Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_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: 17174986
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 67 of 78
Found at i:13701932 original size:18 final size:18
Alignment explanation
Indices: 13701909--13701944 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
13701899 AAGCCGGTTG
*
13701909 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
13701927 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
13701945 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:13702923 original size:18 final size:18
Alignment explanation
Indices: 13702900--13702936 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
13702890 CGAAATTTAT
13702900 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
13702918 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
13702936 A
1 A
13702937 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:13703164 original size:20 final size:20
Alignment explanation
Indices: 13703141--13703179 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
13703131 TTCGGTTTGC
13703141 GAATTTGACTTTCGCGTTGT
1 GAATTTGACTTTCGCGTTGT
13703161 GAATTTGACTTTCGCGTTG
1 GAATTTGACTTTCGCGTTG
13703180 ATCACAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.15, G:0.26, T:0.44
Consensus pattern (20 bp):
GAATTTGACTTTCGCGTTGT
Found at i:13705782 original size:24 final size:24
Alignment explanation
Indices: 13705750--13705801 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
13705740 ATCACATCAC
13705750 CAAAATCTGAGTATTGACCAAGAT
1 CAAAATCTGAGTATTGACCAAGAT
* *
13705774 CAAAGTCTGGGTATTGACCAAGAT
1 CAAAATCTGAGTATTGACCAAGAT
13705798 CAAA
1 CAAA
13705802 TTTCGAATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.23
Consensus pattern (24 bp):
CAAAATCTGAGTATTGACCAAGAT
Found at i:13705959 original size:12 final size:12
Alignment explanation
Indices: 13705926--13705960 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
13705916 AGGTTGTGGG
*
13705926 TTTTGAGATTGT
1 TTTTGATATTGT
13705938 TTTTGATATTGT
1 TTTTGATATTGT
*
13705950 TTTTGGTATTG
1 TTTTGATATTG
13705961 GAAATGTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.23, T:0.63
Consensus pattern (12 bp):
TTTTGATATTGT
Found at i:13706591 original size:14 final size:15
Alignment explanation
Indices: 13706555--13706592 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
13706545 GAAATCATTG
13706555 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
13706570 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
13706585 AAAAATTA
1 AAAAATTA
13706593 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:13706809 original size:19 final size:20
Alignment explanation
Indices: 13706749--13706860 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
13706739 ACTAAAACCT
* *
13706749 GTTGCGAAATT-AAATTCGT
1 GTTGCGAATTTGAAATTCGA
* * * *
13706768 GTTGTGAATTCGAAAATCTA
1 GTTGCGAATTTGAAATTCGA
13706788 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGA
13706807 GTTGCGAATTTGAAATTCCGCA
1 GTTGCGAATTTGAAATT-CG-A
* *
13706829 -TTGCGAATTTG-ACTATCGC
1 GTTGCGAATTTGAAAT-TCGA
13706848 GTTGCGAATTTGA
1 GTTGCGAATTTGA
13706861 CTTATGTGTT
Statistics
Matches: 75, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
19 26 0.35
20 36 0.48
21 12 0.16
22 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGA
Found at i:13706931 original size:20 final size:20
Alignment explanation
Indices: 13706889--13706954 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
13706879 CATATTCGCA
* * *
13706889 TTGCGAAATTGGAAACTGGG
1 TTGCGAAATTGGAGACCGCG
**
13706909 TTGCGAAATTGGAGTTCGCG
1 TTGCGAAATTGGAGACCGCG
*
13706929 TTGCG-AATTTGAGACCGCG
1 TTGCGAAATTGGAGACCGCG
13706948 TTGCGAA
1 TTGCGAA
13706955 TTTGTTGGTC
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
19 16 0.43
20 21 0.57
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.27
Consensus pattern (20 bp):
TTGCGAAATTGGAGACCGCG
Found at i:13708185 original size:11 final size:11
Alignment explanation
Indices: 13708169--13708195 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
13708159 TAGTGCATCG
13708169 GTGCACTAAGA
1 GTGCACTAAGA
13708180 GTGCACTAAGA
1 GTGCACTAAGA
13708191 GTGCA
1 GTGCA
13708196 TCGATGCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.19, G:0.30, T:0.19
Consensus pattern (11 bp):
GTGCACTAAGA
Found at i:13708324 original size:65 final size:65
Alignment explanation
Indices: 13708191--13708398 Score: 201
Period size: 65 Copynumber: 3.2 Consensus size: 65
13708181 TGCACTAAGA
* *
13708191 GTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
* * * *
13708255 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATTG-T
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGCT
*
13708318 AT
65 -G
* * ** ** ** *
13708320 GTGCATCGATGAATGAAATGCATTCGATG--TTCAATTTAATTCATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAT-AGCCACAGTGCATCGATGCATGG-C
13708383 TG
64 TG
13708385 GTGCATCGATGCAT
1 GTGCATCGATGCAT
13708399 GGATTGGTGC
Statistics
Matches: 118, Mismatches: 19, Indels: 13
0.79 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 46 0.39
65 63 0.53
66 4 0.03
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
Found at i:13708388 original size:20 final size:20
Alignment explanation
Indices: 13708363--13708418 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
13708353 ATTTAATTCA
13708363 TGGTGCATCGATGCATGGAT
1 TGGTGCATCGATGCATGGAT
13708383 TGGTGCATCGATGCATGGAT
1 TGGTGCATCGATGCATGGAT
*
13708403 TGGTGCATCGGTGCAT
1 TGGTGCATCGATGCAT
13708419 CACTCTGTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.18, C:0.16, G:0.36, T:0.30
Consensus pattern (20 bp):
TGGTGCATCGATGCATGGAT
Found at i:13708869 original size:2 final size:2
Alignment explanation
Indices: 13708862--13708892 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13708852 TAGCCAATTG
13708862 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13708893 GCTTAAGCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13714282 original size:19 final size:19
Alignment explanation
Indices: 13714258--13714296 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
13714248 TTGAATGCAT
13714258 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
13714277 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
13714296 T
1 T
13714297 GATTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:13714321 original size:64 final size:65
Alignment explanation
Indices: 13714238--13714423 Score: 184
Period size: 64 Copynumber: 2.9 Consensus size: 65
13714228 TCAATGAATA
* * * *
13714238 AATTGAAACATTGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTC-TG-ATT
1 AATTAAAACATCGAATGCATT-CATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGCATT
13714301 T
65 T
* * **
13714302 AATTAAAACATCGAATGCATTTGATGAATCGATGCACAATCCATGCATCGATGCAC-CAGGCTAT
1 AATTAAAACATCGAATGCA-TTCATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGC-AT
13714366 TT
64 TT
* * * *
13714368 -TTTCAAACATCGAATGCACTTCATGCATCGATGCACTCT-TAGTGCACCGATGCACT
1 AATTAAAACATCGAATGCA-TTCATGCATCGATGCACTCTCCA-TGCATCGATGCACT
13714424 AGGAGTCCAA
Statistics
Matches: 99, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
63 1 0.01
64 48 0.48
65 46 0.46
66 4 0.04
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.28
Consensus pattern (65 bp):
AATTAAAACATCGAATGCATTCATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGCATTT
Found at i:13714402 original size:65 final size:63
Alignment explanation
Indices: 13714192--13714403 Score: 176
Period size: 64 Copynumber: 3.2 Consensus size: 63
13714182 TTTTCAAAGG
* * ** * * * *
13714192 CATGCACCGATGCATCAAATACCATGCATCGATGTATCAATGAATAAATTGAAACATTGAATGCA
1 CATGCATCGATGCA-C-AAT-CCATGCATCGATGCA-CGCTGATTTAATTAAAACATCGAATGCA
13714257 TT
62 TT
* ** *
13714259 CCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGATTTAATTAAAACATCGAATGCATTT
1 -CATGCATCGATGCACAATCCATGCATCGATGCACGCTGATTTAATTAAAACATCGAATGCA-TT
* * * *
13714324 GATGAATCGATGCACAATCCATGCATCGATGCACCAGGCT-ATTT-TTTCAAACATCGAATGCAC
1 CATGCATCGATGCACAATCCATGCATCGATGCA-C--GCTGATTTAATTAAAACATCGAATGCA-
13714387 TT
62 TT
13714389 CATGCATCGATGCAC
1 CATGCATCGATGCAC
13714404 TCTTAGTGCA
Statistics
Matches: 120, Mismatches: 20, Indels: 11
0.79 0.13 0.07
Matches are distributed among these distances:
64 50 0.42
65 48 0.40
66 5 0.04
67 3 0.03
68 14 0.12
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.27
Consensus pattern (63 bp):
CATGCATCGATGCACAATCCATGCATCGATGCACGCTGATTTAATTAAAACATCGAATGCATT
Found at i:13714403 original size:17 final size:19
Alignment explanation
Indices: 13714375--13714423 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
13714365 TTTTTTCAAA
13714375 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
13714393 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
13714412 CACCGATGCACT
1 CATCGATGCACT
13714424 AGGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:13722574 original size:20 final size:20
Alignment explanation
Indices: 13722545--13722596 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
13722535 GCAGCCTTCG
*
13722545 TGCATGGATGCATAGCAA-GA
1 TGCATCGATGCATAG-AAGGA
13722565 TGCATCGATGCATAGAAGGA
1 TGCATCGATGCATAGAAGGA
13722585 TGCATCGATGCA
1 TGCATCGATGCA
13722597 CTAATTGCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (20 bp):
TGCATCGATGCATAGAAGGA
Found at i:13722694 original size:21 final size:20
Alignment explanation
Indices: 13722619--13722716 Score: 90
Period size: 21 Copynumber: 4.7 Consensus size: 20
13722609 AGTGTTTGAG
*
13722619 TGCATGGATGCACTGCATGA
1 TGCATGGATGCACTGCAGGA
*
13722639 TGCATCGATGCACTAGTGCAGG-
1 TGCATGGATGCAC---TGCAGGA
* *
13722661 TGTATGAATGCACTGCAGGGA
1 TGCATGGATGCACTGCA-GGA
*
13722682 TGCATGGATGCACTGCAGGGG
1 TGCATGGATGCACTGCA-GGA
*
13722703 TGCATGGAAGCACT
1 TGCATGGATGCACT
13722717 TTGACACCAC
Statistics
Matches: 64, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
19 4 0.06
20 14 0.22
21 31 0.48
22 10 0.16
23 5 0.08
ACGTcount: A:0.24, C:0.19, G:0.34, T:0.22
Consensus pattern (20 bp):
TGCATGGATGCACTGCAGGA
Found at i:13723121 original size:21 final size:21
Alignment explanation
Indices: 13723095--13723191 Score: 140
Period size: 21 Copynumber: 4.6 Consensus size: 21
13723085 GTGTCAAAGA
*
13723095 GCATCCATGTACCCCTGTAGT
1 GCATCCATGCACCCCTGTAGT
*
13723116 GCATCCATGCACTCCTGTAGT
1 GCATCCATGCACCCCTGTAGT
13723137 GCATCCATGCACCCCTGTAGT
1 GCATCCATGCACCCCTGTAGT
* **
13723158 GCATCCATGCATCCCTACAGT
1 GCATCCATGCACCCCTGTAGT
*
13723179 GCAACCATGCACC
1 GCATCCATGCACC
13723192 TGCACTAGTG
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 68 1.00
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.24
Consensus pattern (21 bp):
GCATCCATGCACCCCTGTAGT
Found at i:13723154 original size:42 final size:41
Alignment explanation
Indices: 13723095--13723232 Score: 159
Period size: 42 Copynumber: 3.3 Consensus size: 41
13723085 GTGTCAAAGA
* *
13723095 GCATCCATGTACCCCTGTAGTGCATCCATGCACTCCTGTAGT
1 GCATCCATGCACCCCTGTAGTGCATCCATGCA-TCCTGCAGT
*
13723137 GCATCCATGCACCCCTGTAGTGCATCCATGCATCCCTACAGT
1 GCATCCATGCACCCCTGTAGTGCATCCATGCAT-CCTGCAGT
* * ** * * *
13723179 GCAACCATGCACCTGCACTAGTGCATCGATACATCATGCAGT
1 GCATCCATGCACC-CCTGTAGTGCATCCATGCATCCTGCAGT
13723221 GCATCCATGCAC
1 GCATCCATGCAC
13723233 TCAAACATCG
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
41 1 0.01
42 66 0.80
43 15 0.18
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24
Consensus pattern (41 bp):
GCATCCATGCACCCCTGTAGTGCATCCATGCATCCTGCAGT
Found at i:13723305 original size:21 final size:21
Alignment explanation
Indices: 13723271--13723314 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
13723261 ATGCATCCTT
**
13723271 CTGTGCATTGATGCATC-AAGG
1 CTGTGCATCCATGCA-CGAAGG
13723292 CTGTGCATCCATGCACGAAGG
1 CTGTGCATCCATGCACGAAGG
13723313 CT
1 CT
13723315 ACAACGGCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25
Consensus pattern (21 bp):
CTGTGCATCCATGCACGAAGG
Found at i:13723457 original size:20 final size:22
Alignment explanation
Indices: 13723419--13723458 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
13723409 TTTTAGTAGA
13723419 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
13723441 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
13723459 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:13728608 original size:23 final size:23
Alignment explanation
Indices: 13728578--13728622 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
13728568 ATATGTATTT
*
13728578 AAGTTAGGGATGTTAAAGGAGGC
1 AAGTTAGGGATGTTAAAAGAGGC
13728601 AAGTTAGGGATGTTAAAAGAGG
1 AAGTTAGGGATGTTAAAAGAGG
13728623 TGAAATATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.02, G:0.38, T:0.22
Consensus pattern (23 bp):
AAGTTAGGGATGTTAAAAGAGGC
Found at i:13738958 original size:31 final size:31
Alignment explanation
Indices: 13738891--13738950 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
13738881 CAATTTAAGG
*
13738891 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
13738922 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
13738951 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:13739038 original size:19 final size:19
Alignment explanation
Indices: 13739014--13739061 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
13739004 AAATGTTTTA
**
13739014 TGAACAGTAAATTACTATT
1 TGAACAGTAAAGCACTATT
*
13739033 TGAACAGTAAAGCACTGTT
1 TGAACAGTAAAGCACTATT
13739052 TGAACAGTAA
1 TGAACAGTAA
13739062 CCCGAGGCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (19 bp):
TGAACAGTAAAGCACTATT
Found at i:13739192 original size:21 final size:21
Alignment explanation
Indices: 13739166--13739207 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
13739156 ATTTGAATAT
*
13739166 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
13739187 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
13739208 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:13739269 original size:21 final size:21
Alignment explanation
Indices: 13739236--13739275 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
13739226 TTTTTGCAGA
*
13739236 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
13739258 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
13739276 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:13741293 original size:13 final size:15
Alignment explanation
Indices: 13741274--13741306 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
13741264 ATTGCCACCA
13741274 ATATT-AAACCATAT
1 ATATTAAAACCATAT
13741288 -TATTAAAACCATAT
1 ATATTAAAACCATAT
13741302 ATATT
1 ATATT
13741307 GTTCATTTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 4 0.24
14 9 0.53
15 4 0.24
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (15 bp):
ATATTAAAACCATAT
Found at i:13741411 original size:14 final size:15
Alignment explanation
Indices: 13741385--13741414 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
13741375 CCATATTACA
13741385 AAATAATAACCCAAT
1 AAATAATAACCCAAT
13741400 AAATAA-AACCCAAT
1 AAATAATAACCCAAT
13741414 A
1 A
13741415 CTCATTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.63, C:0.20, G:0.00, T:0.17
Consensus pattern (15 bp):
AAATAATAACCCAAT
Found at i:13744655 original size:25 final size:25
Alignment explanation
Indices: 13744623--13744675 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
13744613 TATTAGGGAT
13744623 TTTATTATTTTAAAAT-AATTAAATA
1 TTTATTA-TTTAAAATAAATTAAATA
**
13744648 TTTATTATTTAATTTAAATTAAATA
1 TTTATTATTTAAAATAAATTAAATA
13744673 TTT
1 TTT
13744676 GGGAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TTTATTATTTAAAATAAATTAAATA
Found at i:13748143 original size:8 final size:8
Alignment explanation
Indices: 13748132--13748247 Score: 205
Period size: 8 Copynumber: 14.5 Consensus size: 8
13748122 AAAAAATGCA
*
13748132 TACATACA
1 TACATACG
*
13748140 TACATACA
1 TACATACG
13748148 TACATACG
1 TACATACG
13748156 TACATACG
1 TACATACG
13748164 TACATACG
1 TACATACG
13748172 TACATACG
1 TACATACG
13748180 TACATACG
1 TACATACG
13748188 TACATACG
1 TACATACG
13748196 TACATACG
1 TACATACG
13748204 TACATACG
1 TACATACG
13748212 TACATACG
1 TACATACG
*
13748220 TACATACA
1 TACATACG
13748228 TACATACG
1 TACATACG
13748236 TACATACG
1 TACATACG
13748244 TACA
1 TACA
13748248 AAATCATATA
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 105 1.00
ACGTcount: A:0.41, C:0.25, G:0.09, T:0.25
Consensus pattern (8 bp):
TACATACG
Found at i:13748503 original size:22 final size:22
Alignment explanation
Indices: 13748477--13748559 Score: 112
Period size: 22 Copynumber: 3.8 Consensus size: 22
13748467 GGTATGTGAA
* *
13748477 ATTTTTCCTGAAGGACCTATGT
1 ATTTTTCCCGAAAGACCTATGT
13748499 ATTTTTCCCGAAAGACCTATGT
1 ATTTTTCCCGAAAGACCTATGT
* *
13748521 ATTTGTCCCGAATGACCTATGT
1 ATTTTTCCCGAAAGACCTATGT
* *
13748543 ATTTGTCCCGAATGACC
1 ATTTTTCCCGAAAGACC
13748560 GCGTAGAACC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 57 1.00
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (22 bp):
ATTTTTCCCGAAAGACCTATGT
Found at i:13755146 original size:23 final size:21
Alignment explanation
Indices: 13755094--13755155 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
13755084 TTTTGGTGCA
*
13755094 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
13755114 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
13755135 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
13755156 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:13760352 original size:18 final size:19
Alignment explanation
Indices: 13760318--13760353 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
13760308 ATATTGTTAT
*
13760318 AATTTTATTTTTATATAAC
1 AATTTTATTTGTATATAAC
13760337 AATTTT-TTTGTATATAA
1 AATTTTATTTGTATATAA
13760354 TAAGATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (19 bp):
AATTTTATTTGTATATAAC
Found at i:13761663 original size:25 final size:25
Alignment explanation
Indices: 13761634--13761683 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
13761624 AATAGGACAT
*
13761634 GAAGCAACTTCAAAGTATAAACTTC
1 GAAGCAACTTCAAAGCATAAACTTC
*
13761659 GAAGCAACTTCAAAGCGTAAACTTC
1 GAAGCAACTTCAAAGCATAAACTTC
13761684 AAAACAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.22
Consensus pattern (25 bp):
GAAGCAACTTCAAAGCATAAACTTC
Found at i:13761691 original size:25 final size:25
Alignment explanation
Indices: 13761638--13761691 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
13761628 GGACATGAAG
* * *
13761638 CAACTTCAAAGTATAAACTTCGAAG
1 CAACTTCAAAGCATAAACTTCAAAA
*
13761663 CAACTTCAAAGCGTAAACTTCAAAA
1 CAACTTCAAAGCATAAACTTCAAAA
13761688 CAAC
1 CAAC
13761692 AATCCACAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.46, C:0.24, G:0.09, T:0.20
Consensus pattern (25 bp):
CAACTTCAAAGCATAAACTTCAAAA
Found at i:13775678 original size:19 final size:19
Alignment explanation
Indices: 13775654--13775691 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
13775644 TTTTCTCTCT
*
13775654 ACATGGAGAATTTATTTTA
1 ACATGGAGAAATTATTTTA
13775673 ACATGGAGAAATTATTTTA
1 ACATGGAGAAATTATTTTA
13775692 TATACTCTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.39
Consensus pattern (19 bp):
ACATGGAGAAATTATTTTA
Found at i:13775843 original size:12 final size:12
Alignment explanation
Indices: 13775826--13775856 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
13775816 TTAAATCTCC
13775826 ATCTCTTCTTCA
1 ATCTCTTCTTCA
13775838 ATCTCTTCTTCA
1 ATCTCTTCTTCA
13775850 ATCTCTT
1 ATCTCTT
13775857 AACTCCCTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (12 bp):
ATCTCTTCTTCA
Found at i:13776869 original size:31 final size:31
Alignment explanation
Indices: 13776834--13776937 Score: 84
Period size: 31 Copynumber: 3.2 Consensus size: 31
13776824 TCAGTCGGTG
13776834 CTGAACCTATACAAGGAATTACCAACAACTA
1 CTGAACCTATACAAGGAATTACCAACAACTA
* * ** *
13776865 CTGAACCTGCTAGCTATAAGGAAGTACCAATC-GGTG
1 CTGAA-C--CTA--TACAAGGAATTACCAA-CAACTA
* *
13776901 CTGAACCTATGCAAGGAATTACCAACAACGA
1 CTGAACCTATACAAGGAATTACCAACAACTA
13776932 CTGAAC
1 CTGAAC
13776938 TTGTTAGAGT
Statistics
Matches: 54, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
30 1 0.02
31 24 0.44
32 1 0.02
33 3 0.06
34 3 0.06
35 1 0.02
36 20 0.37
37 1 0.02
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (31 bp):
CTGAACCTATACAAGGAATTACCAACAACTA
Found at i:13780738 original size:31 final size:31
Alignment explanation
Indices: 13780703--13780801 Score: 81
Period size: 36 Copynumber: 3.0 Consensus size: 31
13780693 CACTCGTTGT
*
13780703 TGAACATATACAATGAATTACCAGTAGAGAC
1 TGAACATATACAAGGAATTACCAGTAGAGAC
* * * *
13780734 TGAACCTACCAGATATAAGGAATTACCAGTTGATAC
1 TG-A---A-CATATACAAGGAATTACCAGTAGAGAC
* * *
13780770 TGAACCTATACAAGGAATTACTAGTAGCGAC
1 TGAACATATACAAGGAATTACCAGTAGAGAC
13780801 T
1 T
13780802 AAACCTGCCA
Statistics
Matches: 51, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
31 23 0.45
32 2 0.04
35 2 0.04
36 24 0.47
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.24
Consensus pattern (31 bp):
TGAACATATACAAGGAATTACCAGTAGAGAC
Found at i:13799923 original size:2 final size:2
Alignment explanation
Indices: 13799916--13799947 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
13799906 ATTATAACCC
13799916 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
13799948 CCATTTTCGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13802939 original size:19 final size:20
Alignment explanation
Indices: 13802900--13802941 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
13802890 CTGACATGAC
13802900 ATTTTTAAATCATTATCTTA
1 ATTTTTAAATCATTATCTTA
*
13802920 ATTTTTAAATTATTAT-TTA
1 ATTTTTAAATCATTATCTTA
13802939 ATT
1 ATT
13802942 AATTTTATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTTTAAATCATTATCTTA
Found at i:13803282 original size:33 final size:33
Alignment explanation
Indices: 13803240--13803322 Score: 157
Period size: 33 Copynumber: 2.5 Consensus size: 33
13803230 TAGAAAATAC
13803240 AATTTAAAATTATTTATATTTTATTAAAATTAA
1 AATTTAAAATTATTTATATTTTATTAAAATTAA
13803273 AATTTAAAATTATTTATATTTTATTAAAATTAA
1 AATTTAAAATTATTTATATTTTATTAAAATTAA
*
13803306 AATTTATAATTATTTAT
1 AATTTAAAATTATTTAT
13803323 TAAAATAAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
AATTTAAAATTATTTATATTTTATTAAAATTAA
Found at i:13804999 original size:2 final size:2
Alignment explanation
Indices: 13804992--13805018 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13804982 ATTATATCAT
13804992 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
13805019 TAATGATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13806006 original size:19 final size:20
Alignment explanation
Indices: 13805984--13806022 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
13805974 TATAAAATCA
*
13805984 ATGTTTAAG-GACCTATTTG
1 ATGTTTAAGTGACCAATTTG
*
13806003 ATGTTTTAGTGACCAATTTG
1 ATGTTTAAGTGACCAATTTG
13806023 TTACTTTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.26, C:0.10, G:0.21, T:0.44
Consensus pattern (20 bp):
ATGTTTAAGTGACCAATTTG
Found at i:13808470 original size:15 final size:15
Alignment explanation
Indices: 13808438--13808493 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
13808428 TACCTTCATT
**
13808438 ATCACCACCAAGATC
1 ATCACCACCACCATC
*
13808453 ATCACCACCACCACC
1 ATCACCACCACCATC
* *
13808468 ATCACCATCATCATC
1 ATCACCACCACCATC
*
13808483 ATTACCACCAC
1 ATCACCACCAC
13808494 TTGATGTCAA
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.36, C:0.46, G:0.02, T:0.16
Consensus pattern (15 bp):
ATCACCACCACCATC
Found at i:13811800 original size:199 final size:202
Alignment explanation
Indices: 13811421--13811828 Score: 680
Period size: 199 Copynumber: 2.0 Consensus size: 202
13811411 GATGAAAGGT
* *
13811421 TTACACTTTGAAACTAAAGTTTCTCTACTTCCTCCCGTTGCCTTCTTTACTTCTTACTTTGGTTG
1 TTACACTTTGAAACTAAAGTTTCTATACTTCCTCCCGTTGCCTTCTTTACTTCTTACTTTGATTG
*
13811486 TGAATTTTTTTTAATATTTTGATTTTTAAATTCATTTTTTTTCAATTATTTTTAACACTTCCAAA
66 TGAATTTTTTTTAATATTTTGATTTTTAAATT-ATATTTTTTCAATTATTTTTAACACTTCCAAA
* ** *
13811551 CAAATCCTCTACTATTTGCTTTAGTACTTTCTTACACACCTACATCATCTACTACTTGCTTTACT
130 AAAATCCTCTACTATTTGCTCCAGTACTTTCTTACACACCTACATCATCTACTACATGCTTTACT
13811616 ACTTTTAC
195 ACTTTTAC
* * *
13811624 TTACCCTTTGAAACTAGAGTTTCTATGCTTCCTCCCGTTGCCTTCTTTACTTCTTACTTTGATTG
1 TTACACTTTGAAACTAAAGTTTCTATACTTCCTCCCGTTGCCTTCTTTACTTCTTACTTTGATTG
13811689 TG-ATTTTTTTTAATATTTTGATTTTTAAATT-TATTTTTTCAATTA-TTTTAACACTTCCAAAA
66 TGAATTTTTTTTAATATTTTGATTTTTAAATTATATTTTTTCAATTATTTTTAACACTTCC-AAA
13811751 AAAAT-CTCTACTATTTGCTCCAGTACTTTCTTACACACCTACATCATCTACTACATGCTTTACT
130 AAAATCCTCTACTATTTGCTCCAGTACTTTCTTACACACCTACATCATCTACTACATGCTTTACT
13811815 ACTTTTAC
195 ACTTTTAC
13811823 TTACAC
1 TTACAC
13811829 CCTTTTTTTT
Statistics
Matches: 193, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
199 82 0.42
200 20 0.10
202 29 0.15
203 62 0.32
ACGTcount: A:0.24, C:0.22, G:0.06, T:0.48
Consensus pattern (202 bp):
TTACACTTTGAAACTAAAGTTTCTATACTTCCTCCCGTTGCCTTCTTTACTTCTTACTTTGATTG
TGAATTTTTTTTAATATTTTGATTTTTAAATTATATTTTTTCAATTATTTTTAACACTTCCAAAA
AAATCCTCTACTATTTGCTCCAGTACTTTCTTACACACCTACATCATCTACTACATGCTTTACTA
CTTTTAC
Found at i:13811886 original size:12 final size:12
Alignment explanation
Indices: 13811865--13811900 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
13811855 CCAAGAATCA
13811865 TATTTTTTATTT
1 TATTTTTTATTT
* *
13811877 TATTTATTATAT
1 TATTTTTTATTT
13811889 TATTTTTTATTT
1 TATTTTTTATTT
13811901 ACATGCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
TATTTTTTATTT
Found at i:13811927 original size:17 final size:17
Alignment explanation
Indices: 13811883--13811933 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
13811873 ATTTTATTTA
13811883 TTATATTATTTTTTA-T
1 TTATATTATTTTTTATT
* *
13811899 TTACATGCATTTTTTATT
1 TTATAT-TATTTTTTATT
13811917 TTATATTATTTTTTATT
1 TTATATTATTTTTTATT
13811934 ATGAATAGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 5 0.17
17 18 0.62
18 6 0.21
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (17 bp):
TTATATTATTTTTTATT
Found at i:13815850 original size:17 final size:17
Alignment explanation
Indices: 13815806--13815873 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 17
13815796 ATTCATGCAT
13815806 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
* *
13815823 GTTATTTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
*
13815841 CTAGTTCATT-CTTCAAA
1 CTAGTTCATTAATT-AAA
*
13815858 CTAGTTCATTTATTAA
1 CTAGTTCATTAATTAA
13815874 TCTAACTCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
16 2 0.05
17 25 0.61
18 14 0.34
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.44
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:13820140 original size:15 final size:15
Alignment explanation
Indices: 13820120--13820149 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
13820110 GGCAGTAGAA
13820120 AAACACGCATTGCAT
1 AAACACGCATTGCAT
13820135 AAACACGCATTGCAT
1 AAACACGCATTGCAT
13820150 TACATAGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.20
Consensus pattern (15 bp):
AAACACGCATTGCAT
Found at i:13833747 original size:2 final size:2
Alignment explanation
Indices: 13833740--13833798 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
13833730 AAATATAGAA
13833740 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
13833782 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
13833799 GTTTGATGTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13834899 original size:135 final size:134
Alignment explanation
Indices: 13834651--13834960 Score: 332
Period size: 135 Copynumber: 2.3 Consensus size: 134
13834641 TCAGATCGAG
* * * * * *
13834651 AAACTTTGATTCATTTCACTATTCTTCAGGGAAGATTGAATTGAACTTGATTTGCTTCGCTGCTC
1 AAACTTTAATCCACTTCACTACTCTTCAGGGAAGATTGAATCGAACTTGATTTACTTCGCTGCTC
* ** ** * *
13834716 TTCAGGAAGATCAACTCTGAAACACGAAGAATCTGCTCTAATACTCTTTAGGGGCGATCAAACTC
66 TTCAGGAAGACCAACTCTGAAACAAAAAGAATCTAATCCAATACTCTTTAGGGGAGATCAAACTC
13834781 GAAA
131 GAAA
* * ** * * *
13834785 AAACTTTTGATTCACTTTGCTTCTCTTCAGGGAAGATTGAATCGAATTTGATTTACTTTGCTGCT
1 AAAC-TTTAATCCACTTCACTACTCTTCAGGGAAGATTGAATCGAACTTGATTTACTTCGCTGCT
* * * ** * * *
13834850 CTTCAGGAAGACCAATTCTGAAAGAAAAAGAATTTAATCCGCTATTCTTTAGGGGAGATTATACT
65 CTTCAGGAAGACCAACTCTGAAACAAAAAGAATCTAATCCAATACTCTTTAGGGGAGATCAAACT
*
13834915 CGAGA
130 CGAAA
* *
13834920 AATCTTTAATCCACTTCACTACTCTTCAGGGAATATTGAAT
1 AAACTTTAATCCACTTCACTACTCTTCAGGGAAGATTGAAT
13834961 ATGAAAATCA
Statistics
Matches: 143, Mismatches: 32, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
134 35 0.24
135 108 0.76
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34
Consensus pattern (134 bp):
AAACTTTAATCCACTTCACTACTCTTCAGGGAAGATTGAATCGAACTTGATTTACTTCGCTGCTC
TTCAGGAAGACCAACTCTGAAACAAAAAGAATCTAATCCAATACTCTTTAGGGGAGATCAAACTC
GAAA
Found at i:13835665 original size:89 final size:89
Alignment explanation
Indices: 13835572--13835857 Score: 276
Period size: 89 Copynumber: 3.2 Consensus size: 89
13835562 TCTTCTTCCC
* *
13835572 GAGAAAGTCAAGAATAACACCACTAAAAGGTTTACTTC-TCTTCACGAGAAAGTCAAGAAGGACA
1 GAGAAAGTCAAGAATAACACCACTAAAAGATTGAC-TCATCTTCACGAGAAAGTCAAGAAGGACA
*
13835636 ACACTAAAATTTGACTTCTCTTCGT
65 ACACTAAAATTTGACTTCTCTTCAT
* ** * * * *
13835661 GAGAAAGTCAAAAACGACAACACTAAAATATTGACTCATCTTCGCGAGAAAGTCAATAAGGACAA
1 GAGAAAGTCAAGAATAACACCACTAAAAGATTGACTCATCTTCACGAGAAAGTCAAGAAGGACAA
* * *
13835726 CACCAAAATATTGACTCCTCTTCAC
66 CACTAAAAT-TTGACTTCTCTTCAT
* * * * * * * * * *
13835751 AATAAATTCAAGGA-AA-A-CATTGAAAGATTGACTCTTCTTCACGACAAAGTTAAGAATGACAA
1 GAGAAAGTCAAGAATAACACCACTAAAAGATTGACTCATCTTCACGAGAAAGTCAAGAAGGACAA
* *
13835813 AACTGATAGA-TTGACTTCTCTTCAT
66 CACT-A-AAATTTGACTTCTCTTCAT
13835838 GAGAAAGTCAAGAATAACAC
1 GAGAAAGTCAAGAATAACAC
13835858 TGAAAGAATG
Statistics
Matches: 153, Mismatches: 37, Indels: 13
0.75 0.18 0.06
Matches are distributed among these distances:
87 61 0.40
88 6 0.04
89 65 0.42
90 21 0.14
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (89 bp):
GAGAAAGTCAAGAATAACACCACTAAAAGATTGACTCATCTTCACGAGAAAGTCAAGAAGGACAA
CACTAAAATTTGACTTCTCTTCAT
Found at i:13835668 original size:44 final size:45
Alignment explanation
Indices: 13835547--13835851 Score: 228
Period size: 45 Copynumber: 6.9 Consensus size: 45
13835537 TTGATAATGT
** * ** *
13835547 CACTAAAAGGTTGAC-TCTTCTTCCCGAGAAAGTCAAGAATAACAC
1 CACTAAAATATTGACTTC-TCTTCGCGAGAAAGTCAAGAAGGACAA
** * *
13835592 CACTAAAAGGTTTACTTCTCTTCACGAGAAAGTCAAGAAGGACAA
1 CACTAAAATATTGACTTCTCTTCGCGAGAAAGTCAAGAAGGACAA
* * *
13835637 CACTAAAAT-TTGACTTCTCTTCGTGAGAAAGTCAAAAACGACAA
1 CACTAAAATATTGACTTCTCTTCGCGAGAAAGTCAAGAAGGACAA
*
13835681 CACTAAAATATTGAC-TCATCTTCGCGAGAAAGTCAATAAGGACAA
1 CACTAAAATATTGACTTC-TCTTCGCGAGAAAGTCAAGAAGGACAA
* * * * * * *
13835726 CACCAAAATATTGACTCCTCTTCACAATAAATTC---AAGGAAAA
1 CACTAAAATATTGACTTCTCTTCGCGAGAAAGTCAAGAAGGACAA
* * * * * * *
13835768 CATTGAAAGATTGAC-TCTTCTTCACGACAAAGTTAAGAATGACAA
1 CACTAAAATATTGACTTC-TCTTCGCGAGAAAGTCAAGAAGGACAA
* * * * **
13835813 AACTGATAGATTGACTTCTCTTCATGAGAAAGTCAAGAA
1 CACTAAAATATTGACTTCTCTTCGCGAGAAAGTCAAGAA
13835852 TAACACTGAA
Statistics
Matches: 213, Mismatches: 38, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
41 1 0.00
42 30 0.14
44 41 0.19
45 136 0.64
46 5 0.02
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (45 bp):
CACTAAAATATTGACTTCTCTTCGCGAGAAAGTCAAGAAGGACAA
Found at i:13835914 original size:38 final size:38
Alignment explanation
Indices: 13835820--13836202 Score: 452
Period size: 38 Copynumber: 10.0 Consensus size: 38
13835810 CAAAACTGAT
* *
13835820 AGATTGACTTCTCTTCATGAGAAAGTCAAGAATAACACTGAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAAT-A-AC--AA
* * *
13835862 AGAATGA-TTCCTCTTCACGAGGGAGTCAAGGAA-GACAA
1 AGATTGACTT-CTCTTCACGAGGAAGTCAA-GAATAACAA
13835900 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* * *
13835938 AGATTGCCTTCTCTTCACGAGGAAATCAAGGAA-GACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAA-GAATAACAA
* *
13835976 ATATTGACTTCTCTTCACAAGGAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
*
13836014 AGACTTG-CTTCTCTTCACGAGGAAGTCATA-AATAAAAA
1 AGA-TTGACTTCTCTTCACGAGGAAGTCA-AGAATAACAA
* * * *
13836052 AAATTGACTTCTCTTCACCAGAAAGTCAAGAACAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* *
13836090 AGATTGACTTCTCTTCATGAGGAAGTCAAGTATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* *
13836128 ATATTGACTTCTCTTTACGAGGAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* **
13836166 AGATCGACTTCTCTTCGTGAGGAAGTCAAGAATAACA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACA
13836203 TTGGAAAATT
Statistics
Matches: 292, Mismatches: 39, Indels: 24
0.82 0.11 0.07
Matches are distributed among these distances:
37 10 0.03
38 244 0.84
39 9 0.03
40 2 0.01
41 2 0.01
42 22 0.08
43 3 0.01
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.25
Consensus pattern (38 bp):
AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
Found at i:13838225 original size:18 final size:18
Alignment explanation
Indices: 13838204--13838242 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
13838194 TTTCTTCTTA
*
13838204 TTTTTCTATATTTTCTCT
1 TTTTTCTATATTTTCCCT
*
13838222 TTTTTCTATCTTTTCCCT
1 TTTTTCTATATTTTCCCT
13838240 TTT
1 TTT
13838243 CCCTTTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTCTATATTTTCCCT
Found at i:13844666 original size:16 final size:16
Alignment explanation
Indices: 13844647--13844696 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
13844637 AATTTTGAAA
13844647 TTTTGGTTTTTTTTGT
1 TTTTGGTTTTTTTTGT
13844663 TTTTGG--TTTTTTG-
1 TTTTGGTTTTTTTTGT
*
13844676 TTTTGCCTTTTTTTTGT
1 TTTTG-GTTTTTTTTGT
13844693 TTTT
1 TTTT
13844697 TTTTTGAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
13 5 0.17
14 7 0.24
16 13 0.45
17 4 0.14
ACGTcount: A:0.00, C:0.04, G:0.16, T:0.80
Consensus pattern (16 bp):
TTTTGGTTTTTTTTGT
Found at i:13844700 original size:14 final size:14
Alignment explanation
Indices: 13844653--13844701 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
13844643 GAAATTTTGG
13844653 TTTTTTTTGTTTTT
1 TTTTTTTTGTTTTT
** *
13844667 GGTTTTTTGTTTTGCC
1 TTTTTTTTGTTTT--T
13844683 TTTTTTTTGTTTTT
1 TTTTTTTTGTTTTT
13844697 TTTTT
1 TTTTT
13844702 GAAAAAAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
14 16 0.59
16 11 0.41
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.84
Consensus pattern (14 bp):
TTTTTTTTGTTTTT
Found at i:13849378 original size:16 final size:16
Alignment explanation
Indices: 13849359--13849407 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
13849349 AATTTTGAAA
13849359 TTTGGTTTTTTTTGTT
1 TTTGGTTTTTTTTGTT
13849375 TTTGG--TTTTTTG-T
1 TTTGGTTTTTTTTGTT
*
13849388 TTTGCCTTTTTTTTGTT
1 TTTG-GTTTTTTTTGTT
13849405 TTT
1 TTT
13849408 TTTTTTTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
13 5 0.18
14 7 0.25
16 12 0.43
17 4 0.14
ACGTcount: A:0.00, C:0.04, G:0.16, T:0.80
Consensus pattern (16 bp):
TTTGGTTTTTTTTGTT
Found at i:13849411 original size:14 final size:14
Alignment explanation
Indices: 13849364--13849414 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
13849354 TGAAATTTGG
13849364 TTTTTTTTGTTTTT
1 TTTTTTTTGTTTTT
** *
13849378 GGTTTTTTGTTTTGCC
1 TTTTTTTTGTTTT--T
13849394 TTTTTTTTGTTTTT
1 TTTTTTTTGTTTTT
13849408 TTTTTTT
1 TTTTTTT
13849415 GAAAAAAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
14 18 0.62
16 11 0.38
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.84
Consensus pattern (14 bp):
TTTTTTTTGTTTTT
Found at i:13850196 original size:15 final size:17
Alignment explanation
Indices: 13850171--13850204 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
13850161 TAAAGGTCCT
13850171 AAATAACTAATAAA-TA
1 AAATAACTAATAAACTA
13850187 AAATAA-TAATAAACTA
1 AAATAACTAATAAACTA
13850203 AA
1 AA
13850205 CATGTCTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAACTAATAAACTA
Found at i:13855757 original size:3 final size:3
Alignment explanation
Indices: 13855749--13855792 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
13855739 AAAAGTAGGT
13855749 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
13855793 TAAAGATGTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:13856316 original size:134 final size:133
Alignment explanation
Indices: 13855949--13856654 Score: 773
Period size: 134 Copynumber: 5.3 Consensus size: 133
13855939 ACTGTTTATG
* * * * **
13855949 TAGGGTAGATCAGA-TCGA-AAAAATTTGATTCA-TTCTGTTGTTCTTCAGGGAAGATTGAATCG
1 TAGGGGAGATCAGACTCGAGAAAATTTTGATCCACTTC-GATGCACTTCAGGGAAGATTGAATC-
* * * * * * **
13856011 AACTTGATTTGCTTCACTGCTCTTCAGGAAGACCAACTATGAAACACGAAGAATCTGCTCTGCTA
64 AAATTGATTTGCTTCATTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTA
13856076 CTCTT
129 CTCTT
* * * * * * * *
13856081 TAGGGGAGATCAGACTTGAAAAAACTTTTGATTCACTTCGCTCCTCTTTAGAGAAGATTGAATCG
1 TAGGGGAGATCAGACTCGAGAAAA-TTTTGATCCACTTCGATGCACTTCAGGGAAGATTGAATC-
* * * * *
13856146 AATTTGATTTACTTCACTGCTCTTTAGGAAGACCAAATCTGAAAGAAGAAGAATTTGCTCCACTA
64 AAATTGATTTGCTTCATTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTA
13856211 CTCTT
129 CTCTT
*
13856216 TAGGGGAGATCAGACTCGAGAAAATTTTGATCCACTTCGATGCACTTCAGGGAAGATCGAATCAA
1 TAGGGGAGATCAGACTCGAGAAAATTTTGATCCACTTCGATGCACTTCAGGGAAGATTGAATCAA
* * * * * *
13856281 ACTTGATTTGCTTCGTTGCTCTTCAAGAAGACCAAATCAGAAAGAAGAAGAATATGATCCTCTAC
66 A-TTGATTTGCTTCATTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTAC
*
13856346 TCTA
130 TCTT
* * *
13856350 TAGGGGAGATCAGACTCGAGGAAATTTTGATCTACTTC-ACTGCACTTCTGGGAAGATTGAATCG
1 TAGGGGAGATCAGACTCGAGAAAATTTTGATCCACTTCGA-TGCACTTCAGGGAAGATTGAATC-
* * *
13856414 AAATCGATTTGCTTCATTGCTCTTCAGGAAGACCAAATTTGAAAGAAGAATAATCTGCTCCACTA
64 AAATTGATTTGCTTCATTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTA
13856479 -TCCTT
129 CT-CTT
* * ** *
13856484 TAGGGGAGATCAAACTCGAGAAAA-CTTGATCCACTTCTCTGCTA-TTCATGGAAGATTGAATCA
1 TAGGGGAGATCAGACTCGAGAAAATTTTGATCCACTTCGATGC-ACTTCAGGGAAGATTGAATCA
* * * * *
13856547 GAATCGATTTGCTTCACTT-CTCTTCAGGAAGACCAAATCTGAATGAAGAAGAATCTTCTTCGCT
65 -AATTGATTTGCTTCA-TTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACT
*
13856611 ATTCTT
128 ACTCTT
13856617 TAGGGGAGATCAGACTCGAG-AAATCTTTGATCCACTTC
1 TAGGGGAGATCAGACTCGAGAAAAT-TTTGATCCACTTC
13856655 ACTACTCTTC
Statistics
Matches: 492, Mismatches: 67, Indels: 28
0.84 0.11 0.05
Matches are distributed among these distances:
132 17 0.03
133 114 0.23
134 243 0.49
135 115 0.23
136 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (133 bp):
TAGGGGAGATCAGACTCGAGAAAATTTTGATCCACTTCGATGCACTTCAGGGAAGATTGAATCAA
ATTGATTTGCTTCATTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTACT
CTT
Found at i:13857296 original size:50 final size:47
Alignment explanation
Indices: 13857222--13857438 Score: 132
Period size: 45 Copynumber: 4.7 Consensus size: 47
13857212 GATACTACTG
* * *
13857222 AAAA-GTTGACTCCTC-TCCGCGAGAAAGTCAAGTTGATAATGACATCACT
1 AAAAGGTTGACTCTTCTTCC-CGAGAAAGTCAA---GATAATAACACCACT
13857271 AAAAGGTTGACTCTTCTTCCCGAGAAAGTC-A-ATAATAACACCACT
1 AAAAGGTTGACTCTTCTTCCCGAGAAAGTCAAGATAATAACACCACT
* * ** *
13857316 AAAAGGTTTACT-TCTCTTCACGAGAAAGTCAAG--AAGGACAACACT
1 AAAAGGTTGACTCT-TCTTCCCGAGAAAGTCAAGATAATAACACCACT
* ** ** * *
13857361 AAAA-TTTGACT-TCTCTTCATGAGAAAGTCAA-A-AAGGACAACATT
1 AAAAGGTTGACTCT-TCTTCCCGAGAAAGTCAAGATAATAACACCACT
** * *
13857405 AAAATATTGACTCCTCTTCGCGAGAAAGTCAAGA
1 AAAAGGTTGACTCTTCTTCCCGAGAAAGTCAAGA
13857439 AGGACACCAC
Statistics
Matches: 143, Mismatches: 16, Indels: 21
0.79 0.09 0.12
Matches are distributed among these distances:
44 40 0.28
45 73 0.51
46 2 0.01
49 5 0.03
50 20 0.14
51 3 0.02
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (47 bp):
AAAAGGTTGACTCTTCTTCCCGAGAAAGTCAAGATAATAACACCACT
Found at i:13857385 original size:89 final size:90
Alignment explanation
Indices: 13857292--13857577 Score: 307
Period size: 89 Copynumber: 3.2 Consensus size: 90
13857282 TCTTCTTCCC
* * * *
13857292 GAGAAAGTCAATAATAACACCACTAAAAGGTTTACTTCTCTTCACGAGAAAGTCAAGAAGGACAA
1 GAGAAAGTCAAGAATAACACCATTAAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAAGGACAA
13857357 CACTAAAAT-TTGACTTCTCTTCAT
66 CACTAAAATATTGACTTCTCTTCAT
* ** * * * * *
13857381 GAGAAAGTCAAAAAGGACAACATTAAAATATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAC
1 GAGAAAGTCAAGAATAACACCATTAAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAAGGACAA
*
13857446 CACCAAAATATTGA-TTACTCTTCAT
66 CACTAAAATATTGACTT-CTCTTCAT
* * * *
13857471 GAGAAATTCAAGGAA-AA-A--ATTGAAAGATTGAC-TCTTCTTCACGACAAAGTCAAGAATGAC
1 GAGAAAGTCAA-GAATAACACCATTAAAAGATTGACTTC-TCTTCACGAGAAAGTCAAGAAGGAC
* * * *
13857531 AAAACTGATATATTGACTTCTCTTTAT
64 AACACTAAAATATTGACTTCTCTTCAT
13857558 GAGAAAGTCAAGAATAACAC
1 GAGAAAGTCAAGAATAACAC
13857578 TAAAATATTG
Statistics
Matches: 161, Mismatches: 28, Indels: 16
0.79 0.14 0.08
Matches are distributed among these distances:
86 4 0.02
87 64 0.40
88 3 0.02
89 65 0.40
90 23 0.14
91 2 0.01
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.24
Consensus pattern (90 bp):
GAGAAAGTCAAGAATAACACCATTAAAAGATTGACTTCTCTTCACGAGAAAGTCAAGAAGGACAA
CACTAAAATATTGACTTCTCTTCAT
Found at i:13857522 original size:87 final size:87
Alignment explanation
Indices: 13857315--13857598 Score: 279
Period size: 87 Copynumber: 3.2 Consensus size: 87
13857305 ATAACACCAC
* * * *
13857315 TAAAAGGTTTACTTCTCTTCACGAGAAAGTCAAGAAGGACAACACTAAAATTTGACTTCTCTTCA
1 TAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAACACCAAAATTTGACTTCTCTTCA
* *
13857380 TGAGAAAGTCAAAAAGGACAACAT
66 TGAGAAAGTC--AAAGGAAAAAAT
* * *
13857404 TAAAATATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACACCACCAAAATATTGA-TTACTCTT
1 TAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAACACCAAAAT-TTGACTT-CTCTT
*
13857468 CATGAGAAATTC-AAGGAAAAAAT
64 CATGAGAAAGTCAAAGGAAAAAAT
* * * * * ** * *
13857491 TGAAAGATTGACTCTTCTTCACGACAAAGTCAAGAATGACAAAACTGATATATTGACTTCTCTTT
1 TAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAACACCAAAAT-TTGACTTCTCTTC
* *
13857556 ATGAGAAAGTC-AA-GAATAACAC
65 ATGAGAAAGTCAAAGGAA-AAAAT
* *
13857578 TAAAATATTGATTCCTCTTCA
1 TAAAAGATTGACTCCTCTTCA
13857599 GGTGGGAGTC
Statistics
Matches: 162, Mismatches: 29, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
86 3 0.02
87 91 0.56
88 2 0.01
89 46 0.28
90 20 0.12
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (87 bp):
TAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAACACCAAAATTTGACTTCTCTTCA
TGAGAAAGTCAAAGGAAAAAAT
Found at i:13857569 original size:45 final size:45
Alignment explanation
Indices: 13857262--13857598 Score: 266
Period size: 45 Copynumber: 7.6 Consensus size: 45
13857252 AGTTGATAAT
* ** * * *
13857262 GACATCACTAAAAGGTTGAC-TCTTCTTCCCGAGAAAGTCAATAAT
1 GACAACACTAAAATATTGACTTC-TCTTCACGAGAAAGTCAAGAAG
* * ** *
13857307 AACACCACTAAAAGGTTTACTTCTCTTCACGAGAAAGTCAAGAAG
1 GACAACACTAAAATATTGACTTCTCTTCACGAGAAAGTCAAGAAG
* *
13857352 GACAACACTAAAAT-TTGACTTCTCTTCATGAGAAAGTCAAAAAG
1 GACAACACTAAAATATTGACTTCTCTTCACGAGAAAGTCAAGAAG
* * *
13857396 GACAACATTAAAATATTGACTCCTCTTCGCGAGAAAGTCAAGAAG
1 GACAACACTAAAATATTGACTTCTCTTCACGAGAAAGTCAAGAAG
* * * *
13857441 GACACCACCAAAATATTGA-TTACTCTTCATGAGAAATTCAAGGAA-
1 GACAACACTAAAATATTGACTT-CTCTTCACGAGAAAGTCAA-GAAG
* * * * *
13857486 -A-AA-ATTGAAAGATTGAC-TCTTCTTCACGACAAAGTCAAGAAT
1 GACAACACTAAAATATTGACTTC-TCTTCACGAGAAAGTCAAGAAG
* * * * *
13857528 GACAAAACTGATATATTGACTTCTCTTTATGAGAAAGTCAAG-A-
1 GACAACACTAAAATATTGACTTCTCTTCACGAGAAAGTCAAGAAG
*
13857571 -ATAACACTAAAATATTGA-TTCCTCTTCA
1 GACAACACTAAAATATTGACTT-CTCTTCA
13857599 GGTGGGAGTC
Statistics
Matches: 237, Mismatches: 43, Indels: 27
0.77 0.14 0.09
Matches are distributed among these distances:
41 6 0.03
42 45 0.19
43 2 0.01
44 45 0.19
45 132 0.56
46 7 0.03
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.26
Consensus pattern (45 bp):
GACAACACTAAAATATTGACTTCTCTTCACGAGAAAGTCAAGAAG
Found at i:13857635 original size:38 final size:37
Alignment explanation
Indices: 13857579--13857839 Score: 145
Period size: 38 Copynumber: 6.9 Consensus size: 37
13857569 GAATAACACT
* * *
13857579 AAAATATTGA-TTCCTCTTCAGGTGGGAGTCAAGGAAG
1 AAAAAATTGACTT-CTCTTCACGTGGAAGTCAAGGAAG
* *
13857616 AAATAAATTGACTTCTCTTCACGTAGAAGTCAA-GAAT
1 AAA-AAATTGACTTCTCTTCACGTGGAAGTCAAGGAAG
** *
13857653 AACAAAGATTGACTTCTCTTCACAAGGAAATCAAGGAAG
1 AA-AAA-ATTGACTTCTCTTCACGTGGAAGTCAAGGAAG
* *** * *
13857692 ACAAATATTGACTTCTCTTCATAAGAAAGTCAA-GAATA
1 A-AAAAATTGACTTCTCTTCACGTGGAAGTCAAGGAA-G
* * * *
13857730 AAAAAGACTGACTTCTCTTCACGAGGAAGTC-ACGAAT
1 AAAAA-ATTGACTTCTCTTCACGTGGAAGTCAAGGAAG
** * * * *
13857767 AAAAAAGTTTGACTTCTCTAAATGAGAAAGTCAA-GAACA
1 AAAAAA--TTGACTTCTCTTCACGTGGAAGTCAAGGAA-G
* * *
13857806 AAAAAGATCGACTTCTCTTCATGAGGAAGTCAAG
1 AAAAA-ATTGACTTCTCTTCACGTGGAAGTCAAG
13857840 TATAACAAAG
Statistics
Matches: 178, Mismatches: 31, Indels: 28
0.75 0.13 0.12
Matches are distributed among these distances:
36 1 0.01
37 22 0.12
38 139 0.78
39 14 0.08
40 2 0.01
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (37 bp):
AAAAAATTGACTTCTCTTCACGTGGAAGTCAAGGAAG
Found at i:13857703 original size:76 final size:76
Alignment explanation
Indices: 13857542--13857915 Score: 327
Period size: 76 Copynumber: 4.9 Consensus size: 76
13857532 AAACTGATAT
* * * * * *
13857542 ATTGACTTCTCTTTATG-AGAAAGTCAAGAATAACACTAAAATATTGA-TTCCTCTTCAGGTGGG
1 ATTGACTTCTCTTAATGTAGAAAGTCAAGAAT-A-A--AAAAGATCGACTT-CTCTTCACGAGGA
13857605 AGTCAAGGAAGAAATAA
61 AGTCAAGGAAGAAA-AA
* * * * * *
13857622 ATTGACTTCTCTTCACGTAG-AAGTCAAGAATAACAAAGATTGACTTCTCTTCACAAGGAAATCA
1 ATTGACTTCTCTTAATGTAGAAAGTCAAGAATAAAAAAGATCGACTTCTCTTCACGAGGAAGTCA
*
13857686 AGGAAGACAAAT
66 AGGAAGA-AAAA
* *
13857698 ATTGACTTCTCTTCAT-AAGAAAGTCAAGAATAAAAAAGA-CTGACTTCTCTTCACGAGGAAGTC
1 ATTGACTTCTCTTAATGTAGAAAGTCAAGAATAAAAAAGATC-GACTTCTCTTCACGAGGAAGTC
* *
13857761 -ACGAATAAAAA
65 AAGGAAGAAAAA
* * *
13857772 AGTTTGACTTCTCTAAATG-AGAAAGTCAAGAACAAAAAAGATCGACTTCTCTTCATGAGGAAGT
1 A--TTGACTTCTCTTAATGTAGAAAGTCAAGAATAAAAAAGATCGACTTCTCTTCACGAGGAAGT
*
13857836 CAAGTATA-ACAAAGA
64 CAAGGA-AGA-AAA-A
* * ***
13857851 A-TGACTTCTCTTAATG-AAAAAGTCAAGAATAACAAAGATCGACTTCTCTTCGTTAGGAAGTCA
1 ATTGACTTCTCTTAATGTAGAAAGTCAAGAATAAAAAAGATCGACTTCTCTTCACGAGGAAGTCA
13857914 AG
66 AG
13857916 AATGACATTG
Statistics
Matches: 250, Mismatches: 31, Indels: 30
0.80 0.10 0.10
Matches are distributed among these distances:
74 4 0.02
75 7 0.03
76 195 0.78
77 8 0.03
78 5 0.02
79 3 0.01
80 26 0.10
81 2 0.01
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26
Consensus pattern (76 bp):
ATTGACTTCTCTTAATGTAGAAAGTCAAGAATAAAAAAGATCGACTTCTCTTCACGAGGAAGTCA
AGGAAGAAAAA
Found at i:13857850 original size:38 final size:38
Alignment explanation
Indices: 13857625--13857918 Score: 281
Period size: 38 Copynumber: 7.7 Consensus size: 38
13857615 GAAATAAATT
* *
13857625 GACTTCTCTTCACGTA-GAAGTCAAGAATAACAAAGATT
1 GACTTCTCTTCATG-AGGAAGTCAAGAATAACAAAGATC
** * * * *
13857663 GACTTCTCTTCACAAGGAAATCAAGGAA-GACAAATATT
1 GACTTCTCTTCATGAGGAAGTCAA-GAATAACAAAGATC
* * *
13857701 GACTTCTCTTCATAAGAAAGTCAAGAATAAAAAAGA-C
1 GACTTCTCTTCATGAGGAAGTCAAGAATAACAAAGATC
* * * * *
13857738 TGACTTCTCTTCACGAGGAAGTCACGAATAAAAAAGTTT
1 -GACTTCTCTTCATGAGGAAGTCAAGAATAACAAAGATC
** * * *
13857777 GACTTCTCTAAATGAGAAAGTCAAGAACAAAAAAGATC
1 GACTTCTCTTCATGAGGAAGTCAAGAATAACAAAGATC
*
13857815 GACTTCTCTTCATGAGGAAGTCAAGTATAACAAAGAAT-
1 GACTTCTCTTCATGAGGAAGTCAAGAATAACAAAG-ATC
* **
13857853 GACTTCTCTTAATGAAAAAGTCAAGAATAACAAAGATC
1 GACTTCTCTTCATGAGGAAGTCAAGAATAACAAAGATC
* *
13857891 GACTTCTCTTCGTTAGGAAGTCAAGAAT
1 GACTTCTCTTCATGAGGAAGTCAAGAAT
13857919 GACATTGGAA
Statistics
Matches: 209, Mismatches: 40, Indels: 14
0.79 0.15 0.05
Matches are distributed among these distances:
37 6 0.03
38 198 0.95
39 5 0.02
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.25
Consensus pattern (38 bp):
GACTTCTCTTCATGAGGAAGTCAAGAATAACAAAGATC
Found at i:13857912 original size:114 final size:113
Alignment explanation
Indices: 13857624--13857917 Score: 336
Period size: 114 Copynumber: 2.6 Consensus size: 113
13857614 AGAAATAAAT
* * *
13857624 TGACTTCTCTTCACGTAGAAGTCAAGAATAACAAAGATTGACTTCTCTTCACAAGGAAATCAAGG
1 TGACTTCTCTTCACGAAGAAGTCAAGAATAACAAAGATTGACTTCTCTTCATAAGGAAGTCAA-G
* * * * *
13857689 AAGACAAATATTGACTTCTCTTCATAAGAAAGTCAAGAATAAAAAAGAC
65 AAAAAAAAGATCGACTTCTCTTCATAAGAAAGTCAAGAATAAAAAAGAA
* * * * ** * *
13857738 TGACTTCTCTTCACGAGGAAGTCACGAATAAAAAAGTTTGACTTCTCTAAATGAGAAAGTCAAGA
1 TGACTTCTCTTCACGAAGAAGTCAAGAATAACAAAGATTGACTTCTCTTCATAAGGAAGTCAAGA
* * * *
13857803 ACAAAAAAGATCGACTTCTCTTCATGAGGAAGTCAAGTATAACAAAGAA
66 A-AAAAAAGATCGACTTCTCTTCATAAGAAAGTCAAGAATAAAAAAGAA
* * * * * *
13857852 TGACTTCTCTTAATGAAAAAGTCAAGAATAACAAAGATCGACTTCTCTTCGTTAGGAAGTCAAGA
1 TGACTTCTCTTCACGAAGAAGTCAAGAATAACAAAGATTGACTTCTCTTCATAAGGAAGTCAAGA
13857917 A
66 A
13857918 TGACATTGGA
Statistics
Matches: 146, Mismatches: 33, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
113 3 0.02
114 143 0.98
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.25
Consensus pattern (113 bp):
TGACTTCTCTTCACGAAGAAGTCAAGAATAACAAAGATTGACTTCTCTTCATAAGGAAGTCAAGA
AAAAAAAGATCGACTTCTCTTCATAAGAAAGTCAAGAATAAAAAAGAA
Found at i:13859916 original size:23 final size:23
Alignment explanation
Indices: 13859890--13859945 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
13859880 ATTTTCTCTA
*
13859890 TTTTTTTCTTTTTCCTCTTTTTC
1 TTTTTTTCTTTTTCCTATTTTTC
*
13859913 TTTTTTTCTTTTTCTTATTTTTC
1 TTTTTTTCTTTTTCCTATTTTTC
13859936 TTATTTTTCT
1 TT-TTTTTCT
13859946 CTCTTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 23 0.77
24 7 0.23
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTTTTCTTTTTCCTATTTTTC
Found at i:13859933 original size:15 final size:14
Alignment explanation
Indices: 13859892--13859937 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 14
13859882 TTTCTCTATT
*
13859892 TTTTTCTTTTTCCTC
1 TTTTTCTTTTT-TTC
13859907 TTTTTCTTTTTTTC
1 TTTTTCTTTTTTTC
13859921 TTTTTCTTATTTTTC
1 TTTTTCTT-TTTTTC
13859936 TT
1 TT
13859938 ATTTTTCTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 10 0.34
15 19 0.66
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTCTTTTTTTC
Found at i:13859970 original size:28 final size:29
Alignment explanation
Indices: 13859939--13860015 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 29
13859929 ATTTTTCTTA
13859939 TTTTTCTCTCTTTTTTATATCT-TTTCC-C
1 TTTTTCTCTCTTTTTTAT-TCTCTTTCCTC
* *
13859967 TTTTTTTCTCTTGTTTTCTTCTCTTTCCTC
1 TTTTTCTCTCTT-TTTTATTCTCTTTCCTC
* *
13859997 TTTATCTCTATATTTTTAT
1 TTTTTCTCTCT-TTTTTAT
13860016 GAATTTATTG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
28 14 0.36
29 10 0.26
30 14 0.36
31 1 0.03
ACGTcount: A:0.08, C:0.22, G:0.01, T:0.69
Consensus pattern (29 bp):
TTTTTCTCTCTTTTTTATTCTCTTTCCTC
Found at i:13862122 original size:13 final size:13
Alignment explanation
Indices: 13862104--13862128 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13862094 TCATCCCTGG
13862104 TTGTCTACTCCTA
1 TTGTCTACTCCTA
13862117 TTGTCTACTCCT
1 TTGTCTACTCCT
13862129 CAAGGGACGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.32, G:0.08, T:0.48
Consensus pattern (13 bp):
TTGTCTACTCCTA
Found at i:13865331 original size:45 final size:45
Alignment explanation
Indices: 13865279--13865540 Score: 312
Period size: 45 Copynumber: 5.8 Consensus size: 45
13865269 GAACACAAAC
* *
13865279 GAAAATGCATAATGGTGCATTATCGGCATAAAAGGTGCCACATAT
1 GAAAATGCATAACGGTGCATTATCGACATAAAAGGTGCCACATAT
* * * *
13865324 AAAAATGCATAACGGTGCATTATCGGCATAAAATGTCCCAC-TAGT
1 GAAAATGCATAACGGTGCATTATCGACATAAAAGGTGCCACATA-T
* * * * * *
13865369 GAAAATGCATAATGGTGCATTATCGGCGTAAAAAGTGTCACAAAT
1 GAAAATGCATAACGGTGCATTATCGACATAAAAGGTGCCACATAT
* *
13865414 GAAAATGCATAACGATGCATTATCGACATAAAAGGTGCCACAAAT
1 GAAAATGCATAACGGTGCATTATCGACATAAAAGGTGCCACATAT
* * * *
13865459 GAAAATGCATAACGGTGCATTATCGAAATAAAAAGTGTCA-TTAAT
1 GAAAATGCATAACGGTGCATTATCGACATAAAAGGTGCCACAT-AT
* *
13865504 GAAAATGTATAACGGTGCATTAACGACATAAAAGGTG
1 GAAAATGCATAACGGTGCATTATCGACATAAAAGGTG
13865541 TTACTCATGG
Statistics
Matches: 187, Mismatches: 27, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
44 2 0.01
45 184 0.98
46 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (45 bp):
GAAAATGCATAACGGTGCATTATCGACATAAAAGGTGCCACATAT
Found at i:13865433 original size:90 final size:90
Alignment explanation
Indices: 13865272--13865539 Score: 365
Period size: 90 Copynumber: 3.0 Consensus size: 90
13865262 AATGGATGAA
* * * * *
13865272 CACAAACGAAAATGCATAATGGTGCATTATCGGCATAAAAGGTGCCACATATAAAAATGCATAAC
1 CACAAATGAAAATGCATAATGGTGCATTATCGGCATAAAAAGTGTCACAAATGAAAATGCATAAC
* *
13865337 GGTGCATTATCGGCATAAAATGTCC
66 GGTGCATTATCGACATAAAAGGTCC
* * *
13865362 CACTAGTGAAAATGCATAATGGTGCATTATCGGCGTAAAAAGTGTCACAAATGAAAATGCATAAC
1 CACAAATGAAAATGCATAATGGTGCATTATCGGCATAAAAAGTGTCACAAATGAAAATGCATAAC
* *
13865427 GATGCATTATCGACATAAAAGGTGC
66 GGTGCATTATCGACATAAAAGGTCC
* ** ** *
13865452 CACAAATGAAAATGCATAACGGTGCATTATCGAAATAAAAAGTGTCATTAATGAAAATGTATAAC
1 CACAAATGAAAATGCATAATGGTGCATTATCGGCATAAAAAGTGTCACAAATGAAAATGCATAAC
*
13865517 GGTGCATTAACGACATAAAAGGT
66 GGTGCATTATCGACATAAAAGGT
13865540 GTTACTCATG
Statistics
Matches: 155, Mismatches: 23, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
90 155 1.00
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (90 bp):
CACAAATGAAAATGCATAATGGTGCATTATCGGCATAAAAAGTGTCACAAATGAAAATGCATAAC
GGTGCATTATCGACATAAAAGGTCC
Found at i:13865521 original size:135 final size:135
Alignment explanation
Indices: 13865272--13865525 Score: 373
Period size: 135 Copynumber: 1.9 Consensus size: 135
13865262 AATGGATGAA
* * * *
13865272 CACAAACGAAAATGCATAATGGTGCATTATCGGCATAAAAGGTGCCACATATAAAAATGCATAAC
1 CACAAACGAAAATGCATAACGATGCATTATCGACATAAAAGGTGCCACAAATAAAAATGCATAAC
** * * *
13865337 GGTGCATTATCGGCATAAAATGTCCCACTAGTGAAAATGCATAATGGTGCATTATCGGCGTAAAA
66 GGTGCATTATCGAAATAAAAAGTCCCACTAATGAAAATGCATAACGGTGCATTATCGGCGTAAAA
13865402 AGTGT
131 AGTGT
* *
13865407 CACAAATGAAAATGCATAACGATGCATTATCGACATAAAAGGTGCCACAAATGAAAATGCATAAC
1 CACAAACGAAAATGCATAACGATGCATTATCGACATAAAAGGTGCCACAAATAAAAATGCATAAC
** * *
13865472 GGTGCATTATCGAAATAAAAAGTGTCATTAATGAAAATGTATAACGGTGCATTA
66 GGTGCATTATCGAAATAAAAAGTCCCACTAATGAAAATGCATAACGGTGCATTA
13865526 ACGACATAAA
Statistics
Matches: 104, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
135 104 1.00
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (135 bp):
CACAAACGAAAATGCATAACGATGCATTATCGACATAAAAGGTGCCACAAATAAAAATGCATAAC
GGTGCATTATCGAAATAAAAAGTCCCACTAATGAAAATGCATAACGGTGCATTATCGGCGTAAAA
AGTGT
Found at i:13865524 original size:24 final size:24
Alignment explanation
Indices: 13865456--13865526 Score: 62
Period size: 24 Copynumber: 3.1 Consensus size: 24
13865446 AGGTGCCACA
*
13865456 AATGAAAATGCATAACGGTGCATT
1 AATGAAAATGTATAACGGTGCATT
**
13865480 -ATCG-AAA--TA-AAAAGTGTCATT
1 AAT-GAAAATGTATAACGGTG-CATT
13865501 AATGAAAATGTATAACGGTGCATT
1 AATGAAAATGTATAACGGTGCATT
13865525 AA
1 AA
13865527 CGACATAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 14
0.65 0.09 0.26
Matches are distributed among these distances:
20 5 0.14
21 6 0.17
22 5 0.14
23 5 0.14
24 9 0.26
25 5 0.14
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.27
Consensus pattern (24 bp):
AATGAAAATGTATAACGGTGCATT
Found at i:13884210 original size:18 final size:18
Alignment explanation
Indices: 13884173--13884215 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
13884163 GGTATTTTTA
* *
13884173 AAATAAAAGATAAGATTT
1 AAATAAAAGAAAAGAATT
*
13884191 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
*
13884209 AATTAAA
1 AAATAAA
13884216 TGATATAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:13885075 original size:41 final size:40
Alignment explanation
Indices: 13885015--13885091 Score: 109
Period size: 41 Copynumber: 1.9 Consensus size: 40
13885005 TTCCTAATGA
* *
13885015 AAAATAATTAAACTATTTAAACTAAAATACTAAAAAAGAT
1 AAAATAAATAAAATATTTAAACTAAAATACTAAAAAAGAT
* *
13885055 AAAATAAAATAAAATATTTAAACTAATATTCTAAAAA
1 AAAAT-AAATAAAATATTTAAACTAAAATACTAAAAA
13885092 TATGGGTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
40 5 0.16
41 27 0.84
ACGTcount: A:0.64, C:0.06, G:0.01, T:0.29
Consensus pattern (40 bp):
AAAATAAATAAAATATTTAAACTAAAATACTAAAAAAGAT
Found at i:13905116 original size:2 final size:2
Alignment explanation
Indices: 13905111--13905174 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
13905101 ATATATCGTA
13905111 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
13905153 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
13905175 GTGTGTCTAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13916874 original size:25 final size:27
Alignment explanation
Indices: 13916823--13916875 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 27
13916813 TGCACCCGAA
13916823 AAAAAGTAAGGAAAAGTTAACATTTTAAG
1 AAAAAGTAAGGAAAA--TAACATTTTAAG
13916852 AAAAAGTAA-GAAAA-AACATTTTAA
1 AAAAAGTAAGGAAAATAACATTTTAA
13916876 ATTGTGTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 10 0.42
28 5 0.21
29 9 0.38
ACGTcount: A:0.60, C:0.04, G:0.13, T:0.23
Consensus pattern (27 bp):
AAAAAGTAAGGAAAATAACATTTTAAG
Found at i:13916929 original size:22 final size:22
Alignment explanation
Indices: 13916904--13916946 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
13916894 TATTATGTTG
*
13916904 TTATAACATTTTAGTTCACGCT
1 TTATAACATTTTAGGTCACGCT
*
13916926 TTATAATATTTTAGGTCACGC
1 TTATAACATTTTAGGTCACGC
13916947 ATTTCTTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (22 bp):
TTATAACATTTTAGGTCACGCT
Found at i:13922040 original size:29 final size:29
Alignment explanation
Indices: 13921998--13922099 Score: 186
Period size: 29 Copynumber: 3.5 Consensus size: 29
13921988 GGGTTGTGTC
13921998 TTTGTAAAGTTTGCACTTCGGTGCTTTGT
1 TTTGTAAAGTTTGCACTTCGGTGCTTTGT
*
13922027 TTTGTAAAGTTTGCACTTCGGTGTTTTGT
1 TTTGTAAAGTTTGCACTTCGGTGCTTTGT
*
13922056 TTTGTAAAGTTTGCACTTCAGTGCTTTGT
1 TTTGTAAAGTTTGCACTTCGGTGCTTTGT
13922085 TTTGTAAAGTTTGCA
1 TTTGTAAAGTTTGCA
13922100 TTATAGTCAC
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 70 1.00
ACGTcount: A:0.17, C:0.12, G:0.23, T:0.49
Consensus pattern (29 bp):
TTTGTAAAGTTTGCACTTCGGTGCTTTGT
Found at i:13925698 original size:20 final size:20
Alignment explanation
Indices: 13925669--13925717 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
13925659 GATTTTAGAT
*
13925669 AATCGCAATGTGAATATGTA
1 AATCGCAATGCGAATATGTA
*
13925689 AATTGCAATGCGAATATGTA
1 AATCGCAATGCGAATATGTA
13925709 AATCGCAAT
1 AATCGCAAT
13925718 ACGATAACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (20 bp):
AATCGCAATGCGAATATGTA
Found at i:13925762 original size:20 final size:20
Alignment explanation
Indices: 13925734--13925795 Score: 106
Period size: 20 Copynumber: 3.1 Consensus size: 20
13925724 ACACTTGATT
*
13925734 GCAATGCGATTCTGACTATC
1 GCAACGCGATTCTGACTATC
13925754 GCAACGCGATTCTGACTATC
1 GCAACGCGATTCTGACTATC
*
13925774 GCAACGAGATTCTGACTATC
1 GCAACGCGATTCTGACTATC
13925794 GC
1 GC
13925796 GTTGTGATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (20 bp):
GCAACGCGATTCTGACTATC
Found at i:13925990 original size:22 final size:22
Alignment explanation
Indices: 13925973--13926037 Score: 94
Period size: 22 Copynumber: 3.0 Consensus size: 22
13925963 ACATCCGTAT
*
13925973 CCATCTCCGACGAAATCCGTCC
1 CCATCTCCGGCGAAATCCGTCC
* *
13925995 CCATTTCCGGCGAAATCCATCC
1 CCATCTCCGGCGAAATCCGTCC
*
13926017 CCATCTCTGGCGAAATCCGTC
1 CCATCTCCGGCGAAATCCGTC
13926038 TATCTCCATC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.22, C:0.42, G:0.15, T:0.22
Consensus pattern (22 bp):
CCATCTCCGGCGAAATCCGTCC
Found at i:13926441 original size:20 final size:20
Alignment explanation
Indices: 13926376--13926464 Score: 66
Period size: 20 Copynumber: 4.8 Consensus size: 20
13926366 TGAAAAGACA
13926376 AAATTCGCGTTGCGATAG-C
1 AAATTCGCGTTGCGATAGTC
* *
13926395 CATTTCGCGTTGCGAT--T-
1 AAATTCGCGTTGCGATAGTC
*
13926412 --A-TCTCGTTGCGATAGTC
1 AAATTCGCGTTGCGATAGTC
*
13926429 AAATTCGCGTTGCGATAATC
1 AAATTCGCGTTGCGATAGTC
** *
13926449 ATTTTCGTGTTGCGAT
1 AAATTCGCGTTGCGAT
13926465 TTTCATTTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
14 11 0.20
16 1 0.02
19 15 0.28
20 27 0.50
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (20 bp):
AAATTCGCGTTGCGATAGTC
Found at i:13926470 original size:20 final size:21
Alignment explanation
Indices: 13926432--13926488 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
13926422 GATAGTCAAA
* **
13926432 TTCGCGTTGCGATAATCA-TT
1 TTCGTGTTGCGATTTTCATTT
13926452 TTCGTGTTGCGATTTTCATTT
1 TTCGTGTTGCGATTTTCATTT
13926473 TTCGTGTTGCGATTTT
1 TTCGTGTTGCGATTTT
13926489 AAGTTTCAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.12, C:0.16, G:0.21, T:0.51
Consensus pattern (21 bp):
TTCGTGTTGCGATTTTCATTT
Found at i:13928310 original size:31 final size:31
Alignment explanation
Indices: 13928254--13928315 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
13928244 TTGTCTTTGT
*
13928254 TTTGTCTTTTGGTTGAAGTTAGTAAATTCATA
1 TTTGTCTTTTGGTTG-ACTTAGTAAATTCATA
13928286 TTTGTCTTTTGGATTG-CTTAGTAAATTCAT
1 TTTGTCTTTTGG-TTGACTTAGTAAATTCAT
13928316 TCGGTAGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 13 0.46
32 12 0.43
33 3 0.11
ACGTcount: A:0.23, C:0.08, G:0.18, T:0.52
Consensus pattern (31 bp):
TTTGTCTTTTGGTTGACTTAGTAAATTCATA
Found at i:13928586 original size:74 final size:73
Alignment explanation
Indices: 13928488--13928655 Score: 257
Period size: 74 Copynumber: 2.3 Consensus size: 73
13928478 AACGCAAATT
*
13928488 TGACTATCGCAACGCAAATTTGACTATCGCAACGCAAATTTGACTATCGCAACAGGATAATCGTA
1 TGACTATCGCAACGCAAA-TTGACTATCGCAACGCAAATTTGACTATCGCAACAGGATAATCGCA
13928553 ATGCGAAAA
65 ATGCGAAAA
* *
13928562 TGACTATCGCAACGCTGAAA-TGACTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGC
1 TGACTATCGCAACGC--AAATTGACTATCGCAACGCAAATTTGACTATCGCAACAGGATAATCGC
*
13928626 AATGTGAAAA
64 AATGCGAAAA
*
13928636 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCAAATT
13928656 TAGTTTCGTG
Statistics
Matches: 86, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
72 2 0.02
73 1 0.01
74 80 0.93
76 3 0.03
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.23
Consensus pattern (73 bp):
TGACTATCGCAACGCAAATTGACTATCGCAACGCAAATTTGACTATCGCAACAGGATAATCGCAA
TGCGAAAA
Found at i:13928615 original size:20 final size:20
Alignment explanation
Indices: 13928452--13928615 Score: 182
Period size: 20 Copynumber: 8.5 Consensus size: 20
13928442 CGAAAATGAT
13928452 TATCGCAACGCGAATTTGAC
1 TATCGCAACGCGAATTTGAC
*
13928472 TATCGCAACGCAAATTTGAC
1 TATCGCAACGCGAATTTGAC
*
13928492 TATCGCAACGCAAATTTGAC
1 TATCGCAACGCGAATTTGAC
*
13928512 TATCGCAACGCAAATTTGAC
1 TATCGCAACGCGAATTTGAC
13928532 TATCGCAACAG-G-A--T-A-
1 TATCGCAAC-GCGAATTTGAC
* * **
13928547 -ATCGTAATGCGAAAATGAC
1 TATCGCAACGCGAATTTGAC
*
13928566 TATCGCAACGCTGAA-ATGAC
1 TATCGCAACGC-GAATTTGAC
13928586 TATCGCAACGCGAATTTGAC
1 TATCGCAACGCGAATTTGAC
13928606 TATCGCAACG
1 TATCGCAACG
13928616 GGATAATCGC
Statistics
Matches: 127, Mismatches: 7, Indels: 20
0.82 0.05 0.13
Matches are distributed among these distances:
13 1 0.01
14 7 0.06
15 1 0.01
16 1 0.01
17 2 0.02
18 1 0.01
19 4 0.03
20 106 0.83
21 4 0.03
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
TATCGCAACGCGAATTTGAC
Found at i:13928722 original size:20 final size:20
Alignment explanation
Indices: 13928697--13928746 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
13928687 GTGATTTTCT
*
13928697 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCA
13928717 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCA
13928737 CGTTGCGATA
1 CGTTGCGATA
13928747 ATCATTTTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCA
Found at i:13929302 original size:21 final size:21
Alignment explanation
Indices: 13929256--13929360 Score: 104
Period size: 21 Copynumber: 5.0 Consensus size: 21
13929246 GACTCACCTG
*
13929256 TCATCGTTCAAGAGGCCTCTC
1 TCATCGTTCAAGAGGCCCCTC
*
13929277 -CTATCGTTCAAGAGGCCCCTA
1 TC-ATCGTTCAAGAGGCCCCTC
* ** *
13929298 TTATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
13929319 TCACCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTC
* *
13929340 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
13929361 CCAACATTCT
Statistics
Matches: 65, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
20 1 0.02
21 64 0.98
ACGTcount: A:0.20, C:0.35, G:0.19, T:0.26
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:13929360 original size:42 final size:44
Alignment explanation
Indices: 13929252--13929360 Score: 120
Period size: 42 Copynumber: 2.6 Consensus size: 44
13929242 GCCCGACTCA
*
13929252 CCTGTCATCGTTCAAGAGG--CCTCTCCTATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGTCCCTCTCCTACCGTTCAAGAGGCC
* * **
13929294 CCTATTATCCCTCAAGA-GTCCC-CT-CTCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGTCCCTCTCCT-ACCGTTCAAGAGGCC
*
13929336 CCTGTCATCGTTGAAGAGGTCCCTC
1 CCTGTCATCGTTCAAGAGGTCCCTC
13929361 CCAACATTCT
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
41 3 0.06
42 41 0.79
43 7 0.13
44 1 0.02
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.26
Consensus pattern (44 bp):
CCTGTCATCGTTCAAGAGGTCCCTCTCCTACCGTTCAAGAGGCC
Found at i:13930772 original size:30 final size:30
Alignment explanation
Indices: 13930738--13930796 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
13930728 AGAGTTGATT
13930738 TGTTTAATTGATGTGTAAATAATTCTTATG
1 TGTTTAATTGATGTGTAAATAATTCTTATG
13930768 TGTTTAATTGATGTGTAAATAATTCTTAT
1 TGTTTAATTGATGTGTAAATAATTCTTAT
13930797 TTGTGCTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.31, C:0.03, G:0.15, T:0.51
Consensus pattern (30 bp):
TGTTTAATTGATGTGTAAATAATTCTTATG
Found at i:13930790 original size:15 final size:15
Alignment explanation
Indices: 13930742--13930791 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
13930732 TTGATTTGTT
13930742 TAATTGATGTGTAAA
1 TAATTGATGTGTAAA
* *
13930757 TAATTCTTATGTGT--T
1 TAA-T-TGATGTGTAAA
13930772 TAATTGATGTGTAAA
1 TAATTGATGTGTAAA
13930787 TAATT
1 TAATT
13930792 CTTATTTGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
13 7 0.26
14 1 0.04
15 11 0.41
16 1 0.04
17 7 0.26
ACGTcount: A:0.34, C:0.02, G:0.16, T:0.48
Consensus pattern (15 bp):
TAATTGATGTGTAAA
Found at i:13930975 original size:20 final size:20
Alignment explanation
Indices: 13930950--13931227 Score: 234
Period size: 20 Copynumber: 14.8 Consensus size: 20
13930940 GTGATTTTCT
*
13930950 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
*
13930970 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
13930990 CGTTGCGATAGTC-ATTTCG
1 CGTTGCGATAGTCAAATTCG
*
13931009 CGTTGCGAT--T----TTCT
1 CGTTGCGATAGTCAAATTCG
13931023 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
13931043 CGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
13931063 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
13931083 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
13931097 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
** *
13931117 CGTTGCGATAGTCATTTTCA
1 CGTTGCGATAGTCAAATTCG
* *
13931137 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
* * *
13931151 CGTTACGATATTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
13931171 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
* *
13931191 CATTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
13931211 CGCTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
13931228 GAATGTGTAA
Statistics
Matches: 208, Mismatches: 32, Indels: 36
0.75 0.12 0.13
Matches are distributed among these distances:
14 31 0.15
16 3 0.01
17 1 0.00
18 2 0.01
19 16 0.08
20 155 0.75
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:13931031 original size:53 final size:54
Alignment explanation
Indices: 13930970--13931071 Score: 170
Period size: 53 Copynumber: 1.9 Consensus size: 54
13930960 GTCAAATTCC
* *
13930970 CGTTGCGATAATCAAATTCGCGTTGCGATAG-TCATTTCGCGTTGCGATTTTCT
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTTAAATTCGCGTTGCGATTTTCT
*
13931023 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTTAAATTCGCGTTGCGAT
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTTAAATTCGCGTTGCGAT
13931072 AGTCATTTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
53 30 0.67
54 15 0.33
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.35
Consensus pattern (54 bp):
CGTTGCGATAATCAAATTCGCGTTGCGATAGTTAAATTCGCGTTGCGATTTTCT
Found at i:13931037 original size:73 final size:74
Alignment explanation
Indices: 13930942--13931126 Score: 309
Period size: 73 Copynumber: 2.5 Consensus size: 74
13930932 TACACTTTGT
*
13930942 GATTTTCTCGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCGCGTTGCGATAGTCA-TT
1 GATTTTCTCGTTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCGCGTTGCGATAGTCATTT
*
13931006 TCGCGTTGC
66 TCGCATTGC
* *
13931015 GATTTTCTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTTAAATTCGCGTTGCGATAGTCATTT
1 GATTTTCTCGTTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCGCGTTGCGATAGTCATTT
13931080 TCGCATTGC
66 TCGCATTGC
* *
13931089 GATTATCCCGTTGCGATAGTCAAATTCGCGTTGCGATA
1 GATTTTCTCGTTGCGATAGTCAAATTCGCGTTGCGATA
13931127 GTCATTTTCA
Statistics
Matches: 105, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
73 59 0.56
74 46 0.44
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.36
Consensus pattern (74 bp):
GATTTTCTCGTTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCGCGTTGCGATAGTCATTT
TCGCATTGC
Found at i:13931101 original size:54 final size:54
Alignment explanation
Indices: 13931043--13931199 Score: 253
Period size: 54 Copynumber: 2.9 Consensus size: 54
13931033 GTCAAATTCG
13931043 CGTTGCGATAGTTAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
1 CGTTGCGATAGTTAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
* *
13931097 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCACATTGCGATTATCC
1 CGTTGCGATAGTTAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
* * *
13931151 CGTTACGATA-TTCAAATTCACGTTGCGATAGTCATATTCGCATTGCGAT
1 CGTTGCGATAGTT-AAATTCGCGTTGCGATAGTCATTTTCGCATTGCGAT
13931200 AGTCATATTC
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
53 1 0.01
54 94 0.99
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (54 bp):
CGTTGCGATAGTTAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
Found at i:13931143 original size:74 final size:73
Alignment explanation
Indices: 13930950--13931224 Score: 304
Period size: 74 Copynumber: 3.7 Consensus size: 73
13930940 GTGATTTTCT
* * *
13930950 CGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCGCGTTGCGATAGTCATTTCGCGTTGC
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTCGCATTGC
* *
13931015 GATTTTCT
66 GATTATCC
*
13931023 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTTAAATTCGCGTTGCGATAGTCATTTTCGCATTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCA-TTTCGCATTG
13931088 CGATTATCC
65 CGATTATCC
** * * * *
13931097 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCACATTGCGATTA-TCCCGTTACG-AT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGA-TAGT--CATTTCGCAT
* * * *
13931160 ATTCAAAT-TCA
63 -TGCGATTATCC
* * * *
13931171 CGTTGCGATAGTCATATTCGCATTGCGATAGTCATATTCGCGCTGCGATAGTCA
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCA
13931225 AATGAATGTG
Statistics
Matches: 172, Mismatches: 24, Indels: 13
0.82 0.11 0.06
Matches are distributed among these distances:
72 1 0.01
73 53 0.31
74 107 0.62
75 10 0.06
76 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (73 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTCGCATTGC
GATTATCC
Found at i:13931425 original size:18 final size:18
Alignment explanation
Indices: 13931402--13931436 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
13931392 AAGCCGGTTG
*
13931402 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
13931420 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
13931437 GCCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:13933493 original size:14 final size:14
Alignment explanation
Indices: 13933474--13933510 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
13933464 TCTCGTGGCA
13933474 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
13933488 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
13933502 TTCTTCTTC
1 TT-TTCTTC
13933511 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:13934285 original size:29 final size:30
Alignment explanation
Indices: 13934243--13934314 Score: 119
Period size: 29 Copynumber: 2.4 Consensus size: 30
13934233 CCCGAAGGAC
*
13934243 CTATCCAGAGGTCATAAAGAT-CTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGATAA
13934272 CTATCCAGAGGTCATAAAGATCCTCGATAA
1 CTATCCAGAGGTCATAAAGATCCTCGATAA
*
13934302 CTATCCATAGGTC
1 CTATCCAGAGGTC
13934315 CCGAAGAACC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 21 0.52
30 19 0.47
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGATAA
Found at i:13934354 original size:31 final size:31
Alignment explanation
Indices: 13934300--13934381 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 31
13934290 GATCCTCGAT
* *
13934300 AACTATCCATAGGTCCCGAAGAACCTAAGTA
1 AACTATCCATATGTCCCGAAGAACATAAGTA
* ** *
13934331 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTCCCGAAGAACATAAGTA
* * *
13934362 TACTGTCCATATGTCTCGAA
1 AACTATCCATATGTCCCGAA
13934382 AGACATAGGT
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (31 bp):
AACTATCCATATGTCCCGAAGAACATAAGTA
Found at i:13936420 original size:24 final size:24
Alignment explanation
Indices: 13936393--13936439 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
13936383 ATCATTAAAA
13936393 TCCGAGTATTGACCAAGATCAAAG
1 TCCGAGTATTGACCAAGATCAAAG
*
13936417 TCCGGGTATTGACCAAGATCAAA
1 TCCGAGTATTGACCAAGATCAAA
13936440 TTTTGAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (24 bp):
TCCGAGTATTGACCAAGATCAAAG
Found at i:13937297 original size:21 final size:20
Alignment explanation
Indices: 13937273--13937347 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 20
13937263 GTTAGTCAGA
13937273 ATCGCGTTGCGATCACGTATT
1 ATCGCGTTGCGATCA-GTATT
* ***
13937294 ATCGCGTTGTGAT-AGTCCGA
1 ATCGCGTTGCGATCAGT-ATT
*
13937314 ATCGCGTTGCGATCAAGTGTT
1 ATCGCGTTGCGATC-AGTATT
13937335 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
13937348 TTACATATTT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.05
20 13 0.30
21 25 0.58
22 3 0.07
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.32
Consensus pattern (20 bp):
ATCGCGTTGCGATCAGTATT
Found at i:13937310 original size:41 final size:41
Alignment explanation
Indices: 13937265--13937343 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
13937255 AGTGATGCGT
*
13937265 TAGTCAGAATCGCGTTGCGATCACGTATTATCGCGTTGTGA
1 TAGTCAGAATCGCGTTGCGATCAAGTATTATCGCGTTGTGA
* *
13937306 TAGTCCGAATCGCGTTGCGATCAAGTGTTATCGCGTTG
1 TAGTCAGAATCGCGTTGCGATCAAGTATTATCGCGTTG
13937344 CGATTTACAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (41 bp):
TAGTCAGAATCGCGTTGCGATCAAGTATTATCGCGTTGTGA
Found at i:13937366 original size:20 final size:20
Alignment explanation
Indices: 13937336--13937388 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
13937326 TCAAGTGTTA
*
13937336 TCGCGTTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
13937356 TTGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
13937376 TCGCATTGCGATT
1 TCGCATTGCGATT
13937389 ATCTAAAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:13937498 original size:19 final size:19
Alignment explanation
Indices: 13937474--13937510 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
13937464 TGCGATAATG
13937474 GAGATCGCATTGAGATTTA
1 GAGATCGCATTGAGATTTA
*
13937493 GAGATCGCATTGCGATTT
1 GAGATCGCATTGAGATTT
13937511 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGAGATTTA
Found at i:13938381 original size:15 final size:16
Alignment explanation
Indices: 13938361--13938390 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
13938351 ATCAAATCAA
13938361 AACAAAGA-AAAAAAC
1 AACAAAGAGAAAAAAC
13938376 AACAAAGAGAAAAAA
1 AACAAAGAGAAAAAA
13938391 GAAAAAGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (16 bp):
AACAAAGAGAAAAAAC
Found at i:13938446 original size:54 final size:49
Alignment explanation
Indices: 13938386--13938511 Score: 137
Period size: 54 Copynumber: 2.4 Consensus size: 49
13938376 AACAAAGAGA
* *
13938386 AAAAAGAAAAAGCAAAGAAAAAAAGGAAAAATAAAGAGTAAAGAAAAATAGAG
1 AAAAAGAAAAAG-AAAGAAAAAAA-GAAAAACAAAGAGCAAAGAAAAA-A-AG
*
13938439 AGCAAAGAAAAAAGAGAA-AAGAAAAAGAAAAACAAAGAGCAAAGAAAAAAAG
1 A-AAAAG-AAAAAGA-AAGAA-AAAAAGAAAAACAAAGAGCAAAGAAAAAAAG
*
13938491 AAAAAGAAAAAAAAAGAAAAA
1 AAAAAGAAAAAGAAAGAAAAA
13938512 GGGGACAAGA
Statistics
Matches: 63, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
49 5 0.08
50 8 0.13
51 4 0.06
52 3 0.05
53 2 0.03
54 28 0.44
55 13 0.21
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.02
Consensus pattern (49 bp):
AAAAAGAAAAAGAAAGAAAAAAAGAAAAACAAAGAGCAAAGAAAAAAAG
Found at i:13938466 original size:37 final size:37
Alignment explanation
Indices: 13938425--13938505 Score: 121
Period size: 37 Copynumber: 2.2 Consensus size: 37
13938415 AATAAAGAGT
* *
13938425 AAAGAAAAATAGAGAGCAAAG-AAAAAAGAGAAAAGAA
1 AAAGAAAAACAAAGAGCAAAGAAAAAAAGA-AAAAGAA
13938462 AAAGAAAAACAAAGAGCAAAGAAAAAAAGAAAAAGAA
1 AAAGAAAAACAAAGAGCAAAGAAAAAAAGAAAAAGAA
13938499 AAA-AAAA
1 AAAGAAAA
13938506 GAAAAAGGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
36 4 0.10
37 29 0.71
38 8 0.20
ACGTcount: A:0.78, C:0.04, G:0.17, T:0.01
Consensus pattern (37 bp):
AAAGAAAAACAAAGAGCAAAGAAAAAAAGAAAAAGAA
Found at i:13940177 original size:131 final size:134
Alignment explanation
Indices: 13939990--13940350 Score: 374
Period size: 131 Copynumber: 2.7 Consensus size: 134
13939980 CATTATCCCT
* * * * * * *
13939990 AAAGATGGCCAACCGTCCTCATCGCGTAGGAACCATGTCATCCCCCAACCATACCTCCTCATCAC
1 AAAGATGGCCAGCCGTCCTCATCACGTAGGAACTATGTCATCCACCGACCAAACCTCCTCATCAA
* * * *
13940055 GTATGAGCCGTGTCATCCTTAGATAACCAGTCGTCCTCATCACGTAGGAACCAG-GTTATCA-A-
66 GTAAGAGCCGTGTCACCCTTAGATAACCAGCCGTCCTCATCACGTAGGAACC-GTATTATCACAT
13940117 GCC-C
130 GCCTC
* * * *
13940121 AAGGATGG-CATGCTGTCCTCATCACGTAGGAACTGTGTCATTCACCGACCAAACCTCCTCATCA
1 AAAGATGGCCA-GCCGTCCTCATCACGTAGGAACTATGTCATCCACCGACCAAACCTCCTCATCA
* ** * ** *
13940185 AGTAGGAGTTGTGTCACCCATAGATAACCAGCCGTCCTCATCGTGTAGGAATCGTATTATCATCA
65 AGTAAGAGCCGTGTCACCCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTATTATCA-CA
* *
13940250 TTCCTT
129 TGCCTC
* * * * *
13940256 AAATATGGCCAGCCGTCCTCATCCCGTAGGAACTATGTCATCCACTGACCAGATCTCCTCATCAT
1 AAAGATGGCCAGCCGTCCTCATCACGTAGGAACTATGTCATCCACCGACCAAACCTCCTCATCA-
*
13940321 A-TAAGAGCCGTGTCACCCTTAGATGACCAG
65 AGTAAGAGCCGTGTCACCCTTAGATAACCAG
13940351 AACTCTTCAT
Statistics
Matches: 185, Mismatches: 37, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
130 3 0.02
131 100 0.54
133 1 0.01
134 2 0.01
135 76 0.41
136 3 0.02
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (134 bp):
AAAGATGGCCAGCCGTCCTCATCACGTAGGAACTATGTCATCCACCGACCAAACCTCCTCATCAA
GTAAGAGCCGTGTCACCCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTATTATCACATG
CCTC
Found at i:13940539 original size:10 final size:10
Alignment explanation
Indices: 13940524--13940558 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
13940514 GTCTAAAAAT
13940524 ATTATTTATA
1 ATTATTTATA
13940534 ATTATTTATA
1 ATTATTTATA
*
13940544 ATTA-TTATT
1 ATTATTTATA
13940553 ATTATT
1 ATTATT
13940559 CTATTAACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
ATTATTTATA
Found at i:13942238 original size:2 final size:2
Alignment explanation
Indices: 13942233--13942257 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13942223 GCCGAATAAG
13942233 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
13942258 CCATAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13949220 original size:21 final size:19
Alignment explanation
Indices: 13949192--13949237 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
13949182 TCATTGAATC
13949192 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
13949212 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
13949231 ACTTAGT
1 A-TTAGT
13949238 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Done.