 AAATGATAATAAATATAAG
290126 AAATGA-AATAAA-ATAA
1 AAATGATAATAAATATAA
290142 AGAAGGGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 6 0.38
19 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.23
Consensus pattern (19 bp):
AAATGATAATAAATATAAG
Found at i:291352 original size:12 final size:12
Alignment explanation
Indices: 291337--291376 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
291327 ATATAAATTT
291337 ATATAATGTATA
1 ATATAATGTATA
291349 ATATAAAT-T-T-
1 ATAT-AATGTATA
291359 ATATAATGTATA
1 ATATAATGTATA
291371 ATATAA
1 ATATAA
291377 GAACGTGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
9 3 0.12
10 5 0.21
11 2 0.08
12 11 0.46
13 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (12 bp):
ATATAATGTATA
Found at i:291353 original size:22 final size:22
Alignment explanation
Indices: 291327--291376 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
291317 TAAACTAAGT
291327 ATATAAATTTATATAATGTATA
1 ATATAAATTTATATAATGTATA
291349 ATATAAATTTATATAATGTATA
1 ATATAAATTTATATAATGTATA
291371 ATATAA
1 ATATAA
291377 GAACGTGAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (22 bp):
ATATAAATTTATATAATGTATA
Found at i:294156 original size:18 final size:17
Alignment explanation
Indices: 294133--294167 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
294123 TAGGTTAGGG
294133 TAGAAAGAATAGAAGAAA
1 TAGAAAG-ATAGAAGAAA
*
294151 TAGAAAGGTAGAAGAAA
1 TAGAAAGATAGAAGAAA
294168 GGAATCAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.11
Consensus pattern (17 bp):
TAGAAAGATAGAAGAAA
Found at i:294398 original size:19 final size:18
Alignment explanation
Indices: 294376--294423 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
294366 CTTTTTTGAA
*
294376 TTTCTTTTTCTTTTCTTCT
1 TTTCTTTTT-TTATCTTCT
*
294395 TTTCTTATTTTTATCTTTT
1 TTTCTT-TTTTTATCTTCT
294414 TTTCTTTTTT
1 TTTCTTTTTT
294424 GCACTCCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 4 0.15
19 19 0.73
20 3 0.12
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTCTTTTTTTATCTTCT
Found at i:294422 original size:8 final size:8
Alignment explanation
Indices: 294380--294423 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
294370 TTTGAATTTC
294380 TTTTTCTT
1 TTTTTCTT
*
294388 TTCTTCTT
1 TTTTTCTT
* *
294396 TTCTTATT
1 TTTTTCTT
*
294404 TTTATCTT
1 TTTTTCTT
294412 TTTTTCTT
1 TTTTTCTT
294420 TTTT
1 TTTT
294424 GCACTCCAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTCTT
Found at i:294683 original size:21 final size:22
Alignment explanation
Indices: 294659--294703 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
294649 TAAGAAAGGA
*
294659 ATAATAAATGAAAT-AATAAAG
1 ATAAGAAATGAAATAAATAAAG
294680 ATAAGAAATGAAATGAAATAAAG
1 ATAAGAAATGAAAT-AAATAAAG
294703 A
1 A
294704 AGGGATAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.62
23 8 0.38
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (22 bp):
ATAAGAAATGAAATAAATAAAG
Found at i:300210 original size:2 final size:2
Alignment explanation
Indices: 300205--300276 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
300195 TTAAAAAGTA
300205 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
300247 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
300277 TATTCATTCA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:303185 original size:30 final size:30
Alignment explanation
Indices: 303151--303217 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
303141 ATTTTTTCCA
303151 TAAACTTCTCCAAATTTATAATTTAGCCAC
1 TAAACTTCTCCAAATTTATAATTTAGCCAC
*
303181 TAAACTTCTCCAAATTTATACTTTAGCCAC
1 TAAACTTCTCCAAATTTATAATTTAGCCAC
303211 TAAACTT
1 TAAACTT
303218 TGAAAACTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (30 bp):
TAAACTTCTCCAAATTTATAATTTAGCCAC
Found at i:308434 original size:25 final size:25
Alignment explanation
Indices: 308406--308471 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 25
308396 CACTAGGTAC
*
308406 CTAGCTAACTACCTACA-CTACCTAG
1 CTAGCTAACTACCTA-AGCTACATAG
308431 CTAG-T---TACCTAAGCTACATAG
1 CTAGCTAACTACCTAAGCTACATAG
* *
308452 CTAGCTAACCACCTATGCTA
1 CTAGCTAACTACCTAAGCTA
308472 GCTTCTTACT
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
20 1 0.03
21 17 0.52
22 1 0.03
24 1 0.03
25 13 0.39
ACGTcount: A:0.32, C:0.32, G:0.11, T:0.26
Consensus pattern (25 bp):
CTAGCTAACTACCTAAGCTACATAG
Found at i:308439 original size:21 final size:21
Alignment explanation
Indices: 308403--308458 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
308393 CGACACTAGG
*
308403 TACCTAGCTAACTACCTACA-C
1 TACCTAGCTAGCTACCTA-AGC
*
308424 TACCTAGCTAGTTACCTAAGC
1 TACCTAGCTAGCTACCTAAGC
*
308445 TACATAGCTAGCTA
1 TACCTAGCTAGCTA
308459 ACCACCTATG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.32, C:0.30, G:0.11, T:0.27
Consensus pattern (21 bp):
TACCTAGCTAGCTACCTAAGC
Found at i:308630 original size:20 final size:21
Alignment explanation
Indices: 308589--308630 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
308579 CTACCATATG
* *
308589 ATTCATTAATATGGCATGTGC
1 ATTCATTAATAAGGCATCTGC
308610 ATTCATTAA-AAGGCATCTGC
1 ATTCATTAATAAGGCATCTGC
308630 A
1 A
308631 CTCTTTGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (21 bp):
ATTCATTAATAAGGCATCTGC
Found at i:319780 original size:22 final size:21
Alignment explanation
Indices: 319755--319797 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
319745 TTAGCCACCT
*
319755 ATTAAAATTATTAATTTCCAAA
1 ATTAAAATTAATAA-TTCCAAA
319777 ATTAAAATTAATAATTCCAAA
1 ATTAAAATTAATAATTCCAAA
319798 CCATTTAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (21 bp):
ATTAAAATTAATAATTCCAAA
Found at i:327468 original size:22 final size:21
Alignment explanation
Indices: 327440--327495 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
327430 ACTGAAAGGG
*
327440 AGTATCGATACCATAATATAGA
1 AGTATCGATACCATAAGATA-A
327462 AGTATCGATA-C-TAAGATAA
1 AGTATCGATACCATAAGATAA
327481 AGGTATCGATACCAT
1 A-GTATCGATACCAT
327496 GAATTACAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.07
20 15 0.50
21 2 0.07
22 11 0.37
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (21 bp):
AGTATCGATACCATAAGATAA
Found at i:327532 original size:34 final size:34
Alignment explanation
Indices: 327482--327560 Score: 122
Period size: 34 Copynumber: 2.3 Consensus size: 34
327472 CTAAGATAAA
* *
327482 GGTATCGATACCATGAATTACAGAATGTAGAAAT
1 GGTATCGATACAATGAATTACAGAATGTAGAAAG
* *
327516 GTTATCGATACAATGAATTATAGAATGTAGAAAG
1 GGTATCGATACAATGAATTACAGAATGTAGAAAG
327550 GGTATCGATAC
1 GGTATCGATAC
327561 TAGAAGGGCG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.28
Consensus pattern (34 bp):
GGTATCGATACAATGAATTACAGAATGTAGAAAG
Found at i:327593 original size:17 final size:17
Alignment explanation
Indices: 327571--327614 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
327561 TAGAAGGGCG
327571 TATCGATACTTCTATAC
1 TATCGATACTTCTATAC
327588 TATCGATACTTCTATAC
1 TATCGATACTTCTATAC
327605 TATCGATACT
1 TATCGATACT
327615 ATTGAGTCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.41
Consensus pattern (17 bp):
TATCGATACTTCTATAC
Found at i:327613 original size:9 final size:9
Alignment explanation
Indices: 327571--327616 Score: 60
Period size: 9 Copynumber: 5.3 Consensus size: 9
327561 TAGAAGGGCG
327571 TATCGATAC
1 TATCGATAC
*
327580 T-TCTATAC
1 TATCGATAC
327588 TATCGATAC
1 TATCGATAC
*
327597 T-TCTATAC
1 TATCGATAC
327605 TATCGATAC
1 TATCGATAC
327614 TAT
1 TAT
327617 TGAGTCTGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
8 14 0.45
9 17 0.55
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (9 bp):
TATCGATAC
Found at i:327994 original size:45 final size:46
Alignment explanation
Indices: 327945--328068 Score: 173
Period size: 45 Copynumber: 2.8 Consensus size: 46
327935 GTTTTCATTA
*
327945 CATAAATGAAATGCATAACGGTGCATTAAAGGCATTAAAAAAAT-T
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATTAAAAAAATGC
* **
327990 CATAAATGAAATGCATAACGGTGCATTAAAGGCA-TGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATTAAAAAAATGC
* *
328035 CAT-GATGAAATGCATAACAGTGCATTAAAGGCAT
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCAT
328069 GAAAGGATGT
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
44 34 0.48
45 37 0.52
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.23
Consensus pattern (46 bp):
CATAAATGAAATGCATAACGGTGCATTAAAGGCATTAAAAAAATGC
Found at i:328058 original size:44 final size:45
Alignment explanation
Indices: 327945--328089 Score: 204
Period size: 44 Copynumber: 3.2 Consensus size: 45
327935 GTTTTCATTA
* ** *
327945 CATAAATGAAATGCATAACGGTGCATTAAAGGCATTAAAAAAAT-T
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCA-TGAAAGGATGC
327990 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* * *
328035 CAT-GATGAAATGCATAACAGTGCATTAAAGGCATGAAAGGATGT
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
328079 CATAAATGAAA
1 CATAAATGAAA
328090 ATAATGAATA
Statistics
Matches: 90, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
44 47 0.52
45 43 0.48
ACGTcount: A:0.46, C:0.12, G:0.21, T:0.22
Consensus pattern (45 bp):
CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
Found at i:341719 original size:15 final size:15
Alignment explanation
Indices: 341701--341733 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
341691 GACTTCTACC
341701 TTTCTTGCTTCATTG
1 TTTCTTGCTTCATTG
*
341716 TTTCTTTCTTCATTG
1 TTTCTTGCTTCATTG
341731 TTT
1 TTT
341734 GGGTACGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.18, G:0.09, T:0.67
Consensus pattern (15 bp):
TTTCTTGCTTCATTG
Found at i:349742 original size:10 final size:11
Alignment explanation
Indices: 349708--349740 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
349698 ATGTTTTAAG
349708 AATATT-AAAA
1 AATATTAAAAA
349718 AATATTAAAAA
1 AATATTAAAAA
349729 AATATATAAAAA
1 AATAT-TAAAAA
349741 TACTATCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 6 0.29
11 9 0.43
12 6 0.29
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AATATTAAAAA
Found at i:359824 original size:30 final size:31
Alignment explanation
Indices: 359765--359840 Score: 100
Period size: 30 Copynumber: 2.4 Consensus size: 31
359755 TTGGGGCATG
*
359765 GGGCCTACCTAAGAATACATCTTAGGGCCGCA
1 GGGCCTA-CTAAGAATACATCTCAGGGCCGCA
*
359797 GGGCCTACTGAGAATA-ATCTCAGGGCCGCA
1 GGGCCTACTAAGAATACATCTCAGGGCCGCA
*
359827 GAGCCTACCTAAGA
1 GGGCCTA-CTAAGA
359841 GTCACATTAG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
30 19 0.49
31 13 0.33
32 7 0.18
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.17
Consensus pattern (31 bp):
GGGCCTACTAAGAATACATCTCAGGGCCGCA
Found at i:364875 original size:19 final size:19
Alignment explanation
Indices: 364839--364875 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
364829 AATAATGAGC
**
364839 TTTTATAATTTTTTTAAAG
1 TTTTATAATTTTCATAAAG
364858 TTTTATAATTTTCATAAA
1 TTTTATAATTTTCATAAA
364876 TCTTAAAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTTATAATTTTCATAAAG
Found at i:367640 original size:17 final size:17
Alignment explanation
Indices: 367599--367639 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
367589 ATAAATAAAT
367599 AAATAATA-AAAATATA
1 AAATAATATAAAATATA
*
367615 AAATCATATAAAATA-A
1 AAATAATATAAAATATA
367631 AAAT-ATATA
1 AAATAATATA
367640 TCTCTCAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 5 0.22
16 12 0.52
17 6 0.26
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATAATATAAAATATA
Found at i:367805 original size:21 final size:21
Alignment explanation
Indices: 367781--367832 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
367771 ACATTACACA
*
367781 TATATTTAACTTAAGCCATAC
1 TATATTTAACCTAAGCCATAC
*
367802 TATATTTAACCTAGGCCATAC
1 TATATTTAACCTAAGCCATAC
*
367823 TATATGTAAC
1 TATATTTAAC
367833 ATATATATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.37
Consensus pattern (21 bp):
TATATTTAACCTAAGCCATAC
Found at i:367863 original size:3 final size:3
Alignment explanation
Indices: 367855--367900 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
367845 ATATAAAAGG
367855 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
367901 GATAAAAACA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:368461 original size:27 final size:27
Alignment explanation
Indices: 368400--368461 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
368390 TTTTATGGAA
* *
368400 CCCTATTTTTCATTTTTTCCTCCCATGT
1 CCCT-TTTTTCATTTTTTCCTACCATCT
* *
368428 GCATTTTTTCATTCTTTTCC-ACCATCT
1 CCCTTTTTTCATT-TTTTCCTACCATCT
368455 CCCTTTT
1 CCCTTTT
368462 GTTTCTCTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.11, C:0.32, G:0.03, T:0.53
Consensus pattern (27 bp):
CCCTTTTTTCATTTTTTCCTACCATCT
Found at i:369421 original size:12 final size:12
Alignment explanation
Indices: 369404--369428 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
369394 TTGCACTGAT
369404 ATAGATACGGGG
1 ATAGATACGGGG
369416 ATAGATACGGGG
1 ATAGATACGGGG
369428 A
1 A
369429 CGGGGATGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.40, T:0.16
Consensus pattern (12 bp):
ATAGATACGGGG
Found at i:370086 original size:21 final size:21
Alignment explanation
Indices: 370060--370100 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
370050 ATATATTGAA
* *
370060 AAAATAAAATATACAGTAAAT
1 AAAATAAAAAATAAAGTAAAT
370081 AAAATAAAAAATAAAGTAAA
1 AAAATAAAAAATAAAGTAAA
370101 ATTCAATAAT
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:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (21 bp):
AAAATAAAAAATAAAGTAAAT
Found at i:379853 original size:196 final size:197
Alignment explanation
Indices: 379519--379913 Score: 783
Period size: 196 Copynumber: 2.0 Consensus size: 197
379509 GAAGGATTAA
379519 AATGTGATTTTCCATTTTTAATAAGCCAAATATGCAATAATAAATAAAATGCAAAAAGTACACAA
1 AATGTGATTTTCCATTTTTAATAAGCCAAATATGCAATAATAAATAAAATGCAAAAAGTACACAA
379584 TTAGGACAACAAGATTTCAAAAAAATAAATAGTCACTACAGGTGGCCAGAATACAAAAACACGCT
66 TTAGGACAACAAGATTTCAAAAAAATAAATAGTCACTACAGGTGGCCAGAATACAAAAACACGCT
379649 AAAACTA-GGGAACTAAAAAGAAAATATTATAAAAAGACATAACACGTATAAAAAAGGGTAAATA
131 AAAACTAGGGGAACTAAAAAGAAAATATTATAAAAAGACATAACACGTATAAAAAAGGGTAAATA
379713 AC
196 AC
379715 AATGTGATTTTCCATTTTTAATAAGCCAAATATGCAATAATAAATAAAATGCAAAAAGTACACAA
1 AATGTGATTTTCCATTTTTAATAAGCCAAATATGCAATAATAAATAAAATGCAAAAAGTACACAA
379780 TTAGGACAACAAGATTTCAAAAAAATAAATAGTCACTACAGGTGGCCAGAATACAAAAACACGCT
66 TTAGGACAACAAGATTTCAAAAAAATAAATAGTCACTACAGGTGGCCAGAATACAAAAACACGCT
379845 AAAACTAGGGGAACTAAAAAGAAAATATTATAAAAAGACATAACACGTATAAAAAAGGGTAAATA
131 AAAACTAGGGGAACTAAAAAGAAAATATTATAAAAAGACATAACACGTATAAAAAAGGGTAAATA
379910 AC
196 AC
379912 AA
1 AA
379914 ATTTGGTCAT
Statistics
Matches: 198, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
196 137 0.69
197 61 0.31
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.21
Consensus pattern (197 bp):
AATGTGATTTTCCATTTTTAATAAGCCAAATATGCAATAATAAATAAAATGCAAAAAGTACACAA
TTAGGACAACAAGATTTCAAAAAAATAAATAGTCACTACAGGTGGCCAGAATACAAAAACACGCT
AAAACTAGGGGAACTAAAAAGAAAATATTATAAAAAGACATAACACGTATAAAAAAGGGTAAATA
AC
Found at i:381201 original size:40 final size:39
Alignment explanation
Indices: 381147--381245 Score: 135
Period size: 40 Copynumber: 2.5 Consensus size: 39
381137 TACTAACCAT
**
381147 ACTCCTTTGTGATGGTTGACCCAAGGTGATGCTGATCCA
1 ACTCCTTTGTGATGGACGACCCAAGGTGATGCTGATCCA
* *
381186 ACTCCTTATGTGATGGACGAGCCAAGGTGATGTTGATCCA
1 ACTCCTT-TGTGATGGACGACCCAAGGTGATGCTGATCCA
*
381226 ACTTCTTTTGTGATGGACGA
1 AC-TCCTTTGTGATGGACGA
381246 GTAAAATGAT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
39 7 0.13
40 42 0.79
41 4 0.08
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.31
Consensus pattern (39 bp):
ACTCCTTTGTGATGGACGACCCAAGGTGATGCTGATCCA
Found at i:381246 original size:40 final size:40
Alignment explanation
Indices: 381167--381367 Score: 170
Period size: 42 Copynumber: 4.9 Consensus size: 40
381157 GATGGTTGAC
* *
381167 CCAAGGTGATGCTGATCCAACTCCTTATGTGATGGACGAG
1 CCAAGGTGATGTTGATCCAACTTCTTATGTGATGGACGAG
*
381207 CCAAGGTGATGTTGATCCAACTTCTTTTGTGATGGACGAG
1 CCAAGGTGATGTTGATCCAACTTCTTATGTGATGGACGAG
** * * * * * *
381247 TAAAATGATTATGCTGATCCAACTCCTTATATGATGAACGAG
1 -CCAA-GGTGATGTTGATCCAACTTCTTATGTGATGGACGAG
* * ** * *
381289 CGAAATGATGATGTTGATCCAACTTCTTATGCAATGGATGAA
1 C-CAA-GGTGATGTTGATCCAACTTCTTATGTGATGGACGAG
* *
381331 CCAAGGTTGATGTTGTTTCAAC-TCTTTATGTGATGGA
1 CCAAGG-TGATGTTGATCCAACTTC-TTATGTGATGGA
381368 ATCGAGCTAA
Statistics
Matches: 128, Mismatches: 28, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
40 40 0.31
41 27 0.21
42 61 0.48
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (40 bp):
CCAAGGTGATGTTGATCCAACTTCTTATGTGATGGACGAG
Found at i:381482 original size:118 final size:117
Alignment explanation
Indices: 381359--381937 Score: 697
Period size: 118 Copynumber: 4.9 Consensus size: 117
381349 CAACTCTTTA
* * * *
381359 TGTGATGGAATCGAGCTAAGGTTGAACAAGTT-TGTCTTATTATGAACTTCATCTCCCTCATCGG
1 TGTGATGGATTCGAACAAAGGTTGAACAAGTTCT-TCTCATTATGAACTTCATCTCCCTCATCGG
* *
381423 ATGAGTTTTTCTCATTATGAACCATTCCATTGAAAATGTTGATCCACCCCCTTC
65 ATGAGTTTTTCTCATTATGAACC-TTCCATTGGAAATGTTGATCCACCTCCTTC
* * *
381477 TGTGATGGATTCGAACAAAGGTTGAACAAGTTTTTCTCATTATGAACTT-ATTCTCCCTCGTCAG
1 TGTGATGGATTCGAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCA-TCTCCCTCATCGG
* * *
381541 ATGAGTTCTTCTCATTATGAA-CTCTCCTATTGGAAATGTTGACCCACCTCCTCC
65 ATGAGTTTTTCTCATTATGAACCT-TCC-ATTGGAAATGTTGATCCACCTCCTTC
* * * ** *
381595 TATGAT-GATTCGAACAAAGGTTAAACAAGTTCTTATCATTATGAACTTTTTCTCCCTCGTCGGA
1 TGTGATGGATTCGAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCATCTCCCTCATCGGA
* * *
381659 TGAGTTCTTT-TTAGTATGAACCCTTCCATTGAAAATGTTGATCCACCTCCTTC
66 TGAGTT-TTTCTCATTATGAA-CCTTCCATTGGAAATGTTGATCCACCTCCTTC
* * * *
381712 TATGATGGATTCGATCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTCCCTCATCGGA
1 TGTGATGGATTCGAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCATCTCCCTCATCGGA
** * *
381777 TGAGTTCATCTCATTATGAACTCTCCCACTGGAAATGTTGATCCACCTCC-TC
66 TGAGTTTTTCTCATTATGAAC-CTTCCATTGGAAATGTTGATCCACCTCCTTC
* *
381829 ATGTGATCGATTCGAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCA-CTCCCTCATCA
1 -TGTGATGGATTCGAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTT-CATCTCCCTCATCG
*
381893 GATGA-TTTCTTCTCAAATATGAACCCTTCCATTGGAAATGTTGAT
64 GATGAGTTT-TTCTC-ATTATGAA-CCTTCCATTGGAAATGTTGAT
381938 TGGTTTATCC
Statistics
Matches: 398, Mismatches: 47, Indels: 31
0.84 0.10 0.07
Matches are distributed among these distances:
116 1 0.00
117 106 0.27
118 261 0.66
119 29 0.07
120 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.36
Consensus pattern (117 bp):
TGTGATGGATTCGAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCATCTCCCTCATCGGA
TGAGTTTTTCTCATTATGAACCTTCCATTGGAAATGTTGATCCACCTCCTTC
Found at i:381688 original size:235 final size:236
Alignment explanation
Indices: 381397--381937 Score: 782
Period size: 235 Copynumber: 2.3 Consensus size: 236
381387 AGTTTGTCTT
* * *
381397 ATTATGAACTTCATCTCCCTCATCGGATGAGTT-TTTCTCATTATGAACCATTCCATTGAAAATG
1 ATTATGAACTTCATCTCCCTCATCGGATGAGTTCTTT-TAAATATGAACCCTTCCATTGAAAATG
* *
381461 TTGATCCACCCCCTTCTGTGATGGATTCGAACAAAGGTTGAACAAGTTTTTCTCATTATGAACTT
65 TTGATCCACCCCCTTCTATGATGGATTCGAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTT
* * * *
381526 ATTCTCCCTCGTCAGATGAGTTCTTCTCATTATGAACTCTCCTATTGGAAATGTTGACCCACCTC
130 ATTCTCCCTCATCAGATGAGTTCATCTCATTATGAACTCTCCCACTGGAAATGTTGACCCACCTC
*
381591 CTCCTATGAT-GATTCGAACAAAGGTTAAACAAGTTCTTATC
195 CTCATATGATCGATTCGAACAAAGGTTAAACAAGTTCTTATC
** * * *
381632 ATTATGAACTTTTTCTCCCTCGTCGGATGAGTTCTTTTTAGTATGAACCCTTCCATTGAAAATGT
1 ATTATGAACTTCATCTCCCTCATCGGATGAGTTCTTTTAAATATGAACCCTTCCATTGAAAATGT
* * *
381697 TGATCCACCTCCTTCTATGATGGATTCGATCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
66 TGATCCACCCCCTTCTATGATGGATTCGAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTA
* * *
381762 TTTTCCCTCATCGGATGAGTTCATCTCATTATGAACTCTCCCACTGGAAATGTTGATCCACCTCC
131 TTCTCCCTCATCAGATGAGTTCATCTCATTATGAACTCTCCCACTGGAAATGTTGACCCACCTCC
* * *
381827 TCATGTGATCGATTCGAACAAAGGTTGAACAAGTTCTTCTC
196 TCATATGATCGATTCGAACAAAGGTTAAACAAGTTCTTATC
* * * *
381868 ATTATGAACTTCCA-CTCCCTCATCAGATGATTTCTTCTCAAATATGAACCCTTCCATTGGAAAT
1 ATTATGAACTT-CATCTCCCTCATCGGATGAGTTCTT-TTAAATATGAACCCTTCCATTGAAAAT
381932 GTTGAT
64 GTTGAT
381938 TGGTTTATCC
Statistics
Matches: 271, Mismatches: 31, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
235 180 0.66
236 62 0.23
237 29 0.11
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.36
Consensus pattern (236 bp):
ATTATGAACTTCATCTCCCTCATCGGATGAGTTCTTTTAAATATGAACCCTTCCATTGAAAATGT
TGATCCACCCCCTTCTATGATGGATTCGAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTA
TTCTCCCTCATCAGATGAGTTCATCTCATTATGAACTCTCCCACTGGAAATGTTGACCCACCTCC
TCATATGATCGATTCGAACAAAGGTTAAACAAGTTCTTATC
Found at i:383014 original size:1 final size:1
Alignment explanation
Indices: 383010--383056 Score: 67
Period size: 1 Copynumber: 47.0 Consensus size: 1
383000 TTTATTTTCC
* * *
383010 TTTTTTTCTTTTTTTTTTTTTTTTCTTTTTTCTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
383057 CTTAAGTGTA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:383032 original size:25 final size:24
Alignment explanation
Indices: 382998--383057 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
382988 TTAAACCCTC
*
382998 TTTTTATTTTCCTTTTTTTCTTTTT
1 TTTTTTTTTTCC-TTTTTTCTTTTT
*
383023 TTTTTTTTTTTCTTTTTTCTTTTT
1 TTTTTTTTTTCCTTTTTTCTTTTT
383047 TTTTTTTTTTC
1 TTTTTTTTTTC
383058 TTAAGTGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
24 22 0.69
25 10 0.31
ACGTcount: A:0.02, C:0.10, G:0.00, T:0.88
Consensus pattern (24 bp):
TTTTTTTTTTCCTTTTTTCTTTTT
Found at i:384457 original size:31 final size:30
Alignment explanation
Indices: 384394--384459 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 30
384384 AGTACAGTTA
* ** *
384394 AATTAAAGAATTTAAAGAATAATGAATGCT
1 AATTAAAGAATTCAAAGAATAAAAAATACT
*
384424 AATTAAATTAATTCAAAGAATAAAAAATACT
1 AATTAAA-GAATTCAAAGAATAAAAAATACT
384455 AATTA
1 AATTA
384460 TGGACATAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 7 0.23
31 23 0.77
ACGTcount: A:0.58, C:0.05, G:0.08, T:0.30
Consensus pattern (30 bp):
AATTAAAGAATTCAAAGAATAAAAAATACT
Found at i:385990 original size:21 final size:22
Alignment explanation
Indices: 385964--386005 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
385954 GAACAGTGAA
385964 GGTATCGATACAC-TGTAGCAG
1 GGTATCGATACACTTGTAGCAG
* *
385985 GGTATCGGTACCCTTGTAGCA
1 GGTATCGATACACTTGTAGCA
386006 TTCTGTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (22 bp):
GGTATCGATACACTTGTAGCAG
Found at i:386505 original size:45 final size:45
Alignment explanation
Indices: 386449--386663 Score: 242
Period size: 45 Copynumber: 4.8 Consensus size: 45
386439 TATAAAATTT
* *
386449 CTTATCATTTA-TCCTATAAGCTCTTAAGCTTATTTTACCGATATA
1 CTTACCATTTATTCC-ATAAGCTCTTAAGCTTATTTTACCAATATA
* * * *
386494 CTTACCATTTATTCCATAAGATCGTAAGCTTATTGTATCAATATA
1 CTTACCATTTATTCCATAAGCTCTTAAGCTTATTTTACCAATATA
* * *
386539 CTTACCATTTATTCCATAAGGT-TGTAAGCTTGTTTTATCAATATA
1 CTTACCATTTATTCCATAAGCTCT-TAAGCTTATTTTACCAATATA
*
386584 CTTACCATTAATTCCATAAGCT-TGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCT-TAAGCTTATTTTACCAATATA
* * *
386629 ATTGTCC--TTATTCCATAAGCTCGTAAGCTTATTTT
1 CTT-ACCATTTATTCCATAAGCTCTTAAGCTTATTTT
386664 CATGATTACC
Statistics
Matches: 148, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
44 25 0.17
45 118 0.80
46 5 0.03
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.43
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCTTAAGCTTATTTTACCAATATA
Found at i:386930 original size:40 final size:40
Alignment explanation
Indices: 386767--386928 Score: 225
Period size: 40 Copynumber: 4.0 Consensus size: 40
386757 ATCGTAGTGC
* *
386767 TACAAATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
** *
386807 TACACATAAAATCGTGCCCACCATATACACCAAAATGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
**
386847 TACACATAAGGTCGTATCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
* * * *
386887 TATACATAAGGTCTTGCCCACAATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
386927 TA
1 TA
386929 TAAACCTGCA
Statistics
Matches: 106, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 106 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.25
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
Found at i:388835 original size:30 final size:30
Alignment explanation
Indices: 388801--388873 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
388791 AAAATTACAT
* *
388801 TTTGGTCCCTAAACTTT-TCAAAGTTTATAC
1 TTTGGTCCCTAAACTTTACCAAA-TTTATAA
388831 TTTGGTCACC-AAACTTTACCAAATTTATAA
1 TTTGGTC-CCTAAACTTTACCAAATTTATAA
*
388861 TTTGGTCACTAAA
1 TTTGGTCCCTAAA
388874 TCAATTTATG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 1 0.03
30 30 0.81
31 6 0.16
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.40
Consensus pattern (30 bp):
TTTGGTCCCTAAACTTTACCAAATTTATAA
Found at i:390669 original size:2 final size:2
Alignment explanation
Indices: 390662--390699 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
390652 CAAAAGTGAA
390662 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
390700 TAATCATATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:393204 original size:40 final size:40
Alignment explanation
Indices: 393160--393240 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
393150 ATCCAATATT
393160 TTACACATAAGGTCGTACCCACCATATACACCGAAGTGTA
1 TTACACATAAGGTCGTACCCACCATATACACCGAAGTGTA
* *
393200 TTACACATAAGGTCGTGCCCATCATATACACCGAAGTGTA
1 TTACACATAAGGTCGTACCCACCATATACACCGAAGTGTA
393240 T
1 T
393241 AATAAACATG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (40 bp):
TTACACATAAGGTCGTACCCACCATATACACCGAAGTGTA
Found at i:402743 original size:26 final size:26
Alignment explanation
Indices: 402712--402762 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
402702 CATTTTGATC
402712 ATCTCTAGGAGTTTTCATAGAAGAAT
1 ATCTCTAGGAGTTTTCATAGAAGAAT
402738 ATCTCTAGGAGTTTTCATAGAAGAA
1 ATCTCTAGGAGTTTTCATAGAAGAA
402763 GAAATATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (26 bp):
ATCTCTAGGAGTTTTCATAGAAGAAT
Found at i:412652 original size:74 final size:74
Alignment explanation
Indices: 412530--412680 Score: 216
Period size: 74 Copynumber: 2.0 Consensus size: 74
412520 GTGGGGCATG
* **
412530 TTACCCGACCAATATGATTTTTGAAATGAATATTTTAAAGAAGCCAAGTTTTCTTTTCAAAGGTT
1 TTACCCGACCAATATGATTTCTGAAATGAATATTTTAAAGAAGCCAAGTTTGATTTTCAAAGGTT
412595 TCT-TGATGA
66 TCTAT-ATGA
* * *
412604 TTACCTGACTAATATGATGTTCTGAAATGAAT-TTTTAAAGAAGTCAAGTTTGATTTTCAAAGGT
1 TTACCCGACCAATATGAT-TTCTGAAATGAATATTTTAAAGAAGCCAAGTTTGATTTTCAAAGGT
412668 TTCTATATGA
65 TTCTATATGA
412678 TTA
1 TTA
412681 AATCCTTCAA
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
74 56 0.81
75 13 0.19
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.40
Consensus pattern (74 bp):
TTACCCGACCAATATGATTTCTGAAATGAATATTTTAAAGAAGCCAAGTTTGATTTTCAAAGGTT
TCTATATGA
Found at i:414246 original size:20 final size:20
Alignment explanation
Indices: 414223--414261 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
414213 GGTTTTAAGT
414223 AAAAGTATTT-GGTCAATGAG
1 AAAAGT-TTTAGGTCAATGAG
414243 AAAAGTTTTACGGTCAATG
1 AAAAGTTTTA-GGTCAATG
414262 TAAAATAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 6 0.35
21 8 0.47
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (20 bp):
AAAAGTTTTAGGTCAATGAG
Found at i:414538 original size:20 final size:20
Alignment explanation
Indices: 414513--414604 Score: 103
Period size: 20 Copynumber: 4.5 Consensus size: 20
414503 TTTTCCCAAT
*
414513 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* **
414533 TCGCAACGCGAATGGGAAAA
1 TCGCAATGCGAATAAGAAAA
*
414553 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* **
414573 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
414594 TCGCAATGCGA
1 TCGCAATGCGA
414605 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
20 43 0.74
21 15 0.26
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.16
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:414557 original size:40 final size:41
Alignment explanation
Indices: 414513--414604 Score: 177
Period size: 40 Copynumber: 2.3 Consensus size: 41
414503 TTTTCCCAAT
414513 TCGCAATGCGAATAAGTAAATCGCAACGCGAA-TGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
414553 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
414594 TCGCAATGCGA
1 TCGCAATGCGA
414605 TACTTACTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 32 0.63
41 19 0.37
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.16
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:414689 original size:20 final size:20
Alignment explanation
Indices: 414639--414690 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
414629 AAAAAAAAAA
* *
414639 TCGCAACGAGATACTTACTT
1 TCGCAACGCGATACTGACTT
*
414659 TCGCAATGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
414679 TCGCAACGCGAT
1 TCGCAACGCGAT
414691 TTACATAGCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:415234 original size:19 final size:18
Alignment explanation
Indices: 415198--415281 Score: 132
Period size: 18 Copynumber: 4.5 Consensus size: 18
415188 TTCGAGAATG
415198 AAAATCGCAACGCGGAAAT
1 AAAATCGCAACGC-GAAAT
415217 AAAAATCGCAACGCGAAAT
1 -AAAATCGCAACGCGAAAT
415236 GAAAATCGCAACGCGAAAT
1 -AAAATCGCAACGCGAAAT
*
415255 AAAATCGCAACGCGAAAC
1 AAAATCGCAACGCGAAAT
415273 AAAATCGCA
1 AAAATCGCA
415282 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
18 26 0.42
19 23 0.37
20 13 0.21
ACGTcount: A:0.50, C:0.23, G:0.18, T:0.10
Consensus pattern (18 bp):
AAAATCGCAACGCGAAAT
Found at i:415248 original size:39 final size:37
Alignment explanation
Indices: 415194--415281 Score: 142
Period size: 37 Copynumber: 2.4 Consensus size: 37
415184 ATATTTCGAG
415194 AATGAAAATCGCAACGCGGAAATAAAAATCGCAACGCGA
1 AATGAAAATCGCAACGC-GAAAT-AAAATCGCAACGCGA
415233 AATGAAAATCGCAACGCGAAATAAAATCGCAACGCGA
1 AATGAAAATCGCAACGCGAAATAAAATCGCAACGCGA
*
415270 AA-CAAAATCGCA
1 AATGAAAATCGCA
415282 TTGCGATTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
36 9 0.19
37 17 0.35
38 5 0.10
39 17 0.35
ACGTcount: A:0.50, C:0.22, G:0.18, T:0.10
Consensus pattern (37 bp):
AATGAAAATCGCAACGCGAAATAAAATCGCAACGCGA
Found at i:415326 original size:19 final size:19
Alignment explanation
Indices: 415277--415366 Score: 146
Period size: 20 Copynumber: 4.7 Consensus size: 19
415267 CGAAACAAAA
*
415277 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
415296 TCGCGTTTGCGATTTTCATT
1 TCGCG-TTGCGATTTTCATT
415316 TCGCGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
415334 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
415354 TCGCGTTGCGATT
1 TCGCGTTGCGATT
415367 GTCTGGTCGC
Statistics
Matches: 67, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
18 11 0.16
19 26 0.39
20 30 0.45
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:415335 original size:38 final size:38
Alignment explanation
Indices: 415277--415366 Score: 153
Period size: 38 Copynumber: 2.3 Consensus size: 38
415267 CGAAACAAAA
* *
415277 TCGCATTGCGATTTTCATTTCGCGTTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATTTCGCGGTTGCGATTTTCATT
415316 TCGCGTTGCGATTTCATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTCATTTCGCGGTTGCGATTTTCATT
415354 TCGCGTTGCGATT
1 TCGCGTTGCGATT
415367 GTCTGGTCGC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 39 0.80
39 10 0.20
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTCATTTCGCGGTTGCGATTTTCATT
Found at i:415376 original size:19 final size:18
Alignment explanation
Indices: 415277--415457 Score: 132
Period size: 19 Copynumber: 10.1 Consensus size: 18
415267 CGAAACAAAA
*
415277 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
415296 TCGCGTTTGCGATTTTCATT
1 TCGCG-TTGCGA-TTTCATT
415316 TCGCGTTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
415334 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGA-TTTCATT
415354 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATT-TCATT
* * *
415370 T-G-GTCGCTA-GTCATT
1 TCGCGTTGCGATTTCATT
415385 TCGCGTTGCGA-TTC---
1 TCGCGTTGCGATTTCATT
* *
415399 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGAT-TTCATT
415418 TCCGCG-TGCGATTCTCATT
1 T-CGCGTTGCGATT-TCATT
*
415437 ATCTCGTTGCGATTTCATT
1 -TCGCGTTGCGATTTCATT
415456 TC
1 TC
415458 AACCAAAAGA
Statistics
Matches: 132, Mismatches: 12, Indels: 37
0.73 0.07 0.20
Matches are distributed among these distances:
12 2 0.02
14 15 0.11
15 2 0.02
16 4 0.03
17 7 0.05
18 15 0.11
19 46 0.35
20 41 0.31
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:415387 original size:31 final size:33
Alignment explanation
Indices: 415311--415433 Score: 117
Period size: 31 Copynumber: 3.6 Consensus size: 33
415301 TTTGCGATTT
* **
415311 TCATTTCGCGTTGCGATTTCATTTCGCGGTTGCGATTT
1 TCATTTCGCGTTGCGA-TTC---TCTCGG-TGCGATAG
* *
415349 TCATTTCGCGTTGCGATTGTCT-GGT-CGCTAG
1 TCATTTCGCGTTGCGATTCTCTCGGTGCGATAG
*
415380 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGGTGCGATAG
415413 TCATTTCCGCG-TGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
415434 ATTATCTCGT
Statistics
Matches: 74, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
31 24 0.32
32 3 0.04
33 23 0.31
34 6 0.08
37 2 0.03
38 16 0.22
ACGTcount: A:0.11, C:0.24, G:0.24, T:0.41
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGGTGCGATAG
Found at i:416352 original size:73 final size:72
Alignment explanation
Indices: 416233--416378 Score: 283
Period size: 73 Copynumber: 2.0 Consensus size: 72
416223 GATGACCGCA
416233 AAAGTTTGCGGGGCGATGGGTCGAAATACACTTTGTCAGGCTTTGTTTGGGCCTTTAAGGTAAGA
1 AAAGTTTGCGGGGCGATGGGTCGAAATACACTTTGTCAGGCTTTGTTTGGGCCTTTAAGGTAAGA
416298 ATTTCTAT
66 A-TTCTAT
416306 AAAGTTTGCGGGGCGATGGGTCGAAATACACTTTGTCAGGCTTTGTTTGGGCCTTTAAGGTAAGA
1 AAAGTTTGCGGGGCGATGGGTCGAAATACACTTTGTCAGGCTTTGTTTGGGCCTTTAAGGTAAGA
416371 ATTCTAT
66 ATTCTAT
416378 A
1 A
416379 TTTGTAGCAC
Statistics
Matches: 73, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
72 7 0.10
73 66 0.90
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.34
Consensus pattern (72 bp):
AAAGTTTGCGGGGCGATGGGTCGAAATACACTTTGTCAGGCTTTGTTTGGGCCTTTAAGGTAAGA
ATTCTAT
Found at i:416780 original size:14 final size:13
Alignment explanation
Indices: 416763--416801 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 13
416753 TAATTTTAAA
416763 AATTTATAAAATAT
1 AATTTATAAAA-AT
416777 AATTTTATAAAAAT
1 AA-TTTATAAAAAT
416791 AATTT-TAAAAA
1 AATTTATAAAAA
416802 ATTAAAAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 3 0.12
14 6 0.25
15 9 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AATTTATAAAAAT
Found at i:416785 original size:15 final size:15
Alignment explanation
Indices: 416765--416803 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
416755 ATTTTAAAAA
416765 TTTATAAAATATAAT
1 TTTATAAAATATAAT
416780 TTTATAAAA-ATAAT
1 TTTATAAAATATAAT
*
416794 TTTAAAAAAT
1 TTTATAAAAT
416804 TAAAAGGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TTTATAAAATATAAT
Found at i:416959 original size:13 final size:15
Alignment explanation
Indices: 416935--416966 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
416925 TATAAAATAT
416935 TTTTTGAAAAAT-TA
1 TTTTTGAAAAATGTA
416949 TTTTTG-AAAATGTA
1 TTTTTGAAAAATGTA
416963 TTTT
1 TTTT
416967 ATTTTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.56
Consensus pattern (15 bp):
TTTTTGAAAAATGTA
Found at i:422183 original size:4 final size:4
Alignment explanation
Indices: 422139--422164 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
422129 AATTAAAAGA
422139 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
422165 CTTTAACTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:425324 original size:17 final size:16
Alignment explanation
Indices: 425297--425348 Score: 81
Period size: 15 Copynumber: 3.4 Consensus size: 16
425287 CAGTAAAAAG
425297 ATATATATATATATAT
1 ATATATATATATATAT
425313 ATATAT-TATATATAT
1 ATATATATATATATAT
*
425328 ATATATAGA-ATATAT
1 ATATATATATATATAT
425343 ATATAT
1 ATATAT
425349 TTAAAGCATA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
15 27 0.79
16 7 0.21
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
ATATATATATATATAT
Found at i:425359 original size:19 final size:19
Alignment explanation
Indices: 425293--425366 Score: 85
Period size: 19 Copynumber: 3.8 Consensus size: 19
425283 AAACCAGTAA
425293 AAAGATATATATATATATAT
1 AAAGA-ATATATATATATAT
* * *
425313 ATATATTATATATATATAT
1 AAAGAATATATATATATAT
* *
425332 ATAGAATATATATATATTT
1 AAAGAATATATATATATAT
*
425351 AAAGCATATATATATA
1 AAAGAATATATATATA
425367 CACCCCATCC
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
19 43 0.93
20 3 0.07
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.43
Consensus pattern (19 bp):
AAAGAATATATATATATAT
Found at i:425366 original size:2 final size:2
Alignment explanation
Indices: 425297--425348 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
425287 CAGTAAAAAG
*
425297 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AG A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
425337 AT AT AT AT AT AT
1 AT AT AT AT AT AT
425349 TTAAAGCATA
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:425552 original size:19 final size:20
Alignment explanation
Indices: 425528--425568 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
425518 GTAAACGGAG
425528 ATATCAGA-ATCAAAACAGA
1 ATATCAGATATCAAAACAGA
*
425547 ATATCAGATATCAGAACAGA
1 ATATCAGATATCAAAACAGA
425567 AT
1 AT
425569 CCAGATCGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.54, C:0.15, G:0.12, T:0.20
Consensus pattern (20 bp):
ATATCAGATATCAAAACAGA
Found at i:425584 original size:22 final size:24
Alignment explanation
Indices: 425556--425614 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
425546 AATATCAGAT
*
425556 ATCAGAACAGAATCCA-G-ATCGA
1 ATCAGAACAGAATCCAGGTAACGA
* *
425578 ATCAGAACAGAATTCAGGTAACGT
1 ATCAGAACAGAATCCAGGTAACGA
425602 ATCAGAACAGAAT
1 ATCAGAACAGAAT
425615 TTAATTCGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
22 15 0.47
23 1 0.03
24 16 0.50
ACGTcount: A:0.46, C:0.19, G:0.19, T:0.17
Consensus pattern (24 bp):
ATCAGAACAGAATCCAGGTAACGA
Found at i:426709 original size:18 final size:18
Alignment explanation
Indices: 426688--426722 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
426678 TGCCATCCGG
*
426688 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
426706 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
426723 GTTCTTTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:428023 original size:21 final size:21
Alignment explanation
Indices: 427997--428042 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
427987 GTTCAACGCC
*
427997 GGTCAACGGGTTAACGGGTCG
1 GGTCAACGGGTAAACGGGTCG
428018 GGTCAACGGGTAAACGGGTCG
1 GGTCAACGGGTAAACGGGTCG
428039 GGTC
1 GGTC
428043 GGGTCGAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.20, G:0.43, T:0.17
Consensus pattern (21 bp):
GGTCAACGGGTAAACGGGTCG
Found at i:432076 original size:49 final size:51
Alignment explanation
Indices: 431969--432081 Score: 142
Period size: 52 Copynumber: 2.2 Consensus size: 51
431959 TATAAAAAAA
* * * *
431969 TAAAAATGTAAATAAGTAATAAAAAACTATTTTAAATAAAGACAATATTTAT
1 TAAAAATGTAAATAAGTAAT-AAAAACTAATTAAAATAAAGACAACATTAAT
*
432021 TAAAAATGTAAATAAGTAAT-AAAATTAATTAAAATATAA-A-AACATTAAT
1 TAAAAATGTAAATAAGTAATAAAAACTAATTAAAATA-AAGACAACATTAAT
432070 TAAAAATGTAAA
1 TAAAAATGTAAA
432082 ACTACTTTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
49 19 0.35
50 14 0.25
51 2 0.04
52 20 0.36
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (51 bp):
TAAAAATGTAAATAAGTAATAAAAACTAATTAAAATAAAGACAACATTAAT
Found at i:432081 original size:21 final size:19
Alignment explanation
Indices: 432036--432082 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
432026 ATGTAAATAA
432036 GTAATAAAATTAATTAAAAT
1 GTAA-AAAATTAATTAAAAT
*
432056 ATAAAAACATTAATTAAAAAT
1 GTAAAAA-ATTAATT-AAAAT
432077 GTAAAA
1 GTAAAA
432083 CTACTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 3 0.13
20 10 0.43
21 10 0.43
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (19 bp):
GTAAAAAATTAATTAAAAT
Found at i:432906 original size:10 final size:10
Alignment explanation
Indices: 432888--432918 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
432878 TTGAGTGACC
*
432888 TTTCCCTTTT
1 TTTCTCTTTT
432898 TTTCTCTTTT
1 TTTCTCTTTT
432908 TTTCTCTTTT
1 TTTCTCTTTT
432918 T
1 T
432919 ATCCTTCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTCTCTTTT
Found at i:432934 original size:15 final size:15
Alignment explanation
Indices: 432909--432946 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
432899 TTCTCTTTTT
432909 TTCTC-TTTTTATCC
1 TTCTCTTTTTTATCC
432923 TTCTCTTTTTTATCC
1 TTCTCTTTTTTATCC
432938 TTCTCTTTT
1 TTCTCTTTT
432947 ACATAACATG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.68
Consensus pattern (15 bp):
TTCTCTTTTTTATCC
Found at i:433776 original size:33 final size:33
Alignment explanation
Indices: 433732--433796 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
433722 GAAGGTATCG
433732 ACACTTCAGTGCATTTGGACCTACGAGTTCATA
1 ACACTTCAGTGCATTTGGACCTACGAGTTCATA
* *
433765 ACACTTTAGTGCATTTGGACCTTCGAGTTCAT
1 ACACTTCAGTGCATTTGGACCTACGAGTTCAT
433797 CTGCTATAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (33 bp):
ACACTTCAGTGCATTTGGACCTACGAGTTCATA
Found at i:433982 original size:36 final size:35
Alignment explanation
Indices: 433923--433998 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 35
433913 TACATTATAT
* * * * *
433923 ATATATATGCTCTTGCTATTGATGAACATATTCATG
1 ATATACATGCGCTTACTACTGATGAA-ATATACATG
433959 ATATACATGCGCTTACTACTGATGAAATATACATG
1 ATATACATGCGCTTACTACTGATGAAATATACATG
*
433994 GTATA
1 ATATA
433999 TATATATATA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
35 12 0.35
36 22 0.65
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (35 bp):
ATATACATGCGCTTACTACTGATGAAATATACATG
Found at i:434002 original size:2 final size:2
Alignment explanation
Indices: 433995--434022 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
433985 ATATACATGG
433995 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
434023 CACTTGCTAT
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):
TA
Found at i:434081 original size:36 final size:36
Alignment explanation
Indices: 434025--434177 Score: 143
Period size: 36 Copynumber: 4.2 Consensus size: 36
434015 TATATATACA
* * *
434025 CTTGCTATTGATGATAATATGAATGATAAACATGTG
1 CTTGCTATTAATGATTATATGAATGATATACATGTG
* * *
434061 -TGTGCTATTAATTATTATATGCATGATACACATGT-
1 CT-TGCTATTAATGATTATATGAATGATATACATGTG
*** *
434096 CTTTGCTACCGATGATTATAT-ACATTATATACATGTG
1 C-TTGCTATTAATGATTATATGA-ATGATATACATGTG
*
434133 CTTGAC-ATTAATGATTATATGCATGATATACATGTG
1 CTTG-CTATTAATGATTATATGAATGATATACATGTG
434169 CTTGCTATT
1 CTTGCTATT
434178 GGGTTTATAT
Statistics
Matches: 92, Mismatches: 17, Indels: 16
0.74 0.14 0.13
Matches are distributed among these distances:
35 2 0.02
36 87 0.95
37 3 0.03
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (36 bp):
CTTGCTATTAATGATTATATGAATGATATACATGTG
Found at i:444067 original size:19 final size:19
Alignment explanation
Indices: 444045--444287 Score: 166
Period size: 19 Copynumber: 12.5 Consensus size: 19
444035 GAAACCAAAT
*
444045 TTTTAGGTTGCAACCTAGA
1 TTTTAGGTTGCAACCCAGA
* * * * *
444064 TTTTAAGTTGTAGCCTAGT
1 TTTTAGGTTGCAACCCAGA
** * *
444083 TTTTAGGTTGGGATCCATA
1 TTTTAGGTTGCAACCCAGA
*
444102 TTTTAGGTTTCAACCCAGA
1 TTTTAGGTTGCAACCCAGA
* * *
444121 TATTTAAGCTGCAACCCATA
1 T-TTTAGGTTGCAACCCAGA
* * *
444141 TTTTTATGTTGGAATCCAGA
1 -TTTTAGGTTGCAACCCAGA
*
444161 TTTTAGGTTGCAACCCATA
1 TTTTAGGTTGCAACCCAGA
* *
444180 TTATTAGGTTACAACCCAAA
1 TT-TTAGGTTGCAACCCAGA
* * *
444200 TTTTTGGGTTGGAACCCATA
1 -TTTTAGGTTGCAACCCAGA
** *
444220 TTTTAGGTTAAAAGCC-GAA
1 TTTTAGGTTGCAACCCAG-A
*
444239 TTTTAGGTTGCAACCCATA
1 TTTTAGGTTGCAACCCAGA
444258 TTTTTAGGTTGACAA-CCAGA
1 -TTTTAGGTTG-CAACCCAGA
444278 TTTTAGGTTG
1 TTTTAGGTTG
444288 AAAACCATAT
Statistics
Matches: 170, Mismatches: 46, Indels: 16
0.73 0.20 0.07
Matches are distributed among these distances:
19 95 0.56
20 69 0.41
21 6 0.04
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (19 bp):
TTTTAGGTTGCAACCCAGA
Found at i:444158 original size:59 final size:58
Alignment explanation
Indices: 444030--444287 Score: 236
Period size: 59 Copynumber: 4.4 Consensus size: 58
444020 AGATTTTAAG
* * * *
444030 GGTTGGAAACCAAATTTTTAGGTTGCAACCTAGATTTTAAGTTG-TAGCC-TAGTTTTTA
1 GGTTGGAAACCAGA-TTTTAGGTTGCAACCCAGATTTTAAGTTGCAACCCATA-TTTTTA
* * * * *
444088 GGTTGGGATCCATATTTTAGGTTTCAACCCAGATATTTAAGCTGCAACCCATATTTTTA
1 GGTTGGAAACCAGATTTTAGGTTGCAACCCAGAT-TTTAAGTTGCAACCCATATTTTTA
* * * * * * *
444147 TGTTGGAATCCAGATTTTAGGTTGCAACCCATATTATTAGGTTACAACCCAAATTTTTG
1 GGTTGGAAACCAGATTTTAGGTTGCAACCCAGATT-TTAAGTTGCAACCCATATTTTTA
* * ** * *
444206 GGTTGGAACCCATATTTTAGGTTAAAAGCC-GAATTTTAGGTTGCAACCCATATTTTTA
1 GGTTGGAAACCAGATTTTAGGTTGCAACCCAG-ATTTTAAGTTGCAACCCATATTTTTA
444264 GGTT-GACAACCAGATTTTAGGTTG
1 GGTTGGA-AACCAGATTTTAGGTTG
444288 AAAACCATAT
Statistics
Matches: 163, Mismatches: 31, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
57 20 0.12
58 58 0.36
59 83 0.51
60 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (58 bp):
GGTTGGAAACCAGATTTTAGGTTGCAACCCAGATTTTAAGTTGCAACCCATATTTTTA
Found at i:444288 original size:19 final size:20
Alignment explanation
Indices: 444097--444299 Score: 140
Period size: 20 Copynumber: 10.4 Consensus size: 20
444087 AGGTTGGGAT
*
444097 CCATATTTTAGGTT-TCAAC
1 CCATATTTTAGGTTGACAAC
* * *
444116 CCAGATATTTAAGCTG-CAAC
1 CCATAT-TTTAGGTTGACAAC
* * *
444136 CCATATTTTTATGTTG-GAAT
1 CCATA-TTTTAGGTTGACAAC
*
444156 CCAGATTTTAGGTTG-CAAC
1 CCATATTTTAGGTTGACAAC
444175 CCATATTATTAGGTT-ACAAC
1 CCATATT-TTAGGTTGACAAC
* * *
444195 CCAAATTTTTGGGTTG-GAAC
1 CCATA-TTTTAGGTTGACAAC
*
444215 CCATATTTTAGGTT-AAAAGC
1 CCATATTTTAGGTTGACAA-C
*
444235 CGA-ATTTTAGGTTG-CAAC
1 CCATATTTTAGGTTGACAAC
444253 CCATATTTTTAGGTTGACAA-
1 CCATA-TTTTAGGTTGACAAC
* *
444273 CCAGATTTTAGGTTGA-AAA
1 CCATATTTTAGGTTGACAAC
444292 CCATATTT
1 CCATATTT
444300 CTGGTTAGAA
Statistics
Matches: 146, Mismatches: 24, Indels: 28
0.74 0.12 0.14
Matches are distributed among these distances:
18 5 0.03
19 63 0.43
20 72 0.49
21 6 0.04
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.36
Consensus pattern (20 bp):
CCATATTTTAGGTTGACAAC
Found at i:444321 original size:39 final size:38
Alignment explanation
Indices: 444030--444324 Score: 193
Period size: 39 Copynumber: 7.6 Consensus size: 38
444020 AGATTTTAAG
* * *
444030 GGTTGGAAACCAAATTTTTAGGTTGCAACCTAGATTTTA
1 GGTTAGAAACCAAA-TTTTAGGTTGCAACCCATATTTTA
* * * ** ** *
444069 AGTT-GTAGCCTAGTTTTTAGGTTGGGATCCATATTTTA
1 GGTTAGAAACC-AAATTTTAGGTTGCAACCCATATTTTA
** * * * *
444107 GGTTTCAACCCAGATATTTAAGCTGCAACCCATATTTTTA
1 GGTTAGAAACCAAAT-TTTAGGTTGCAACCCATA-TTTTA
* * * *
444147 TGTTGGAATCCAGATTTTAGGTTGCAACCCATATTATTA
1 GGTTAGAAACCAAATTTTAGGTTGCAACCCATATT-TTA
* * * *
444186 GGTTACAACCCAAATTTTTGGGTTGGAACCCATATTTTA
1 GGTTAGAAACCAAA-TTTTAGGTTGCAACCCATATTTTA
*
444225 GGTTA-AAAGCCGAATTTTAGGTTGCAACCCATATTTTTA
1 GGTTAGAAA-CCAAATTTTAGGTTGCAACCCATA-TTTTA
* * *
444264 GGTT-GACAACCAGATTTTAGGTTGAAAACCATATTTCT-
1 GGTTAGA-AACCAAATTTTAGGTTGCAACCCATATTT-TA
*
444302 GGTTAGAAATCAAATTTTTAGGT
1 GGTTAGAAACCAAA-TTTTAGGT
444325 GTAAGTTTGT
Statistics
Matches: 200, Mismatches: 43, Indels: 26
0.74 0.16 0.10
Matches are distributed among these distances:
38 62 0.31
39 101 0.50
40 37 0.19
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (38 bp):
GGTTAGAAACCAAATTTTAGGTTGCAACCCATATTTTA
Found at i:451133 original size:17 final size:17
Alignment explanation
Indices: 451111--451149 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
451101 AATTGCATCA
451111 AGGAAATCGATCCATTG
1 AGGAAATCGATCCATTG
451128 AGGAAATCGATCCATTG
1 AGGAAATCGATCCATTG
451145 AGGAA
1 AGGAA
451150 TACTTTCGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (17 bp):
AGGAAATCGATCCATTG
Found at i:452749 original size:3 final size:3
Alignment explanation
Indices: 452729--452788 Score: 77
Period size: 3 Copynumber: 20.0 Consensus size: 3
452719 AAGTCTTGCA
* * *
452729 TAT TAT TAAT TAC CAT TAT TAC TAT TA- TAT TAT TAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
452774 TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT
452789 GAATAAAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 2 0.04
3 44 0.90
4 3 0.06
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:461968 original size:16 final size:18
Alignment explanation
Indices: 461936--461968 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
461926 TACCCTTTCA
461936 CATAGAGCTGAAACCATG
1 CATAGAGCTGAAACCATG
461954 CATAGAG-TG-AACCAT
1 CATAGAGCTGAAACCAT
461969 AGACTAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.18
Consensus pattern (18 bp):
CATAGAGCTGAAACCATG
Found at i:464800 original size:41 final size:40
Alignment explanation
Indices: 464755--464973 Score: 167
Period size: 41 Copynumber: 5.2 Consensus size: 40
464745 ATCTTGGCAG
* * *
464755 CATGCACTAATTCACAATTCGATTCAGTTAAATCATAACAA
1 CATGCAATAATTCACAATTCGATTCAATTCAATCATAAC-A
* * *
464796 CATGCAATAATTCACCATTAGACTT-AATTCGATCATGTAAC-
1 CATGCAATAATTCACAATTCGA-TTCAATTCAATCA--TAACA
*
464837 CATGCAATAATTCACAATTCGATTCAATTCAATCAT-GCA
1 CATGCAATAATTCACAATTCGATTCAATTCAATCATAACA
* **
464876 GTATGCAATAATTCACAATTCGATTCTATTCAATTCAATCATGGCA
1 -CATGCAATAATTCACAATTCG-----ATTCAATTCAATCATAACA
* * **
464922 GCATGCAATAATTCACAATTCAACTT-AATTCGATCATGGCA
1 -CATGCAATAATTCACAATTCGA-TTCAATTCAATCATAACA
464963 GCATGCAATAA
1 -CATGCAATAA
464974 ACCATAATTC
Statistics
Matches: 151, Mismatches: 14, Indels: 26
0.79 0.07 0.14
Matches are distributed among these distances:
38 1 0.01
39 1 0.01
40 22 0.15
41 81 0.54
42 4 0.03
43 4 0.03
45 15 0.10
46 23 0.15
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (40 bp):
CATGCAATAATTCACAATTCGATTCAATTCAATCATAACA
Found at i:464983 original size:41 final size:41
Alignment explanation
Indices: 464817--465008 Score: 138
Period size: 41 Copynumber: 4.6 Consensus size: 41
464807 TCACCATTAG
* ** * ** *
464817 ACTTAATTCGATCATGTAACCATGCAATAATTCACAATTCG
1 ACTTAATTCAATCATGGCAGCATGCAATAAACCACAATTCA
* **
464858 A-TTCAATTCAATCAT-GCAGTATGCAATAATTCACAATTCGA
1 ACTT-AATTCAATCATGGCAGCATGCAATAAACCACAATTC-A
* **
464899 TTCTATTCAATTCAATCATGGCAGCATGCAATAATTCACAATTCA
1 -AC--TT-AATTCAATCATGGCAGCATGCAATAAACCACAATTCA
* *
464944 ACTTAATTCGATCATGGCAGCATGCAATAAACCATAATTCA
1 ACTTAATTCAATCATGGCAGCATGCAATAAACCACAATTCA
* * *
464985 A-TTCACTTCAGTCATGGCAACATG
1 ACTT-AATTCAATCATGGCAGCATG
465009 TATTTATTCA
Statistics
Matches: 126, Mismatches: 17, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
40 24 0.19
41 61 0.48
42 2 0.02
44 1 0.01
45 15 0.12
46 23 0.18
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (41 bp):
ACTTAATTCAATCATGGCAGCATGCAATAAACCACAATTCA
Found at i:465028 original size:41 final size:41
Alignment explanation
Indices: 464903--465089 Score: 119
Period size: 41 Copynumber: 4.5 Consensus size: 41
464893 ATTCGATTCT
* * * **
464903 ATTCAATTCA-ATCATGGCAGCATGCAATAATTCACAATTCA
1 ATTCAATT-AGATCATGGCAACATGTATTAATTCACAAACCA
* * * * ** * **
464944 ACTT-AATTCGATCATGGCAGCATGCAATAAACCATAATTCA
1 A-TTCAATTAGATCATGGCAACATGTATTAATTCACAAACCA
* *
464985 ATTCACTTCAG-TCATGGCAACATGTATTTATTCACAAACCA
1 ATTCAATT-AGATCATGGCAACATGTATTAATTCACAAACCA
* * * *
465026 ATTTAATTAGATCATGGTAACATGTATTAATTCACAATCGA
1 ATTCAATTAGATCATGGCAACATGTATTAATTCACAAACCA
* *
465067 ATTCAATTTAAATCAAGGCAACA
1 ATTCAA-TTAGATCATGGCAACA
465090 AGCAATAACT
Statistics
Matches: 115, Mismatches: 25, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
40 4 0.03
41 95 0.83
42 16 0.14
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (41 bp):
ATTCAATTAGATCATGGCAACATGTATTAATTCACAAACCA
Found at i:468431 original size:24 final size:24
Alignment explanation
Indices: 468399--468446 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
468389 AATGAATACC
468399 ATTTTTAGAAAACTTTATGCATAT
1 ATTTTTAGAAAACTTTATGCATAT
468423 ATTTTTAGAAAACTTTATGCATAT
1 ATTTTTAGAAAACTTTATGCATAT
468447 GCACTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (24 bp):
ATTTTTAGAAAACTTTATGCATAT
Found at i:469069 original size:21 final size:21
Alignment explanation
Indices: 469045--469084 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
469035 TTCTTTGCAG
469045 TATCGATACCACATGAATCGA
1 TATCGATACCACATGAATCGA
469066 TATCGATACCACATGAATC
1 TATCGATACCACATGAATC
469085 TGTATTGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (21 bp):
TATCGATACCACATGAATCGA
Found at i:469094 original size:21 final size:20
Alignment explanation
Indices: 469044--469096 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 20
469034 GTTCTTTGCA
469044 GTATCGATACCACATGAATC
1 GTATCGATACCACATGAATC
469064 GATATCGATACCACATGAATC
1 G-TATCGATACCACATGAATC
*
469085 TGTATTGATACC
1 -GTATCGATACC
469097 CTACTTGTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 1 0.03
21 28 0.93
22 1 0.03
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (20 bp):
GTATCGATACCACATGAATC
Found at i:469669 original size:33 final size:33
Alignment explanation
Indices: 469624--469686 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
469614 AGGGGTTTTG
*
469624 GTTCTAGCTTAGCCTGCT-AAAAGCTAGGGAAAA
1 GTTCTAGCTTAGCCTG-TGAAAAACTAGGGAAAA
*
469657 GTTCTAGTTTAGCCTGTGAAAAACTAGGGA
1 GTTCTAGCTTAGCCTGTGAAAAACTAGGGA
469687 GTTGTAAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 1 0.04
33 26 0.96
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (33 bp):
GTTCTAGCTTAGCCTGTGAAAAACTAGGGAAAA
Found at i:472356 original size:163 final size:164
Alignment explanation
Indices: 472079--472475 Score: 661
Period size: 163 Copynumber: 2.4 Consensus size: 164
472069 ATTTTTATTA
* * *
472079 AAAAACCATATTAATCCCTCCAACCAAACACTCAATAATGTGTAGGTTCCCCAGAACCATACACC
1 AAAAATCATATTATTCCCTCCAACC-AACACTCCATAATGTGTAGGTTCCCCAGAACCATACACC
* *
472144 CACCTACACAGCAAGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCCTGTAGTAACGATAACT
65 CACCTACACACCAAGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCCTGCAGTAACGATAACT
472209 TCCTCCAACAACACCCTCCCAT-AAAACATTTATC
130 TCCTCCAACAACACCCTCCCATAAAAACATTTATC
*
472243 AAAAATCATATTATTTCCTCCAACCAACACTCCATAATGTGTAGGTTCCCCAGAACCATACACCC
1 AAAAATCATATTATTCCCTCCAACCAACACTCCATAATGTGTAGGTTCCCCAGAACCATACACCC
* *
472308 ACCTACACACCAAGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCCTGCAGTAATGGTAACTT
66 ACCTACACACCAAGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCCTGCAGTAACGATAACTT
* * *
472373 CCTCCAACAACACCTTTCTATAAAAACATTTATC
131 CCTCCAACAACACCCTCCCATAAAAACATTTATC
* *
472407 AAAAATCATATTATTCCCTCCAACCAACACTCCATAATGTGTAGGTTCCACAGAACCTTACACCC
1 AAAAATCATATTATTCCCTCCAACCAACACTCCATAATGTGTAGGTTCCCCAGAACCATACACCC
472472 ACCT
66 ACCT
472476 GCACTCCTAC
Statistics
Matches: 218, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
163 118 0.54
164 100 0.46
ACGTcount: A:0.37, C:0.31, G:0.11, T:0.21
Consensus pattern (164 bp):
AAAAATCATATTATTCCCTCCAACCAACACTCCATAATGTGTAGGTTCCCCAGAACCATACACCC
ACCTACACACCAAGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCCTGCAGTAACGATAACTT
CCTCCAACAACACCCTCCCATAAAAACATTTATC
Found at i:475143 original size:17 final size:15
Alignment explanation
Indices: 475121--475163 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 15
475111 TCAAAGTTTT
475121 GGTCAACTATGGTCAAC
1 GGTCAAC-A-GGTCAAC
475138 GGTCAAAGCAGGTCAAC
1 GGTC-AA-CAGGTCAAC
475155 GGTCAACAG
1 GGTCAACAG
475164 TCGACCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 3 0.12
16 2 0.08
17 15 0.62
18 3 0.12
19 1 0.04
ACGTcount: A:0.33, C:0.23, G:0.28, T:0.16
Consensus pattern (15 bp):
GGTCAACAGGTCAAC
Found at i:479286 original size:17 final size:17
Alignment explanation
Indices: 479273--479309 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
479263 CTTTCATGAC
479273 TATTTT-ATTTTCATAA
1 TATTTTGATTTTCATAA
*
479289 TATTTTGATTTT-TTAA
1 TATTTTGATTTTCATAA
479305 TATTT
1 TATTT
479310 ATGGACATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.68
Consensus pattern (17 bp):
TATTTTGATTTTCATAA
Found at i:484201 original size:61 final size:61
Alignment explanation
Indices: 484135--484316 Score: 253
Period size: 61 Copynumber: 3.0 Consensus size: 61
484125 TGAGGCATCA
*
484135 CTGATTCGAAATGTTGTGTGAATTG-GACAAAAGAAATGTTATCCCCTTTGGTGGGGCGTTG
1 CTGATTCGAAATGTTGTGTGAATTGAG-CAAAAGAAATGTTATCCCCTCTGGTGGGGCGTTG
* *
484196 CTGATTCAAAATGTTGTGTGAATTGAGCAAAAGAAATGTTATCCCCTCTAGTGGGGCGTTG
1 CTGATTCGAAATGTTGTGTGAATTGAGCAAAAGAAATGTTATCCCCTCTGGTGGGGCGTTG
** * * *
484257 CTGATTCGAGGTG-T-TGTGAATTGAGCAATAGGAAATGTAATCCCCTCTGGTGGGGTGTTG
1 CTGATTCGAAATGTTGTGTGAATTGAGCAA-AAGAAATGTTATCCCCTCTGGTGGGGCGTTG
484317 TTTGTTTTAA
Statistics
Matches: 109, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
59 14 0.13
60 28 0.26
61 66 0.61
62 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.30, T:0.32
Consensus pattern (61 bp):
CTGATTCGAAATGTTGTGTGAATTGAGCAAAAGAAATGTTATCCCCTCTGGTGGGGCGTTG
Found at i:484582 original size:42 final size:41
Alignment explanation
Indices: 484487--484582 Score: 95
Period size: 42 Copynumber: 2.3 Consensus size: 41
484477 TGGCCTAAAA
* * *
484487 GACTTATCATCTTGCTCGAAATACTTATAGATGACCTGAAG
1 GACTTATCATCATGCTCGAAAGACTTATAGATGACCCGAAG
* * * *
484528 GATTTAAGCATCATGCTTGAAAGACTTACT-GATGGCCCGAAG
1 GACTT-ATCATCATGCTCGAAAGACTTA-TAGATGACCCGAAG
484570 GACTTACTCATCA
1 GACTTA-TCATCA
484583 AGAAACCCTT
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
41 5 0.12
42 37 0.86
43 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (41 bp):
GACTTATCATCATGCTCGAAAGACTTATAGATGACCCGAAG
Found at i:484771 original size:52 final size:52
Alignment explanation
Indices: 484635--484885 Score: 204
Period size: 52 Copynumber: 4.6 Consensus size: 52
484625 TTTTTGGTTG
* ** *
484635 TCATCAAGGAACCCCTAAAAATTAGGCTTAGTTTACTTTAAAATTCTTTGGAGATAA
1 TCATCAAGAAACCCCTAAAAATTAGGCTTAGTTT-C-AAAAAACTCTTT-GA-A-AA
* * *
484692 TCATTAAGAAATCCCTGAAAATTAGGCTTAGTTTCAAAAAACTCATTTGAAAA
1 TCATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCAAAAAACTC-TTTGAAAA
* *
484745 -CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTTTAAAAAATTCTTTGAAAATCA
1 TCATCAAGAAACCCCTAAAAATTAGGCTTAG-----TTTCAAAAAACTCTTTG-AAA--A
* * *
484804 TCATCAATAAACCCCTGAAAATCAGGCTTAGTTT-ATAAAAACTCATTTGAAAA
1 TCATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCA-AAAAACTC-TTTGAAAA
* *
484857 -CATTAAGAAAGCCCTAAAAATTA-GCTTAG
1 TCATCAAGAAACCCCTAAAAATTAGGCTTAG
484886 CTTCTTTTAA
Statistics
Matches: 161, Mismatches: 21, Indels: 30
0.76 0.10 0.14
Matches are distributed among these distances:
51 6 0.04
52 45 0.28
53 3 0.02
54 2 0.01
55 21 0.13
56 12 0.07
57 44 0.27
59 1 0.01
60 27 0.17
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.30
Consensus pattern (52 bp):
TCATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCAAAAAACTCTTTGAAAA
Found at i:484803 original size:109 final size:110
Alignment explanation
Indices: 484636--484972 Score: 395
Period size: 109 Copynumber: 3.0 Consensus size: 110
484626 TTTTGGTTGT
* *
484636 CATCAAGGAACCCCTAAAAATTAGGCTTAG-TT-TACTTT-AAAATTCTTTGGAGATAATCAT-T
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCT-TTTTAAAAATTCTTT-GA-A-AATCATAT
*
484697 -AAGAAATCCCTGAAAATTAGGCTTAGTTTCA-AAAAACTCATTTGAAAA
62 CAAGAAA-CCCTGAAAATCAGGCTTAGTTTCATAAAAACTCATTTGAAAA
484745 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTTTAAAAAATTCTTTGAAAATCATCATCA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTTT-AAAAATTCTTTGAAAATCAT-ATCA
*
484810 ATAAACCCCTGAAAATCAGGCTTAGTTT-ATAAAAACTCATTTGAAAA
64 AGAAA-CCCTGAAAATCAGGCTTAGTTTCATAAAAACTCATTTGAAAA
* * * *
484857 CATTAAGAAAGCCCTAAAAATTA-GCTTAGCTTC-TTTTAAGAATTCATTGAAAATCATCATCAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTTTAAAAATTCTTTGAAAATCAT-ATCAA
* * * *
484920 GAAACCCTTGAAAATCAGACTTAGTTTCTTTAAAAATTCTTTTGAAAA
65 GAAACCC-TGAAAATCAGGCTTAGTTTC-ATAAAAACTCATTTGAAAA
*
484968 TATCA
1 CATCA
484973 TGTTGTTTGG
Statistics
Matches: 201, Mismatches: 16, Indels: 20
0.85 0.07 0.08
Matches are distributed among these distances:
108 3 0.01
109 80 0.40
110 10 0.05
111 34 0.17
112 74 0.37
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (110 bp):
CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTTTAAAAATTCTTTGAAAATCATATCAAG
AAACCCTGAAAATCAGGCTTAGTTTCATAAAAACTCATTTGAAAA
Found at i:484831 original size:112 final size:112
Alignment explanation
Indices: 484577--484972 Score: 428
Period size: 112 Copynumber: 3.5 Consensus size: 112
484567 AAGGACTTAC
* * * * ****
484577 TCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAAAATATTTCATTTTTGGTTGTCATCAA
1 TCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCATAAAA-A-CTCA--TTT-GAAAACATCAA
* * * * *
484642 GGAACCCCTAAAAATTAGGCTTAG-TT-TACTTT-AAAATTCTTTGGAGATAA
61 GAAACCCCTAAAAATTAGGCTTAGCTTCT-TTTTAAAAATTCTTTGAAAATCA
* * *
484692 TCATTAAGAAATCCCTGAAAATTAGGCTTAGTTTCA-AAAAACTCATTTGAAAACATCAAGAAAC
1 TCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCATAAAAACTCATTTGAAAACATCAAGAAAC
484756 CCCTAAAAATTAGGCTTAGCTTCTTTTTAAAAAATTCTTTGAAAATCA
66 CCCTAAAAATTAGGCTTAGCTTCTTTTT-AAAAATTCTTTGAAAATCA
* * *
484804 TCATCAATAAACCCCTGAAAATCAGGCTTAGTTT-ATAAAAACTCATTTGAAAACATTAAGAAAG
1 TCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCATAAAAACTCATTTGAAAACATCAAGAAAC
* *
484868 CCCTAAAAATTA-GCTTAGCTTC-TTTTAAGAATTCATTGAAAATCA
66 CCCTAAAAATTAGGCTTAGCTTCTTTTTAAAAATTCTTTGAAAATCA
* * * * * *
484913 TCATCAAGAAACCCTTGAAAATCAGACTTAGTTTCTTTAAAAATTCTTTTGAAAATATCA
1 TCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTC-ATAAAAACTCATTTGAAAACATCA
484973 TGTTGTTTGG
Statistics
Matches: 242, Mismatches: 32, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
109 78 0.32
110 12 0.05
111 31 0.13
112 86 0.36
113 1 0.00
114 4 0.02
115 30 0.12
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.33
Consensus pattern (112 bp):
TCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCATAAAAACTCATTTGAAAACATCAAGAAAC
CCCTAAAAATTAGGCTTAGCTTCTTTTTAAAAATTCTTTGAAAATCA
Found at i:484973 original size:57 final size:55
Alignment explanation
Indices: 484577--484973 Score: 278
Period size: 57 Copynumber: 7.1 Consensus size: 55
484567 AAGGACTTAC
* * * ** *
484577 TCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTC-TTAAAATATTTCATTTTTG-GTTG
1 TCATCAAGAAACCCCTGAAAATTAGGCTTAGTTTCTTTAAAA-A-TTC---TTTGAAATA
* * *
484635 TCATCAAGGAACCCCTAAAAATTAGGCTTAGTTTACTTT-AAAATTCTTTGGAGATAA
1 TCATCAAGAAACCCCTGAAAATTAGGCTTAGTTT-CTTTAAAAATTCTTT-GAAAT-A
* * * *
484692 TCATTAAGAAATCCCTGAAAATTAGGCTTAGTTTC--AAAAAACTCATTTGAAA-A
1 TCATCAAGAAACCCCTGAAAATTAGGCTTAGTTTCTTTAAAAATTC-TTTGAAATA
* *
484745 -CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTTTAAAAAATTCTTTGAAAATCA
1 TCATCAAGAAACCCCTGAAAATTAGGCTTAG-TT-TCTTT-AAAAATTCTTTG-AAAT-A
* * * *
484804 TCATCAATAAACCCCTGAAAATCAGGCTTAG-TT-TATAAAAACTCATTTGAAA-A
1 TCATCAAGAAACCCCTGAAAATTAGGCTTAGTTTCTTTAAAAATTC-TTTGAAATA
* * * * * *
484857 -CATTAAGAAAGCCCTAAAAATTA-GCTTAGCTTCTTTTAAGAATTCATTGAAAATCA
1 TCATCAAGAAACCCCTGAAAATTAGGCTTAGTTTC-TTTAAAAATTCTTTG-AAAT-A
* * *
484913 TCATCAAGAAACCCTTGAAAATCAGACTTAGTTTCTTTAAAAATTCTTTTGAAAATA
1 TCATCAAGAAACCCCTGAAAATTAGGCTTAGTTTCTTTAAAAATTC-TTTG-AAATA
484970 TCAT
1 TCAT
484974 GTTGTTTGGG
Statistics
Matches: 270, Mismatches: 43, Indels: 53
0.74 0.12 0.14
Matches are distributed among these distances:
51 6 0.02
52 47 0.17
53 7 0.03
54 15 0.06
55 20 0.07
56 17 0.06
57 77 0.29
58 47 0.17
59 5 0.02
60 29 0.11
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.33
Consensus pattern (55 bp):
TCATCAAGAAACCCCTGAAAATTAGGCTTAGTTTCTTTAAAAATTCTTTGAAATA
Found at i:486256 original size:28 final size:27
Alignment explanation
Indices: 486224--486284 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
486214 TAAAATGATT
*
486224 AGGTTGACTTGGGAAGGTAATGTGTTTC
1 AGGTTGACTTGGG-AGGTAATATGTTTC
* *
486252 AGGTTAATTTGGGAGGTAATATGTTTC
1 AGGTTGACTTGGGAGGTAATATGTTTC
486279 AGGTTG
1 AGGTTG
486285 GCTTCTTGCG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 18 0.62
28 11 0.38
ACGTcount: A:0.23, C:0.05, G:0.34, T:0.38
Consensus pattern (27 bp):
AGGTTGACTTGGGAGGTAATATGTTTC
Done.