Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_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: 20687664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 22 of 91
Found at i:4408965 original size:20 final size:20
Alignment explanation
Indices: 4408940--4408990 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
4408930 TACGTAGTAC
*
4408940 CGATATTGTTCCTACAATAT
1 CGATATTGTTCCAACAATAT
* *
4408960 CGATATTATAT-GAACAATAT
1 CGATATTGT-TCCAACAATAT
4408980 CGATATTGTTC
1 CGATATTGTTC
4408991 ATGTGGTACC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.04
20 23 0.92
21 1 0.04
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (20 bp):
CGATATTGTTCCAACAATAT
Found at i:4409249 original size:21 final size:22
Alignment explanation
Indices: 4409212--4409252 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
4409202 TTAAATATTA
4409212 TAAAGGTAGTATCGATACTCAT
1 TAAAGGTAGTATCGATACTCAT
*
4409234 TAAAGG-AGTATGGATACTC
1 TAAAGGTAGTATCGATACTC
4409253 CCTGTCTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (22 bp):
TAAAGGTAGTATCGATACTCAT
Found at i:4413585 original size:54 final size:54
Alignment explanation
Indices: 4413166--4413554 Score: 546
Period size: 54 Copynumber: 7.2 Consensus size: 54
4413156 CGAATGAGTA
* *
4413166 TATGTGTGCAACTTAAGAAATTCATAATTAGTTTATGAATTTCCCTATTGGCAC
1 TATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGCAC
* *
4413220 TATGTGTGCAACTTAAGAAATTTATAAT-AGTTTATGAATTTTCATATTTGGCAC
1 TATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCATA-TTGGCAC
* * *
4413274 TCTGTGTGCAACTTAAGAAATTCATAATTAGTTTATGAATTTCCCTATTGGCAC
1 TATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGCAC
* *
4413328 TATGTGTGCAACTTAAGAAATTTATAATAAGTTTATGAATTTTCATATTTGGCAC
1 TATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCATA-TTGGCAC
* * **
4413383 TCTGTGTGCAACTTAAGAAATACATAATAAGTTTATGAATTTATATATTGGCAC
1 TATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGCAC
* * * * **
4413437 TATGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTTCGTATTAACAC
1 TATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGCAC
* * * *
4413491 TATTTGTGCAACCTAAGAAATTCATAATAAATTTATGAATTTCCATATTGACAC
1 TATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGCAC
4413545 TATGTGTGCA
1 TATGTGTGCA
4413555 CCCTCACGTA
Statistics
Matches: 299, Mismatches: 33, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
53 16 0.05
54 218 0.73
55 65 0.22
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (54 bp):
TATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGCAC
Found at i:4413600 original size:54 final size:51
Alignment explanation
Indices: 4413166--4413600 Score: 377
Period size: 54 Copynumber: 8.0 Consensus size: 51
4413156 CGAATGAGTA
* * *
4413166 TATGTGTGCAACTTAAGAAATTCATAATTAGTTTATGAATTTCCCTATTGGCAC
1 TATGTGTGCAACCTAAGAAATTCATAATAAG-TTATGAATTT-CGTATT-GCAC
* * *
4413220 TATGTGTGCAACTTAAGAAATTTATAAT-AGTTTATGAATTTTCATATTTGGCAC
1 TATGTGTGCAACCTAAGAAATTCATAATAAG-TTATGAA-TTTCGTA-TT-GCAC
* * * *
4413274 TCTGTGTGCAACTTAAGAAATTCATAATTAGTTTATGAATTTCCCTATTGGCAC
1 TATGTGTGCAACCTAAGAAATTCATAATAAG-TTATGAATTT-CGTATT-GCAC
* * *
4413328 TATGTGTGCAACTTAAGAAATTTATAATAAGTTTATGAATTTTCATATTTGGCAC
1 TATGTGTGCAACCTAAGAAATTCATAATAAG-TTATGAA-TTTCGTA-TT-GCAC
* * * **
4413383 TCTGTGTGCAACTTAAGAAATACATAATAAGTTTATGAATTTATATATTGGCAC
1 TATGTGTGCAACCTAAGAAATTCATAATAAG-TTATGAATTT-CGTATT-GCAC
* *
4413437 TATGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTTCGTATTAACAC
1 TATGTGTGCAACCTAAGAAATTCATAATAAG-TTATGAA-TTTCGTATT-GCAC
* * *
4413491 TATTTGTGCAACCTAAGAAATTCATAATAAATTTATGAATTTCCATATTGACAC
1 TATGTGTGCAACCTAAGAAATTCATAAT-AAGTTATGAATTT-CGTATTG-CAC
* * * * *
4413545 TATGTGTGCACCCTCACGTAATTCATAATGAGTTGTGAATTATCGTATCTGCAC
1 TATGTGTGCAACCT-AAGAAATTCATAATAAGTTATGAATT-TCGTAT-TGCAC
4413599 TA
1 TA
4413601 CGTATGAGAA
Statistics
Matches: 333, Mismatches: 34, Indels: 28
0.84 0.09 0.07
Matches are distributed among these distances:
53 16 0.05
54 236 0.71
55 81 0.24
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (51 bp):
TATGTGTGCAACCTAAGAAATTCATAATAAGTTATGAATTTCGTATTGCAC
Found at i:4414464 original size:118 final size:121
Alignment explanation
Indices: 4414339--4414562 Score: 341
Period size: 118 Copynumber: 1.9 Consensus size: 121
4414329 TATCTTTATC
* *
4414339 TTCACTTAAAAATATATTT-CATTCTTTTCGTAATTTTTATAATATATATTTTT-AAA-ATCTTA
1 TTCACTTAAAAATATATTTAAATT-TTTT-GTAATTTTTAAAATATATATTTTTAAAATATCTTA
*
4414401 ACTCAAAATATATTTAAATA-TTT-TTATTATTTTAATATAATTTTTTTTATTTTTTA
64 ACTCAAAATATATTTAAATATTTTATTATTACTTTAATATAATTTTTTTTATTTTTTA
*
4414457 TTCACTTAAAAATATATTTAGAATTTTTTTTAATTTTTAAAATATATATTTTTAAAATATCTTAA
1 TTCACTTAAAAATATATTTA-AATTTTTTGTAATTTTTAAAATATATATTTTTAAAATATCTTAA
*
4414522 CTTAAAATATATTTAAATATTTTATTATTACTTTAATATAA
65 CTCAAAATATATTTAAATATTTTATTATTACTTTAATATAA
4414563 AAATATATAT
Statistics
Matches: 95, Mismatches: 5, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
118 41 0.43
119 7 0.07
120 28 0.29
121 3 0.03
122 16 0.17
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (121 bp):
TTCACTTAAAAATATATTTAAATTTTTTGTAATTTTTAAAATATATATTTTTAAAATATCTTAAC
TCAAAATATATTTAAATATTTTATTATTACTTTAATATAATTTTTTTTATTTTTTA
Found at i:4414473 original size:60 final size:60
Alignment explanation
Indices: 4414376--4414562 Score: 168
Period size: 60 Copynumber: 3.1 Consensus size: 60
4414366 TCGTAATTTT
* * *
4414376 TATAATATATATTTTTAAA-ATCTTAACTCAAAATATATTTAAATATTTTTATTATTTTAA
1 TATAATATAT-TTTTAAAATATATTAACTTAAAATATATTTAAATATTTTTATTATTTTAA
* *** * *
4414436 TATAAT-TTTTTTTATTTTTTATTCACTTAAAAATATATTTAGAAT-TTTTT-TTAATTTTTAA
1 TATAATATATTTTTAAAATATATTAACTT-AAAATATATTTA-AATATTTTTATT-A-TTTTAA
* * *
4414497 AAT-ATATATTTTTAAAATATCTTAACTTAAAATATATTTAAATATTTTATTATTACTTTAA
1 TATAATATATTTTTAAAATATATTAACTTAAAATATATTTAAATA-TTT-TTATTATTTTAA
4414558 TATAA
1 TATAA
4414563 AAATATATAT
Statistics
Matches: 97, Mismatches: 19, Indels: 20
0.71 0.14 0.15
Matches are distributed among these distances:
58 4 0.04
59 13 0.13
60 38 0.39
61 36 0.37
62 4 0.04
63 2 0.02
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.55
Consensus pattern (60 bp):
TATAATATATTTTTAAAATATATTAACTTAAAATATATTTAAATATTTTTATTATTTTAA
Found at i:4414570 original size:29 final size:31
Alignment explanation
Indices: 4414538--4414601 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
4414528 ATATATTTAA
*
4414538 ATATTTTATTATTA-CTTTAATATAAAAATAT
1 ATATTTTATTATTATCTTCAAT-TAAAAATAT
* * *
4414569 ATATTTTGTTCTTATCTTCACTTAAAAATAT
1 ATATTTTATTATTATCTTCAATTAAAAATAT
4414600 AT
1 AT
4414602 TTTAACATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.52
Consensus pattern (31 bp):
ATATTTTATTATTATCTTCAATTAAAAATAT
Found at i:4414698 original size:30 final size:30
Alignment explanation
Indices: 4414662--4414749 Score: 97
Period size: 29 Copynumber: 2.9 Consensus size: 30
4414652 TTTTAAAAAC
*
4414662 TTAAAATAAGAATAAAATATATTTTTTAAG
1 TTAAAATAAGAATATAATATATTTTTTAAG
* *
4414692 TTAAAATAAAAATATAATATA-CTTTTAAG
1 TTAAAATAAGAATATAATATATTTTTTAAG
* * * *
4414721 TGAAGATAAGACTGTAATATATGTTTTTA
1 TTAAAATAAGAATATAATATAT-TTTTTA
4414750 CACTAAAAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
29 23 0.49
30 19 0.40
31 5 0.11
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (30 bp):
TTAAAATAAGAATATAATATATTTTTTAAG
Found at i:4414729 original size:29 final size:30
Alignment explanation
Indices: 4414664--4414729 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
4414654 TTAAAAACTT
* * *
4414664 AAAATAAGAATAAAATATATTTTTTAAGTT
1 AAAATAAAAATAAAATATATCTTTTAAGTG
*
4414694 AAAATAAAAATATAATATA-CTTTTAAGTG
1 AAAATAAAAATAAAATATATCTTTTAAGTG
*
4414723 AAGATAA
1 AAAATAA
4414730 GACTGTAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 14 0.45
30 17 0.55
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.35
Consensus pattern (30 bp):
AAAATAAAAATAAAATATATCTTTTAAGTG
Found at i:4425098 original size:24 final size:24
Alignment explanation
Indices: 4425066--4425153 Score: 106
Period size: 24 Copynumber: 3.7 Consensus size: 24
4425056 GATATCAGAA
*
4425066 ATCAAAACAGAATTCAGATAAGAT
1 ATCAGAACAGAATTCAGATAAGAT
* * *
4425090 ATCAGAACAGAATCCAGATCAGAA
1 ATCAGAACAGAATTCAGATAAGAT
*
4425114 ATCAGAACAGAATTCAGGTAATG-T
1 ATCAGAACAGAATTCAGATAA-GAT
*
4425138 ATCAGAACATAATTCA
1 ATCAGAACAGAATTCA
4425154 AGTCGGAAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
24 53 0.98
25 1 0.02
ACGTcount: A:0.49, C:0.16, G:0.15, T:0.20
Consensus pattern (24 bp):
ATCAGAACAGAATTCAGATAAGAT
Found at i:4425130 original size:12 final size:12
Alignment explanation
Indices: 4425061--4425130 Score: 63
Period size: 12 Copynumber: 5.8 Consensus size: 12
4425051 ACGGAGATAT
* *
4425061 CAGAAATCAAAA
1 CAGAATTCAGAA
4425073 CAGAATTCAGATA
1 CAGAATTCAGA-A
4425086 -AG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
4425097 CAGAATCCAGAT
1 CAGAATTCAGAA
*
4425109 CAGAAATCAGAA
1 CAGAATTCAGAA
4425121 CAGAATTCAG
1 CAGAATTCAG
4425131 GTAATGTATC
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
11 3 0.07
12 40 0.87
13 3 0.07
ACGTcount: A:0.51, C:0.17, G:0.16, T:0.16
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:4425163 original size:48 final size:48
Alignment explanation
Indices: 4425059--4425167 Score: 141
Period size: 48 Copynumber: 2.3 Consensus size: 48
4425049 AAACGGAGAT
* *
4425059 ATCAGAAATCAAAACAGAATTCAGATAAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATAAGATATCAGAACAGAATCAAG
* *
4425107 ATCAGAAATCAGAACAGAATTCAGGTAATG-TATCAGAACATAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAGATAA-GATATCAGAACAGAA-TCAAG
*
4425156 -TCGGAAATCAGA
1 ATCAGAAATCAGA
4425168 TAAAATATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
48 49 0.91
49 5 0.09
ACGTcount: A:0.49, C:0.16, G:0.17, T:0.19
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATAAGATATCAGAACAGAATCAAG
Found at i:4434052 original size:22 final size:22
Alignment explanation
Indices: 4433996--4434112 Score: 137
Period size: 22 Copynumber: 5.2 Consensus size: 22
4433986 ATGTATAATG
4433996 TATAGTTTTATAAAAAATAATATATA
1 TATAGTTTT-T-AAAAAT-ATATA-A
*
4434022 TATAATTTTTAAAAATATATAA
1 TATAGTTTTTAAAAATATATAA
*
4434044 TATAG-TTTTAAAAATATATAG
1 TATAGTTTTTAAAAATATATAA
* * *
4434065 TATAATTTTTGAAAATATATTA
1 TATAGTTTTTAAAAATATATAA
*
4434087 TATAGTTTTAAAAAATATATAA
1 TATAGTTTTTAAAAATATATAA
4434109 TATA
1 TATA
4434113 TAATTTTTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
21 19 0.24
22 40 0.51
23 5 0.06
24 6 0.08
25 1 0.01
26 8 0.10
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (22 bp):
TATAGTTTTTAAAAATATATAA
Found at i:4434158 original size:22 final size:22
Alignment explanation
Indices: 4434008--4434159 Score: 116
Period size: 22 Copynumber: 6.8 Consensus size: 22
4433998 TAGTTTTATA
* *
4434008 AAAAATAATATATATATAATTTTT
1 AAAAAT-ATATGTATAT-AGTTTT
*
4434032 AAAAATATAT-AATATAGTTTT
1 AAAAATATATGTATATAGTTTT
*
4434053 AAAAATATATAGTATA-ATTTTT
1 AAAAATATAT-GTATATAGTTTT
*
4434075 GAAAATATAT-TATATAGTTTT
1 AAAAATATATGTATATAGTTTT
* *
4434096 AAAAAATATATAATATATAATTTTTT
1 -AAAAATATAT-GTATAT-A-GTTTT
* *
4434122 TAAAATGTA-GTATATA-TTTT
1 AAAAATATATGTATATAGTTTT
4434142 AAAAATATATGTAATATA
1 AAAAATATATGT-ATATA
4434160 CATATTTTGA
Statistics
Matches: 105, Mismatches: 13, Indels: 22
0.75 0.09 0.16
Matches are distributed among these distances:
20 15 0.14
21 22 0.21
22 33 0.31
23 12 0.11
24 11 0.10
25 8 0.08
26 4 0.04
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.45
Consensus pattern (22 bp):
AAAAATATATGTATATAGTTTT
Found at i:4434185 original size:27 final size:26
Alignment explanation
Indices: 4434135--4434198 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 26
4434125 AATGTAGTAT
4434135 ATATTTTAAAAATATATGTAATATAC
1 ATATTTTAAAAATATATGTAATATAC
*
4434161 ATATTTTGAAAACATAATAT-TATATATAT
1 ATATTTT-AAAA-AT-ATATGTA-ATATAC
*
4434190 ATATATTAA
1 ATATTTTAA
4434199 GCTTATTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 7 0.22
27 4 0.12
28 6 0.19
29 15 0.47
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (26 bp):
ATATTTTAAAAATATATGTAATATAC
Found at i:4434209 original size:3 final size:3
Alignment explanation
Indices: 4434201--4434226 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4434191 TATATTAAGC
4434201 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
4434227 TATTTATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4434237 original size:15 final size:14
Alignment explanation
Indices: 4434204--4434246 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
4434194 ATTAAGCTTA
4434204 TTATTATTA-TTA-
1 TTATTATTATTTAT
4434216 TTATTATTATTTAT
1 TTATTATTATTTAT
*
4434230 TTATTTATTTTTTAT
1 TTA-TTATTATTTAT
4434245 TT
1 TT
4434247 TTTTTCATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 9 0.33
13 3 0.11
14 3 0.11
15 12 0.44
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTATTATTTAT
Found at i:4439095 original size:25 final size:24
Alignment explanation
Indices: 4439061--4439143 Score: 123
Period size: 24 Copynumber: 3.4 Consensus size: 24
4439051 TCATCTATTA
*
4439061 CAAAAACACAAGCTTT-ATTTGCTG
1 CAAAAGCACAAG-TTTCATTTGCTG
4439085 CAAAAAGCACAAGTTTCATTTGCTG
1 C-AAAAGCACAAGTTTCATTTGCTG
*
4439110 CAAAAGCACAAGTTTCGTTTGCTG
1 CAAAAGCACAAGTTTCATTTGCTG
4439134 CAAAAGCACA
1 CAAAAGCACA
4439144 TGCCTCTGTA
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
24 36 0.65
25 19 0.35
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (24 bp):
CAAAAGCACAAGTTTCATTTGCTG
Found at i:4440998 original size:12 final size:12
Alignment explanation
Indices: 4440977--4441002 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4440967 AGGAAGGCAC
4440977 TACTGAAGGTAT
1 TACTGAAGGTAT
4440989 TACTGAAGGTAT
1 TACTGAAGGTAT
4441001 TA
1 TA
4441003 AATCAATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.35
Consensus pattern (12 bp):
TACTGAAGGTAT
Found at i:4454077 original size:20 final size:21
Alignment explanation
Indices: 4454040--4454099 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
4454030 AGTATATAAT
*
4454040 GTATAGTTTTGTCAAAAACAATA
1 GTATAGTTTT-T-GAAAACAATA
*
4454063 -TATAGTTTTTGAAAA-TATA
1 GTATAGTTTTTGAAAACAATA
*
4454082 GTATAGTTTTTTAAAACA
1 GTATAGTTTTTGAAAACA
4454100 TATTGTTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 3 0.10
20 18 0.58
21 1 0.03
22 9 0.29
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.42
Consensus pattern (21 bp):
GTATAGTTTTTGAAAACAATA
Found at i:4454086 original size:22 final size:23
Alignment explanation
Indices: 4454061--4454201 Score: 60
Period size: 21 Copynumber: 5.9 Consensus size: 23
4454051 TCAAAAACAA
4454061 TATATAGTTTTTGAAAATATAG-
1 TATATAGTTTTTGAAAATATAGT
* *
4454083 --TATAGTTTTTTAAAACATATTGT
1 TATATAG-TTTTTGAAA-ATATAGT
* *
4454106 TATATAG-TTTTGAAAACATAAAAT
1 TATATAGTTTTTG-AAA-ATATAGT
* *
4454130 ATATATACTTTTTGAAAAACATATGT
1 -TATATAGTTTTTG-AAAATATA-GT
* *
4454156 AATATATATATATTTTGAAAACATA-T
1 --TATATA-GT-TTTTGAAAATATAGT
*
4454182 TATAT-GATTTTGAAAATATA
1 TATATAGTTTTTGAAAATATA
4454202 ATATATCATA
Statistics
Matches: 93, Mismatches: 14, Indels: 25
0.70 0.11 0.19
Matches are distributed among these distances:
20 5 0.05
21 20 0.22
22 5 0.05
23 4 0.04
24 13 0.14
25 14 0.15
26 11 0.12
27 7 0.08
28 9 0.10
29 5 0.05
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.44
Consensus pattern (23 bp):
TATATAGTTTTTGAAAATATAGT
Found at i:4454171 original size:29 final size:27
Alignment explanation
Indices: 4454106--4454181 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 27
4454096 AACATATTGT
4454106 TATATAGTTTTGAAAACATA-AAATATA
1 TATATA-TTTTGAAAACATATAAATATA
*
4454133 TATACT-TTTTGAAAAACATATGTAATATA
1 TATA-TATTTTG-AAAACATAT-AAATATA
4454162 TATATATTTTGAAAACATAT
1 TATATATTTTGAAAACATAT
4454182 TATATGATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
26 5 0.12
27 12 0.28
28 11 0.26
29 15 0.35
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (27 bp):
TATATATTTTGAAAACATATAAATATA
Found at i:4454191 original size:21 final size:20
Alignment explanation
Indices: 4454157--4454207 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
4454147 AACATATGTA
4454157 ATATATATATATTTTGAAAAC
1 ATAT-TATATATTTTGAAAAC
*
4454178 ATATTATATGATTTTGAAAAT
1 ATATTATAT-ATTTTGAAAAC
*
4454199 ATAATATAT
1 ATATTATAT
4454208 CATATAGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 5 0.19
21 22 0.81
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (20 bp):
ATATTATATATTTTGAAAAC
Found at i:4459020 original size:16 final size:17
Alignment explanation
Indices: 4458984--4459021 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
4458974 TTATGGAGGT
4458984 AATTGAAATATGTAAAGG
1 AATTGAAATATGT-AAGG
*
4459002 AATTGAAATCTGT-AGG
1 AATTGAAATATGTAAGG
4459018 AATT
1 AATT
4459022 AGAATCTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
18 12 0.63
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (17 bp):
AATTGAAATATGTAAGG
Found at i:4459961 original size:37 final size:38
Alignment explanation
Indices: 4459880--4459963 Score: 145
Period size: 38 Copynumber: 2.2 Consensus size: 38
4459870 AAACCCAAAT
4459880 CCGACCCGATCCGACCCGAATATCACACTTAAAAAAAC
1 CCGACCCGATCCGACCCGAATATCACACTTAAAAAAAC
4459918 CCGACCCGA-CTCGACCCGAATATCACACTT-AAAAAAC
1 CCGACCCGATC-CGACCCGAATATCACACTTAAAAAAAC
4459955 CCGACCCGA
1 CCGACCCGA
4459964 ACAAAACAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
37 17 0.38
38 28 0.62
ACGTcount: A:0.37, C:0.39, G:0.12, T:0.12
Consensus pattern (38 bp):
CCGACCCGATCCGACCCGAATATCACACTTAAAAAAAC
Found at i:4460150 original size:38 final size:37
Alignment explanation
Indices: 4460106--4460186 Score: 117
Period size: 38 Copynumber: 2.2 Consensus size: 37
4460096 CTAAACCAGA
4460106 ACCCGACCCAACCCGAATATCACACTTAAAAAAACCCG
1 ACCCGACCCAACCCGAATATCACACTT-AAAAAACCCG
* * * *
4460144 ACCCGACTCGACCCGAATATCACACTTAATAAATCCG
1 ACCCGACCCAACCCGAATATCACACTTAAAAAACCCG
4460181 ACCCGA
1 ACCCGA
4460187 ACAAAATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
37 14 0.36
38 25 0.64
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.14
Consensus pattern (37 bp):
ACCCGACCCAACCCGAATATCACACTTAAAAAACCCG
Found at i:4460169 original size:223 final size:225
Alignment explanation
Indices: 4459755--4460217 Score: 788
Period size: 228 Copynumber: 2.1 Consensus size: 225
4459745 AATCCGATCT
* *
4459755 GACCCGACCCGACCCAAAATAATAAAAAATTATTTTTATTTAATAAAAATAGTGACTTAATCCGA
1 GACCCGACCCGACCCAAAATAATAAAAAATTATTTTTATTTAATAAAAACAATGACTTAATCCGA
*
4459820 CCCGACCCGAATTATATATATTTTCGGGTCGGTCCAGTTTTTTTCACCCTAAACCCAAATCCGAC
66 CCCGACCCGAATTATATATATTTTCGGGTCGGTCCAGTTTTTTTCACCCTAAACCCAAACCCGAC
4459885 CCGATCCGACCCGAATATCACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTTAA
131 CCGA--C-ACCCGAATATCACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTTAA
4459950 AAAACCCGACCCGAACAAAACAAAGTTTCATCC
193 AAAACCCGACCCGAACAAAACAAAGTTTCATCC
*
4459983 GACCCGACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAATGACTTAATCCGA
1 GACCCGACCCGACCCAAAATAATAAAAAATTATTTTTATTTAATAAAAACAATGACTTAATCCGA
* *
4460048 TCCGACCCGAATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAA-CCAGAACCCGA
66 CCCGACCCGAATTATATATATTTTCGGGTCGGTCCAGTTTTTTTCACCCTAAACCCA-AACCCGA
*
4460112 CCC-A-ACCCGAATATCACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTTAATA
130 CCCGACACCCGAATATCACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTTAAAA
* *
4460175 AATCCGACCCGAACAAAATAAAGTTTCATCC
195 AACCCGACCCGAACAAAACAAAGTTTCATCC
4460206 GACCCGACCCGA
1 GACCCGACCCGA
4460218 ATATATGAAT
Statistics
Matches: 225, Mismatches: 9, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
223 99 0.44
227 4 0.02
228 122 0.54
ACGTcount: A:0.37, C:0.29, G:0.11, T:0.23
Consensus pattern (225 bp):
GACCCGACCCGACCCAAAATAATAAAAAATTATTTTTATTTAATAAAAACAATGACTTAATCCGA
CCCGACCCGAATTATATATATTTTCGGGTCGGTCCAGTTTTTTTCACCCTAAACCCAAACCCGAC
CCGACACCCGAATATCACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTTAAAAA
ACCCGACCCGAACAAAACAAAGTTTCATCC
Found at i:4460259 original size:228 final size:224
Alignment explanation
Indices: 4459795--4460217 Score: 627
Period size: 223 Copynumber: 1.9 Consensus size: 224
4459785 TATTTTTATT
* *
4459795 TAATAAAAATAGTGACTTAATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTCCAGTTT
1 TAATAAAAACAATGACTTAATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTCCAGTTT
*
4459860 TTTTCACCCTAAACCCAAATCCGACCCGATCCGACCCGAATATCACACTTAAAAAAACCCGACCC
66 TTTTCACCCTAAACCCAAACCCGACCCGA--C-ACCCGAATATCACACTTAAAAAAACCCGACCC
4459925 GACTCGACCCGAATATCACACTTAAAAAACCCGACCCGAACAAAACAAAGTTTCATCCGACCCGA
128 GACTCGACCCGAATATCACACTTAAAAAACCCGACCCGAACAAAACAAAGTTTCATCCGACCCGA
* * ***** **
4459990 CCCGACCCGAAATAATAAAAAATTATTTTTATT
193 CCCGA-CAGAAATAATAAAAAATGAACCCGAAA
* *
4460023 TAATAAAAACAATGACTTAATCCGATCCGACCCGAATTATATATATTTTCGGGTCGGTCCGGTTT
1 TAATAAAAACAATGACTTAATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTCCAGTTT
4460088 TTTTCACCCTAAA-CCAGAACCCGACCC-A-ACCCGAATATCACACTTAAAAAAACCCGACCCGA
66 TTTTCACCCTAAACCCA-AACCCGACCCGACACCCGAATATCACACTTAAAAAAACCCGACCCGA
* * *
4460150 CTCGACCCGAATATCACACTTAATAAATCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACC
130 CTCGACCCGAATATCACACTTAAAAAACCCGACCCGAACAAAACAAAGTTTCATCCGACCCGACC
4460215 CGA
195 CGA
4460218 ATATATGAAT
Statistics
Matches: 186, Mismatches: 8, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
223 99 0.53
227 4 0.02
228 83 0.45
ACGTcount: A:0.36, C:0.30, G:0.12, T:0.22
Consensus pattern (224 bp):
TAATAAAAACAATGACTTAATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTCCAGTTT
TTTTCACCCTAAACCCAAACCCGACCCGACACCCGAATATCACACTTAAAAAAACCCGACCCGAC
TCGACCCGAATATCACACTTAAAAAACCCGACCCGAACAAAACAAAGTTTCATCCGACCCGACCC
GACAGAAATAATAAAAAATGAACCCGAAA
Found at i:4463135 original size:31 final size:32
Alignment explanation
Indices: 4463110--4463197 Score: 103
Period size: 31 Copynumber: 2.8 Consensus size: 32
4463100 TTATATTATG
*
4463110 ATTATTGA-ATTTATTAAATTATTATAAAATA
1 ATTATTAAGATTTATTAAATTATTATAAAATA
* *
4463141 ATTATTAAGATTTATTAAA-AACTATAAAATA
1 ATTATTAAGATTTATTAAATTATTATAAAATA
*
4463172 ATTATTAA-ACTTATTAAACTT-TTATA
1 ATTATTAAGATTTATTAAA-TTATTATA
4463198 GTTTATGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 9 0.19
31 29 0.60
32 10 0.21
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.45
Consensus pattern (32 bp):
ATTATTAAGATTTATTAAATTATTATAAAATA
Found at i:4476626 original size:13 final size:13
Alignment explanation
Indices: 4476605--4476639 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
4476595 CCCACTTACT
4476605 TTTCACTTTTCAC
1 TTTCACTTTTCAC
* *
4476618 TTTCCCTTTTTAC
1 TTTCACTTTTCAC
4476631 TTTCACTTT
1 TTTCACTTT
4476640 CTAGTTTCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.11, C:0.29, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTCACTTTTCAC
Found at i:4481763 original size:15 final size:16
Alignment explanation
Indices: 4481742--4481787 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
4481732 CATAGCATTT
*
4481742 TTATTTTACTTGTTCA
1 TTATTTTACTTGTTAA
*
4481758 -TATTTT-CTTTTTAA
1 TTATTTTACTTGTTAA
4481772 TTAGTTTTACTTGTTA
1 TTA-TTTTACTTGTTA
4481788 CTTTCCTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
14 6 0.25
15 8 0.33
16 4 0.17
17 6 0.25
ACGTcount: A:0.20, C:0.09, G:0.07, T:0.65
Consensus pattern (16 bp):
TTATTTTACTTGTTAA
Found at i:4493491 original size:17 final size:18
Alignment explanation
Indices: 4493471--4493508 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
4493461 TCTCCCTTAC
4493471 TTTAACACTTC-CCCCCT
1 TTTAACACTTCTCCCCCT
*
4493488 TTTAACAGTTCTCCCCCT
1 TTTAACACTTCTCCCCCT
4493506 TTT
1 TTT
4493509 TGTTAAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.16, C:0.39, G:0.03, T:0.42
Consensus pattern (18 bp):
TTTAACACTTCTCCCCCT
Found at i:4495390 original size:19 final size:18
Alignment explanation
Indices: 4495361--4495396 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4495351 CAGAGAAAAG
*
4495361 TTTGAAAAATTGTTTGTT
1 TTTGAAAAATTGATTGTT
4495379 TTTGACAAAATTGATTGT
1 TTTGA-AAAATTGATTGT
4495397 AAAATATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.50
Consensus pattern (18 bp):
TTTGAAAAATTGATTGTT
Found at i:4495815 original size:21 final size:22
Alignment explanation
Indices: 4495753--4495878 Score: 73
Period size: 24 Copynumber: 5.6 Consensus size: 22
4495743 GCAAGGCCTT
4495753 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTC-AGGA
* *
4495776 GTGCATCGGTGCATC-TTCATGA
1 GTGCATCGATGCA-CATTCAGGA
*
4495798 -TGTATCGATGCACATTCAAAGG-
1 GTGCATCGATGCACATTC--AGGA
* *
4495820 GATGCAACAATGCACATTCAAAGG-
1 G-TGCATCGATGCACATTC--AGGA
* *
4495844 GATGCATCGATGCACTTTCA-TA
1 G-TGCATCGATGCACATTCAGGA
*
4495866 GTGTATCGATGCA
1 GTGCATCGATGCA
4495879 TTATGCACAA
Statistics
Matches: 83, Mismatches: 13, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
20 1 0.01
21 24 0.29
22 5 0.06
23 17 0.20
24 36 0.43
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAGGA
Found at i:4495832 original size:24 final size:24
Alignment explanation
Indices: 4495805--4495863 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
4495795 TGATGTATCG
4495805 ATGCACATTCAAAGGGATGCAACA
1 ATGCACATTCAAAGGGATGCAACA
* *
4495829 ATGCACATTCAAAGGGATGCATCG
1 ATGCACATTCAAAGGGATGCAACA
*
4495853 ATGCACTTTCA
1 ATGCACATTCA
4495864 TAGTGTATCG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (24 bp):
ATGCACATTCAAAGGGATGCAACA
Found at i:4506841 original size:56 final size:57
Alignment explanation
Indices: 4506781--4506905 Score: 139
Period size: 56 Copynumber: 2.2 Consensus size: 57
4506771 GTGGCATTTG
* **
4506781 CTCGTAT-TACGATCATGAATGTCACTAACTTGATTATACAATCAGTGTGAAATTCA
1 CTCGTATATACGACCATGAATGGAACTAACTTGATTATACAATCAGTGTGAAATTCA
* * * * * * *
4506837 CTCGT-TCTACGACCATGTATGGAACTGATTTGATTATACGATCTGTGTGACATTCA
1 CTCGTATATACGACCATGAATGGAACTAACTTGATTATACAATCAGTGTGAAATTCA
4506893 CTCG-ATATACGAC
1 CTCGTATATACGAC
4506906 TTATGCGACA
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
55 1 0.02
56 56 0.98
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.34
Consensus pattern (57 bp):
CTCGTATATACGACCATGAATGGAACTAACTTGATTATACAATCAGTGTGAAATTCA
Found at i:4515155 original size:46 final size:46
Alignment explanation
Indices: 4515055--4515403 Score: 540
Period size: 46 Copynumber: 7.6 Consensus size: 46
4515045 CATTGTGTAC
**
4515055 TTTCATTGGTGGCATCCTTTCATGCCGATAATG-ACCGTTATGCAT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCAT
*
4515100 TTTCATTTATGGCATCCTTTCATTCCGATAATGCACCGTTATGCAT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCAT
* *
4515146 TTTCATTTATGGCATCCTTTCATGCCGATAATGCTCCGTTATGCAA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCAT
* * *
4515192 TTTCATTTATGACATCCTTTCATGACGATAATGCACCGTTATGTAT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCAT
* * *
4515238 TTTTATTTATGGCATCATTTCATGCCTATAATGCACCGTTATGCAT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCAT
*
4515284 TTTCATTTATGGCATCCTTTCGTGCCGATAATGCACCGTTATGCAT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCAT
* * *
4515330 TTTCATTTATGGCATCCTTTTATGCCTATAATCCACCGTTATAG-AT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTAT-GCAT
4515376 TTTCATTTATGGCATCCTTTCATGCCGA
1 TTTCATTTATGGCATCCTTTCATGCCGA
4515404 AGGCATTTAA
Statistics
Matches: 275, Mismatches: 27, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
45 30 0.11
46 244 0.89
47 1 0.00
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (46 bp):
TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCAT
Found at i:4515560 original size:81 final size:81
Alignment explanation
Indices: 4515403--4515552 Score: 205
Period size: 81 Copynumber: 1.9 Consensus size: 81
4515393 TTTCATGCCG
* * * *
4515403 AAGGCATTTAACCTTTCATCTAAATTGCATTATTGACACCTTTCTTCCAGATACACAGTTAGGCA
1 AAGGCATTTAACCTTTCATCTAAACTGCATGATTGACACCTTTCTTCCAAATACACAGCTAGGCA
4515468 ATTAATCTTTTACTCA
66 ATTAATCTTTTACTCA
* * *
4515484 AAGGTATTTAACCTTTCATCT-AACTGACATGATTGCCACCTTTCTGT-CAAATGCACAGCTAGG
1 AAGGCATTTAACCTTTCATCTAAACTG-CATGATTGACACCTTTCT-TCCAAATACACAGCTAGG
4515547 CAATTA
64 CAATTA
4515553 GTTTTTTATT
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
80 4 0.07
81 55 0.92
82 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.35
Consensus pattern (81 bp):
AAGGCATTTAACCTTTCATCTAAACTGCATGATTGACACCTTTCTTCCAAATACACAGCTAGGCA
ATTAATCTTTTACTCA
Found at i:4515985 original size:20 final size:22
Alignment explanation
Indices: 4515960--4516015 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
4515950 AGATTCAATA
*
4515960 GTATCGGTACTCCTAT-C-ATG
1 GTATCGATACTCCTATACTATG
**
4515980 GTATCGATACTTATATACTATG
1 GTATCGATACTCCTATACTATG
4516002 GTATCGATACTCCT
1 GTATCGATACTCCT
4516016 TTTCAGTATC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 13 0.45
21 1 0.03
22 15 0.52
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (22 bp):
GTATCGATACTCCTATACTATG
Found at i:4523260 original size:18 final size:18
Alignment explanation
Indices: 4523239--4523273 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4523229 ACGTCAGTCA
4523239 ACGATAAACAGTCAACGG
1 ACGATAAACAGTCAACGG
* *
4523257 ACGATCAACGGTCAACG
1 ACGATAAACAGTCAACG
4523274 ACTAACCCGT
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:0.40, C:0.26, G:0.23, T:0.11
Consensus pattern (18 bp):
ACGATAAACAGTCAACGG
Found at i:4531965 original size:14 final size:13
Alignment explanation
Indices: 4531937--4531962 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4531927 ATTATTTAAT
4531937 TTCTCTTTTTTCC
1 TTCTCTTTTTTCC
4531950 TTCTCTTTTTTCC
1 TTCTCTTTTTTCC
4531963 CTTTTTTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (13 bp):
TTCTCTTTTTTCC
Found at i:4532018 original size:11 final size:11
Alignment explanation
Indices: 4531998--4532026 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4531988 TCTATTTTTA
4531998 TTTTTC-TCTT
1 TTTTTCTTCTT
4532008 TTTTTCTTCTT
1 TTTTTCTTCTT
4532019 TTTTTCTT
1 TTTTTCTT
4532027 TTAATCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTCTTCTT
Found at i:4532467 original size:258 final size:256
Alignment explanation
Indices: 4532047--4532837 Score: 989
Period size: 238 Copynumber: 3.1 Consensus size: 256
4532037 TTTATTATTT
* ** * ** * *
4532047 TAAATGAGAAACTTTGAAAATCGTTTTCTCATTTTTCAAATTATCATATGAAAGCATCTTGCCCA
1 TAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTGAAA--ATCACGTGAAAACATCTTGCCCG
* * * * **
4532112 AAGGTCTTATAGATGGCACGAAGGACTTATTATCTTGTTCGAAAGATTGACAGATGACTTGAAGG
64 AAGGTCTTATAGATGGCACGAAGGACTTATCATCTTGCTCGAAAGACTAACAGATGACCCGAAGG
*
4532177 ATTTAATCACCATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTACCAATTTTGGAAATAGTT
129 ATTTAATCAACATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTACCAATTTTGGAAATAGTT
*
4532242 TATTGGGTAAGAAACTTTGAAAATCGTTTTCTTACTTTTCAAAAATTTCACTTTCTGAAAATAC
194 TA-TGGGTAAGAAACTTTGAAAATCGTTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATAC
* * *
4532306 TAAATGAGAAACTTTAGAAATCACTTTCTCATTTTTTGAAAATCACGTGAAAACATCCTGCCTGA
1 TAAATGAGAAACTTTGGAAATCACTTTCTCA-TTTTTGAAAATCACGTGAAAACATCTTGCCCGA
* *
4532371 AGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGACTAACAGATGACCCGAAGGA
65 AGGTCTTATAGATGGCACGAAGGACTTATCATCTTGCTCGAAAGACTAACAGATGACCCGAAGGA
4532436 TTTAATCAACATGCTCGAAAGACTTACTGATGGCCTGAAGGACTT----A---T-----TA----
130 TTTAATCAACATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTACCAATTTTGGAAATAGTTT
* * * * *
4532485 A---GTAAGAAACTTT-AGAAATCATTTTCTTACTTTTAAAAAATTTCATTTTC-AAAAGAGATT
195 ATGGGTAAGAAACTTTGA-AAATCGTTTTCTTACTTTTCAAAAATTTCATTTTCTGAAA-ATA-C
**
4532545 TAAATGAGAAACTTTGGAAATTGCTTTCTCATTTTTGAAAATC-CTGTGAAAACATCTTGCCCGA
1 TAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTGAAAATCAC-GTGAAAACATCTTGCCCGA
* * *
4532609 AGGTCTTATAGATGGCTCGAAGAACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGA
65 AGGTCTTATAGATGGCACGAAGGACTTATCATCTTGCTCGAAAGACTAACAGATGACCCGAAGGA
* * ** *
4532674 TTTAATCATCATGCACGAAAGACTTAAAGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTT
130 TTTAATCAACATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTACCAATTTTGGAAATAGTTT
* *
4532739 ACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATAC
195 A-TGGGTAAGAAACTTTGAAAATCGTTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATAC
4532802 TAAATGAGAAACTTTGGAAATCGA-TTTCTCATTTTT
1 TAAATGAGAAACTTTGGAAATC-ACTTTCTCATTTTT
4532838 TTTTAAAATC
Statistics
Matches: 455, Mismatches: 49, Indels: 58
0.81 0.09 0.10
Matches are distributed among these distances:
237 5 0.01
238 176 0.39
239 28 0.06
242 2 0.00
245 1 0.00
246 2 0.00
250 2 0.00
251 1 0.00
254 2 0.00
257 33 0.07
258 165 0.36
259 30 0.07
260 8 0.02
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Consensus pattern (256 bp):
TAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTGAAAATCACGTGAAAACATCTTGCCCGAA
GGTCTTATAGATGGCACGAAGGACTTATCATCTTGCTCGAAAGACTAACAGATGACCCGAAGGAT
TTAATCAACATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTACCAATTTTGGAAATAGTTTA
TGGGTAAGAAACTTTGAAAATCGTTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATAC
Found at i:4532476 original size:42 final size:41
Alignment explanation
Indices: 4532380--4532482 Score: 125
Period size: 42 Copynumber: 2.5 Consensus size: 41
4532370 AAGGTCTTAT
* * *
4532380 AGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGACTAAC
1 AGATGGCCCGAAGGACTTATCAACATGCTCGAAAGACTAAC
* * *
4532421 AGATGACCCGAAGGATTTAATCAACATGCTCGAAAGACTTAC
1 AGATGGCCCGAAGGACTT-ATCAACATGCTCGAAAGACTAAC
* *
4532463 TGATGGCCTGAAGGACTTAT
1 AGATGGCCCGAAGGACTTAT
4532483 TAAGTAAGAA
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 18 0.35
42 33 0.65
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (41 bp):
AGATGGCCCGAAGGACTTATCAACATGCTCGAAAGACTAAC
Found at i:4532663 original size:41 final size:41
Alignment explanation
Indices: 4532597--4532719 Score: 138
Period size: 42 Copynumber: 3.0 Consensus size: 41
4532587 CCTGTGAAAA
* * * * * *
4532597 CATCTTGCCCGAAGGTCTTATAGATGGCTCGAAGAACTTAT
1 CATCTTGCACGAAAGACTTAAAGATGGCCCGAAGGACTTAT
* * * *
4532638 CATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAT
1 CATCTTGCACGAAAGACTTAAAGATGGCCCGAAGGACTT-AT
*
4532680 CATCATGCACGAAAGACTTAAAGATGGCCCGAAGGACTTA
1 CATCTTGCACGAAAGACTTAAAGATGGCCCGAAGGACTTA
4532720 CCAATTTTGG
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
41 32 0.47
42 36 0.53
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (41 bp):
CATCTTGCACGAAAGACTTAAAGATGGCCCGAAGGACTTAT
Found at i:4539384 original size:11 final size:11
Alignment explanation
Indices: 4539360--4539392 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
4539350 TAAAAAAGAC
4539360 ATTTTTAATT-
1 ATTTTTAATTA
*
4539370 ATTTTTGATTA
1 ATTTTTAATTA
4539381 ATTTTTAATTA
1 ATTTTTAATTA
4539392 A
1 A
4539393 AAGTAATGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (11 bp):
ATTTTTAATTA
Found at i:4543238 original size:2 final size:2
Alignment explanation
Indices: 4543231--4543259 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4543221 GATTTTGGGG
4543231 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4543260 TCCCTAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4548615 original size:128 final size:127
Alignment explanation
Indices: 4548385--4548629 Score: 337
Period size: 128 Copynumber: 1.9 Consensus size: 127
4548375 TTGTGATCAC
*
4548385 TGTAGAGGTGAAGGCCACAACAGAAAGCATTATCAAAATCTTCTAAAATATTGACCTAAACGATA
1 TGTAGAGGTGAAGACCACAACAGAAAGCATTATCAAAATCTTCTAAAATATTGACCTAAACGATA
*
4548450 AAACCTTCATAAATGTGTTCAGTTCATGTTTTAAATTGAATTTTTTTTATCTGAGTTTTTAAT
66 AAAACTTCATAAATGTGTTCAGTTCATGTTTTAAATTGAA-TTTTTTTATCTGAGTTTTTAAT
** * ** * * *
4548513 TGTAGAGGTGAAGACCACAACAGCCAGCATTGTCTGAATCTTTTAAAATATTGGCCTAAATGATA
1 TGTAGAGGTGAAGACCACAACAGAAAGCATTATCAAAATCTTCTAAAATATTGACCTAAACGATA
* * ** * *
4548578 AAAACTTCATAATTGTGTTTAGTTTGTGTTTTTAATTGTATTTTTTTATCTG
66 AAAACTTCATAAATGTGTTCAGTTCATGTTTTAAATTGAATTTTTTTATCTG
4548630 TTTTTATGCA
Statistics
Matches: 101, Mismatches: 16, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
127 12 0.12
128 89 0.88
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.39
Consensus pattern (127 bp):
TGTAGAGGTGAAGACCACAACAGAAAGCATTATCAAAATCTTCTAAAATATTGACCTAAACGATA
AAAACTTCATAAATGTGTTCAGTTCATGTTTTAAATTGAATTTTTTTATCTGAGTTTTTAAT
Found at i:4550181 original size:19 final size:17
Alignment explanation
Indices: 4550157--4550203 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
4550147 ATAGCCTGAG
4550157 TGCATCGATGCATGGAGAA
1 TGCATCGATGCAT-GA-AA
4550176 TGCATC-AGTGCATGAAA
1 TGCATCGA-TGCATGAAA
4550193 TGCATTCGATG
1 TGCA-TCGATG
4550204 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
17 6 0.24
18 7 0.28
19 12 0.48
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.26
Consensus pattern (17 bp):
TGCATCGATGCATGAAA
Found at i:4550252 original size:65 final size:64
Alignment explanation
Indices: 4550112--4550253 Score: 171
Period size: 64 Copynumber: 2.2 Consensus size: 64
4550102 GCACCAAGTG
* * * *
4550112 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGATGCATGGAGAA
1 TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAATAGCATGAATGCATCGATGCATGGAGAA
* * * *
4550176 TGCATCAGTGCATGAAATGCATTCGATGTTTCAATTAAT-TCATTAATGCATCGATGCATGGTTG
1 TGCATCGGTGCATGAAATGCATTCGATGTTTCAA--AATAGCATGAATGCATCGATGCATGG-AG
4550240 -A
63 AA
4550241 TGCATCGGTGCAT
1 TGCATCGGTGCAT
4550254 CACCTCAAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
64 31 0.47
65 31 0.47
66 4 0.06
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (64 bp):
TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAATAGCATGAATGCATCGATGCATGGAGAA
Found at i:4559919 original size:31 final size:31
Alignment explanation
Indices: 4559881--4559960 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
4559871 ATCGATTTTG
4559881 AAAAACTTACTCCCCCTTACTATAGCACATC
1 AAAAACTTACTCCCCCTTACTATAGCACATC
4559912 AAAAACTTACTCCCCCTTACTATAGCACATC
1 AAAAACTTACTCCCCCTTACTATAGCACATC
** * *
4559943 TTAAATTTTCTCCCCCTT
1 AAAAACTTACTCCCCCTT
4559961 TTTGTTAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.31, C:0.35, G:0.03, T:0.31
Consensus pattern (31 bp):
AAAAACTTACTCCCCCTTACTATAGCACATC
Found at i:4567953 original size:17 final size:19
Alignment explanation
Indices: 4567917--4567960 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
4567907 GCCTGAGTGA
4567917 ATCGATGCATGGAGAATGC
1 ATCGATGCATGGAGAATGC
*
4567936 ATCGGTGCAT-GA-AATGC
1 ATCGATGCATGGAGAATGC
4567953 ATTCGATG
1 A-TCGATG
4567961 TTTCAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 6 0.27
18 7 0.32
19 9 0.41
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.25
Consensus pattern (19 bp):
ATCGATGCATGGAGAATGC
Found at i:4569351 original size:2 final size:2
Alignment explanation
Indices: 4569344--4569381 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4569334 TATTCAAGGC
4569344 TA TA TA TA TA 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 TA TA TA TA TA
4569382 ACTAGACCAG
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):
TA
Found at i:4570451 original size:24 final size:24
Alignment explanation
Indices: 4570419--4570464 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
4570409 TCTTCCAGAT
4570419 GATGTATAAAACATCTATGTACAC
1 GATGTATAAAACATCTATGTACAC
4570443 GATGTATAAAACATCTATGTAC
1 GATGTATAAAACATCTATGTAC
4570465 CATATCATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (24 bp):
GATGTATAAAACATCTATGTACAC
Found at i:4574512 original size:15 final size:15
Alignment explanation
Indices: 4574494--4574542 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
4574484 AAAACCTATA
*
4574494 TAAAATATTAAAATT
1 TAAAAAATTAAAATT
* **
4574509 TAAAAAAATAAAAAA
1 TAAAAAATTAAAATT
*
4574524 TAAAAAATTTAAATT
1 TAAAAAATTAAAATT
4574539 TAAA
1 TAAA
4574543 CTAATAAAAA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAAAATTAAAATT
Found at i:4574527 original size:30 final size:30
Alignment explanation
Indices: 4574493--4574552 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
4574483 TAAAACCTAT
*
4574493 ATAAAATATTAAAATTTAAAAAAATAAAAA
1 ATAAAAAATTAAAATTTAAAAAAATAAAAA
* **
4574523 ATAAAAAATTTAAATTTAAACTAATAAAAA
1 ATAAAAAATTAAAATTTAAAAAAATAAAAA
4574553 CCTAGAAGCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (30 bp):
ATAAAAAATTAAAATTTAAAAAAATAAAAA
Found at i:4575039 original size:24 final size:24
Alignment explanation
Indices: 4574992--4575038 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
4574982 AAGTGATAAA
* *
4574992 TTTATAAAATTTTAAGATAAAAAT
1 TTTATAAAATTTAAAAATAAAAAT
4575016 TTTATAAAATTTAAAAAATAAAA
1 TTTATAAAATTT-AAAAATAAAA
4575039 TAAATTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
TTTATAAAATTTAAAAATAAAAAT
Found at i:4575062 original size:21 final size:20
Alignment explanation
Indices: 4575018--4575064 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
4575008 ATAAAAATTT
4575018 TATAAAATTTAAAAAATAAA
1 TATAAAATTTAAAAAATAAA
*
4575038 -ATAAATTATTAATAAAA-AAA
1 TATAAAAT-TTAA-AAAATAAA
4575058 TATAAAA
1 TATAAAA
4575065 AGTGTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
19 6 0.27
20 7 0.32
21 9 0.41
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
TATAAAATTTAAAAAATAAA
Found at i:4575850 original size:28 final size:28
Alignment explanation
Indices: 4575807--4575861 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
4575797 TGGGAATTAC
4575807 TTTCAAGCACTAGCTCGACGACATAATA
1 TTTCAAGCACTAGCTCGACGACATAATA
* * * *
4575835 TTTCATGCACTTGCTCGATGTCATAAT
1 TTTCAAGCACTAGCTCGACGACATAAT
4575862 GTAAATAGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.33
Consensus pattern (28 bp):
TTTCAAGCACTAGCTCGACGACATAATA
Found at i:4578675 original size:17 final size:17
Alignment explanation
Indices: 4578653--4578704 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 17
4578643 CAATACTGAG
4578653 TTTTTATATAAATAATT
1 TTTTTATATAAATAATT
*
4578670 TTTTTAAGTATATAATGATT
1 TTTTT-A-TATA-AATAATT
4578690 TTTTTATACTAAATA
1 TTTTTATA-TAAATA
4578705 GGTGATCATC
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
17 5 0.17
18 6 0.21
19 7 0.24
20 11 0.38
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (17 bp):
TTTTTATATAAATAATT
Found at i:4578692 original size:20 final size:21
Alignment explanation
Indices: 4578657--4578695 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
4578647 ACTGAGTTTT
4578657 TATATAAATAATTTTTTTAAG
1 TATATAAATAATTTTTTTAAG
*
4578678 TATAT-AATGATTTTTTTA
1 TATATAAATAATTTTTTTA
4578696 TACTAAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (21 bp):
TATATAAATAATTTTTTTAAG
Found at i:4585447 original size:21 final size:20
Alignment explanation
Indices: 4585388--4585449 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 20
4585378 TGAAGATTTC
4585388 AATTAAAATTTTAATAATCTA
1 AATTAAAATTTTAATAAT-TA
**
4585409 AATTAAAA-AATAATAATTA
1 AATTAAAATTTTAATAATTA
*
4585428 AATTAAAATTGTTCATAATTA
1 AATTAAAATT-TTAATAATTA
4585449 A
1 A
4585450 TTGGCAGAGG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
19 10 0.29
20 7 0.21
21 17 0.50
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (20 bp):
AATTAAAATTTTAATAATTA
Found at i:4597844 original size:27 final size:27
Alignment explanation
Indices: 4597814--4597866 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
4597804 AAGTGACTTT
*
4597814 TACCTTGAACTGT-AGGTAAGTTATTAA
1 TACCTCGAACT-TAAGGTAAGTTATTAA
*
4597841 TACCTCGATCTTAAGGTAAGTTATTA
1 TACCTCGAACTTAAGGTAAGTTATTA
4597867 GTACTGTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (27 bp):
TACCTCGAACTTAAGGTAAGTTATTAA
Found at i:4604013 original size:25 final size:25
Alignment explanation
Indices: 4603985--4604043 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
4603975 AAGTATCTAT
4603985 TTGAATTAAAAAATAAATTTAAAT-A
1 TTGAATTAAAAAAT-AATTTAAATAA
* *
4604010 TTGATTTGAAAAATAATTTAAATAA
1 TTGAATTAAAAAATAATTTAAATAA
4604035 TT-AATTAAA
1 TTGAATTAAA
4604044 TAAAAACTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 14 0.48
25 15 0.52
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (25 bp):
TTGAATTAAAAAATAATTTAAATAA
Found at i:4604298 original size:18 final size:18
Alignment explanation
Indices: 4604275--4604339 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 18
4604265 GTTTCTGAGA
*
4604275 GAATTGGAATCTGTGAAG
1 GAATTAGAATCTGTGAAG
* *
4604293 GAATT-GAAATCGGTGAAT
1 GAATTAG-AATCTGTGAAG
*
4604311 GAATTAGAATCTAT--AG
1 GAATTAGAATCTGTGAAG
4604327 GAATTAGAATCTG
1 GAATTAGAATCTG
4604340 AATTTGAAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
16 13 0.33
17 1 0.03
18 24 0.62
19 1 0.03
ACGTcount: A:0.38, C:0.06, G:0.26, T:0.29
Consensus pattern (18 bp):
GAATTAGAATCTGTGAAG
Found at i:4604949 original size:28 final size:28
Alignment explanation
Indices: 4604917--4604977 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
4604907 CCTAAACCCG
*
4604917 AACCCGACCCGAATATCACACTTAAAAA
1 AACCCGACCCGAATATCAAACTTAAAAA
4604945 AACCCGACCCGAATATCAAACTTAAAAA
1 AACCCGACCCGAATATCAAACTTAAAAA
4604973 AACCC
1 AACCC
4604978 AATCCGAACC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.48, C:0.33, G:0.07, T:0.13
Consensus pattern (28 bp):
AACCCGACCCGAATATCAAACTTAAAAA
Found at i:4604984 original size:28 final size:28
Alignment explanation
Indices: 4604917--4604985 Score: 102
Period size: 28 Copynumber: 2.5 Consensus size: 28
4604907 CCTAAACCCG
* *
4604917 AACCCGACCCGAATATCACACTTAAAAA
1 AACCCAACCCGAATATCAAACTTAAAAA
*
4604945 AACCCGACCCGAATATCAAACTTAAAAA
1 AACCCAACCCGAATATCAAACTTAAAAA
*
4604973 AACCCAATCCGAA
1 AACCCAACCCGAA
4604986 CCCAAAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.48, C:0.32, G:0.07, T:0.13
Consensus pattern (28 bp):
AACCCAACCCGAATATCAAACTTAAAAA
Found at i:4605293 original size:5 final size:5
Alignment explanation
Indices: 4605283--4605314 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
4605273 CAAGGACACT
4605283 TAATA TAATA TAATA TAATA TAATA TAATA TA
1 TAATA TAATA TAATA TAATA TAATA TAATA TA
4605315 GATTTGTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:4607012 original size:13 final size:13
Alignment explanation
Indices: 4606994--4607054 Score: 52
Period size: 13 Copynumber: 4.5 Consensus size: 13
4606984 GATCGTTGAT
4606994 CGTTGACCTGAAC
1 CGTTGACCTGAAC
**
4607007 CGTTGACCTGAGT
1 CGTTGACCTGAAC
*
4607020 CGTTGACTTTG-AC
1 CGTTGAC-CTGAAC
*
4607033 CTGTTGACCGTTAAC
1 C-GTTGACC-TGAAC
4607048 CGTTGAC
1 CGTTGAC
4607055 AAAAAAGTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
13 19 0.51
14 15 0.41
15 3 0.08
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.31
Consensus pattern (13 bp):
CGTTGACCTGAAC
Found at i:4607032 original size:32 final size:32
Alignment explanation
Indices: 4606975--4607035 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
4606965 CGAGTCAACT
4606975 CGTTGACCCGATCGTTGATCGTTGACCTGAAC
1 CGTTGACCCGATCGTTGATCGTTGACCTGAAC
* *
4607007 CGTTGACCTGAGTCGTTGA-CTTTGACCTG
1 CGTTGACCCGA-TCGTTGATCGTTGACCTG
4607036 TTGACCGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 19 0.73
33 7 0.27
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.31
Consensus pattern (32 bp):
CGTTGACCCGATCGTTGATCGTTGACCTGAAC
Found at i:4608245 original size:11 final size:11
Alignment explanation
Indices: 4608203--4608326 Score: 65
Period size: 12 Copynumber: 10.5 Consensus size: 11
4608193 AAAGGAAAAT
4608203 AATAAAATATAA
1 AATAAAATA-AA
**
4608215 AATAATGTTAAA
1 AATAA-AATAAA
*
4608227 AGAGAAAATAAA
1 A-ATAAAATAAA
*
4608239 AATAAAA-CAA
1 AATAAAATAAA
4608249 AATAAAATAAAA
1 AATAAAAT-AAA
4608261 AAGTGGGAAAATAAA
1 AA-T---AAAATAAA
*
4608276 AATAAAATAAG
1 AATAAAATAAA
4608287 AATAATAAATAAA
1 AAT-A-AAATAAA
*
4608300 AA-AGAAAT-AT
1 AATA-AAATAAA
4608310 AATAAAATAATA
1 AATAAAATAA-A
4608322 AATAA
1 AATAA
4608327 TAGTAGTAAA
Statistics
Matches: 86, Mismatches: 13, Indels: 26
0.69 0.10 0.21
Matches are distributed among these distances:
10 16 0.19
11 22 0.26
12 23 0.27
13 14 0.16
14 1 0.01
15 5 0.06
16 5 0.06
ACGTcount: A:0.73, C:0.01, G:0.07, T:0.19
Consensus pattern (11 bp):
AATAAAATAAA
Found at i:4608261 original size:16 final size:16
Alignment explanation
Indices: 4608231--4608260 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4608221 GTTAAAAGAG
4608231 AAAATAAAAATAAAAC
1 AAAATAAAAATAAAAC
4608247 AAAAT-AAAATAAAA
1 AAAATAAAAATAAAA
4608261 AAGTGGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAATAAAAATAAAAC
Found at i:4608280 original size:37 final size:40
Alignment explanation
Indices: 4608230--4608303 Score: 118
Period size: 37 Copynumber: 1.9 Consensus size: 40
4608220 TGTTAAAAGA
4608230 GAAAATAAAAATAAAACAA-AAT-A-AAATAAAAAAGTGG
1 GAAAATAAAAATAAAACAAGAATAATAAATAAAAAAGTGG
*
4608267 GAAAATAAAAATAAAATAAGAATAATAAATAAAAAAG
1 GAAAATAAAAATAAAACAAGAATAATAAATAAAAAAG
4608304 AAATATAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
37 18 0.55
38 3 0.09
39 1 0.03
40 11 0.33
ACGTcount: A:0.74, C:0.01, G:0.09, T:0.15
Consensus pattern (40 bp):
GAAAATAAAAATAAAACAAGAATAATAAATAAAAAAGTGG
Found at i:4608290 original size:17 final size:17
Alignment explanation
Indices: 4608270--4608319 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
4608260 AAAGTGGGAA
4608270 AATAAAAATAAAATAAG
1 AATAAAAATAAAATAAG
4608287 AATAATAAATAAAA-AAG
1 AATAA-AAATAAAATAAG
*
4608304 AA-ATATAATAAAATAA
1 AATA-AAAATAAAATAA
4608320 TAAATAATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
16 8 0.28
17 13 0.45
18 8 0.28
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (17 bp):
AATAAAAATAAAATAAG
Found at i:4608324 original size:17 final size:17
Alignment explanation
Indices: 4608268--4608325 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
4608258 AAAAAGTGGG
*
4608268 AAAATAAAAATAAAATA
1 AAAATATAAATAAAATA
*
4608285 AGAATAATAAATAAAA-A
1 AAAAT-ATAAATAAAATA
4608302 AGAAATAT-AATAAAATA
1 A-AAATATAAATAAAATA
4608319 ATAAATA
1 A-AAATA
4608326 ATAGTAGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 7 0.21
17 15 0.44
18 12 0.35
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (17 bp):
AAAATATAAATAAAATA
Found at i:4608389 original size:18 final size:18
Alignment explanation
Indices: 4608368--4608410 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
4608358 GTTGTTTTTA
*
4608368 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
4608386 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
4608404 AAATAAA
1 AAATAAA
4608411 TAATCTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:4610774 original size:14 final size:14
Alignment explanation
Indices: 4610739--4610776 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
4610729 TATTAAATTT
4610739 TAAAAAAAATGTTA
1 TAAAAAAAATGTTA
*
4610753 TATAAAAAATGTTA
1 TAAAAAAAATGTTA
4610767 -AAAGAAAAAT
1 TAAA-AAAAAT
4610777 AAAATAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 2 0.10
14 19 0.90
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (14 bp):
TAAAAAAAATGTTA
Found at i:4610942 original size:28 final size:28
Alignment explanation
Indices: 4610884--4610951 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
4610874 AAGAAATGGG
4610884 AAAATAA-AAATAAAACAAAATAATAAT
1 AAAATAATAAATAAAACAAAATAATAAT
*
4610911 -AAATAATAAATAAAAGAGAAAT-ATAAT
1 AAAATAATAAATAAAACA-AAATAATAAT
4610938 AAAATAATAAATAA
1 AAAATAATAAATAA
4610952 TAGTAGTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
26 6 0.16
27 14 0.38
28 17 0.46
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.21
Consensus pattern (28 bp):
AAAATAATAAATAAAACAAAATAATAAT
Found at i:4610969 original size:28 final size:26
Alignment explanation
Indices: 4610884--4610969 Score: 68
Period size: 28 Copynumber: 3.2 Consensus size: 26
4610874 AAGAAATGGG
* *
4610884 AAAATAA-AAATAAAACA-AAATAATA
1 AAAATAATAAATAAAAGAGAAA-GATA
*
4610909 ATAAATAATAAATAAAAGAGAAATATAA
1 A-AAATAATAAATAAAAGAGAAAGAT-A
*
4610937 TAAAATAATAAATAATAGTAGTAAAGATA
1 -AAAATAATAAATAAAAG-AG-AAAGATA
4610966 AAAA
1 AAAA
4610970 GATGGTTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
25 1 0.02
26 6 0.12
27 11 0.22
28 23 0.46
29 4 0.08
30 5 0.10
ACGTcount: A:0.72, C:0.01, G:0.06, T:0.21
Consensus pattern (26 bp):
AAAATAATAAATAAAAGAGAAAGATA
Found at i:4611017 original size:18 final size:18
Alignment explanation
Indices: 4610991--4611036 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
4610981 AAAGTTGTTT
4610991 TTAACATAAAAG-ATAAAAA
1 TTAA-ATAAAAGAAT-AAAA
*
4611010 TTAAATAAAAGAATATAA
1 TTAAATAAAAGAATAAAA
4611028 TTAAATAAA
1 TTAAATAAA
4611037 TAATCTAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.26
Consensus pattern (18 bp):
TTAAATAAAAGAATAAAA
Found at i:4616217 original size:30 final size:30
Alignment explanation
Indices: 4616177--4616239 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
4616167 AATAAACAAT
*
4616177 TGCCAGCCCATTGAAATTATGCACATTCGG
1 TGCCAACCCATTGAAATTATGCACATTCGG
* *
4616207 TGCCAACCCATTGAAATTATGCATATTTGG
1 TGCCAACCCATTGAAATTATGCACATTCGG
4616237 TGC
1 TGC
4616240 GTGCATCCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (30 bp):
TGCCAACCCATTGAAATTATGCACATTCGG
Found at i:4620733 original size:30 final size:30
Alignment explanation
Indices: 4620693--4620755 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
4620683 AATAAAAAAT
*
4620693 TGCCAGCCCATTGAAATTATGCACATTCGG
1 TGCCAACCCATTGAAATTATGCACATTCGG
*
4620723 TGCCAACCCATTGAAATTATGCATATTCGG
1 TGCCAACCCATTGAAATTATGCACATTCGG
4620753 TGC
1 TGC
4620756 GTGCATCCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (30 bp):
TGCCAACCCATTGAAATTATGCACATTCGG
Found at i:4624149 original size:52 final size:50
Alignment explanation
Indices: 4624087--4624236 Score: 140
Period size: 52 Copynumber: 2.9 Consensus size: 50
4624077 AAAAATAAGA
* *
4624087 GACCAAAATGTAATAAAACAAAAAATAGTAGCCCAAATCAGAAATAATTAGT
1 GACCAAAATGT-ATAAAACAAAAAACAGTAGCCCAAATCAGAAATAA-TAAT
* ** ** *
4624139 GACCAAAATGTGTAAATTGAAAGGACAATAGCCCAAATCAGAAATACATAAT
1 GACCAAAATGTATAAA-ACAAAAAACAGTAGCCCAAATCAGAAATA-ATAAT
* * * *
4624191 GACTAAAATGCATAAAATAAAAGAACAGTAG-CTAAATCAGAAATAA
1 GACCAAAATGTATAAAACAAAA-AACAGTAGCCCAAATCAGAAATAA
4624237 GGAGTGATTG
Statistics
Matches: 78, Mismatches: 17, Indels: 8
0.76 0.17 0.08
Matches are distributed among these distances:
50 1 0.01
51 20 0.26
52 56 0.72
53 1 0.01
ACGTcount: A:0.55, C:0.13, G:0.13, T:0.19
Consensus pattern (50 bp):
GACCAAAATGTATAAAACAAAAAACAGTAGCCCAAATCAGAAATAATAAT
Found at i:4625521 original size:3 final size:3
Alignment explanation
Indices: 4625513--4625541 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4625503 CTGCAAAATG
4625513 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
4625542 TTTTTGTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4625897 original size:12 final size:12
Alignment explanation
Indices: 4625880--4625904 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4625870 GTGATACAAA
4625880 ATTCATTTTAAG
1 ATTCATTTTAAG
4625892 ATTCATTTTAAG
1 ATTCATTTTAAG
4625904 A
1 A
4625905 AAAACAATCT
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:0.08, T:0.48
Consensus pattern (12 bp):
ATTCATTTTAAG
Found at i:4626132 original size:22 final size:22
Alignment explanation
Indices: 4626104--4626173 Score: 81
Period size: 22 Copynumber: 3.3 Consensus size: 22
4626094 TGGCCTGAAG
*
4626104 GACTTACACATCATGCTCGAAA
1 GACTTACTCATCATGCTCGAAA
* * *
4626126 GACTTACTGA--ATGCCCGAAG
1 GACTTACTCATCATGCTCGAAA
*
4626146 GACATACTCATCATGCTCGAAA
1 GACTTACTCATCATGCTCGAAA
4626168 GACTTA
1 GACTTA
4626174 TTGATGGCCC
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
20 16 0.43
22 21 0.57
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (22 bp):
GACTTACTCATCATGCTCGAAA
Found at i:4626144 original size:20 final size:20
Alignment explanation
Indices: 4626116--4626186 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
4626106 CTTACACATC
*
4626116 ATGCTCGAAAGACTTACTGA
1 ATGCCCGAAAGACTTACTGA
* * *
4626136 ATGCCCGAAGGACATACTCA
1 ATGCCCGAAAGACTTACTGA
* *
4626156 TCATGCTCGAAAGACTTATTG-
1 --ATGCCCGAAAGACTTACTGA
4626177 ATGGCCCGAA
1 AT-GCCCGAA
4626187 GTACTTAAGC
Statistics
Matches: 38, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 2 0.05
20 22 0.58
22 14 0.37
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (20 bp):
ATGCCCGAAAGACTTACTGA
Found at i:4626146 original size:42 final size:42
Alignment explanation
Indices: 4626058--4626193 Score: 154
Period size: 42 Copynumber: 3.3 Consensus size: 42
4626048 ATGGATGGTT
* * *
4626058 CGAAGGACTTA-TCATCTTGTTCGAAAGCCTTAT-AGATGGCC
1 CGAAGGACTTACTCATCATGCTCGAAAGACTTATGA-ATGGCC
* *
4626099 TGAAGGACTTACACATCATGCTCGAAAGACTTACTGAAT-GCC
1 CGAAGGACTTACTCATCATGCTCGAAAGACTTA-TGAATGGCC
*
4626141 CGAAGGACATACTCATCATGCTCGAAAGACTTATTG-ATGGCC
1 CGAAGGACTTACTCATCATGCTCGAAAGACTTA-TGAATGGCC
*
4626183 CGAAGTACTTA
1 CGAAGGACTTA
4626194 AGCTAATTCG
Statistics
Matches: 80, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
41 12 0.15
42 64 0.80
43 3 0.04
44 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (42 bp):
CGAAGGACTTACTCATCATGCTCGAAAGACTTATGAATGGCC
Found at i:4626311 original size:59 final size:59
Alignment explanation
Indices: 4626199--4626352 Score: 254
Period size: 59 Copynumber: 2.6 Consensus size: 59
4626189 ACTTAAGCTA
* *
4626199 ATTCGAAGTGTTATGAATTGAGCAATATGAAATGTTAACCCCTCTGGTAGGGCGTTGCTG
1 ATTCGAAGTGTTGTGAATCGAGCAA-ATGAAATGTTAACCCCTCTGGTAGGGCGTTGCTG
* *
4626259 ATTCGAAGTGTTGTGAATCGAGCAAAGGAAATGTTAACCCCTCTGGTGGGGCGTTGCTG
1 ATTCGAAGTGTTGTGAATCGAGCAAATGAAATGTTAACCCCTCTGGTAGGGCGTTGCTG
*
4626318 ATTCGAAGTGTTGTGAATCGAGTAAATGAAATGTT
1 ATTCGAAGTGTTGTGAATCGAGCAAATGAAATGTT
4626353 GAAAACATCC
Statistics
Matches: 88, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
59 65 0.74
60 23 0.26
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.31
Consensus pattern (59 bp):
ATTCGAAGTGTTGTGAATCGAGCAAATGAAATGTTAACCCCTCTGGTAGGGCGTTGCTG
Found at i:4626434 original size:41 final size:41
Alignment explanation
Indices: 4626374--4626487 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 41
4626364 ACCCAAAGGT
* **
4626374 CTTATGGATGGCCCGAAGGACTTATCATCTTGTTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTTATCATCACGTTCGAAAGA
* * * *
4626415 CTTATAGATGACCCAAAGGATTTCAGCATCACGTTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTT-ATCATCACGTTCGAAAGA
* *
4626457 CTTATTGATGGCCTGAAGGACTTACTCATCA
1 CTTATAGATGGCCCGAAGGACTTA-TCATCA
4626488 AGAAACCCTT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
41 20 0.34
42 38 0.66
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTATCATCACGTTCGAAAGA
Found at i:4626709 original size:52 final size:53
Alignment explanation
Indices: 4626538--4626757 Score: 203
Period size: 52 Copynumber: 4.1 Consensus size: 53
4626528 GGAACCCTTA
4626538 AAAATTAGGCTTAGTTTCATTTTAAAAACTCA-TTGAAAATCATCATCAAGAAACCCCTG
1 AAAATTAGGCTTAGTTT-A-TTT-AAAACTCATTTGAAAA-CAT--T-AAGAAACCCCTG
* * * * * * * * *
4626597 GAAATCAGGCTTAGTTT-CTAAAAACTCATTTGAAAATATCACGAAATCCCTA
1 AAAATTAGGCTTAGTTTATTTAAAACTCATTTGAAAACATTAAGAAACCCCTG
* * *
4626649 AAAATTAGGCTTAATTTATTTAAAATTCATTTGAAAACATTAAGAAATCCCT-
1 AAAATTAGGCTTAGTTTATTTAAAACTCATTTGAAAACATTAAGAAACCCCTG
* * * * *
4626701 AAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAACATTGAGAAACCCCTG
1 AAAATTAGGCTTAGTTTATTTAAAACTCATTTGAAAACATTAAGAAACCCCTG
4626754 AAAA
1 AAAA
4626758 GCAGGCATAG
Statistics
Matches: 134, Mismatches: 24, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
52 69 0.51
53 32 0.24
55 10 0.07
56 8 0.06
59 15 0.11
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.31
Consensus pattern (53 bp):
AAAATTAGGCTTAGTTTATTTAAAACTCATTTGAAAACATTAAGAAACCCCTG
Found at i:4626940 original size:38 final size:37
Alignment explanation
Indices: 4626898--4627027 Score: 115
Period size: 38 Copynumber: 3.5 Consensus size: 37
4626888 ATGAATATTC
4626898 TTGTTTTGAGTAAAAAAATGTCTCAAGCGAGACAAAGT
1 TTGTTTTGAG-AAAAAAATGTCTCAAGCGAGACAAAGT
* ** * *
4626936 TTGTTTTAAGAAAAATAA--TCTGTAGTGAAACGAAATGT
1 TTGTTTTGAGAAAAA-AATGTCTCAAGCGAGAC-AAA-GT
*
4626974 CTTGTTTTGAGAAAAAAAATGTTTCAAGCGAGACAAAGT
1 -TTGTTTTGAG-AAAAAAATGTCTCAAGCGAGACAAAGT
*
4627013 ATGTTTT-A-AAAAAAA
1 TTGTTTTGAGAAAAAAA
4627028 CAATCTTAAG
Statistics
Matches: 73, Mismatches: 12, Indels: 17
0.72 0.12 0.17
Matches are distributed among these distances:
35 7 0.10
36 9 0.12
37 9 0.12
38 19 0.26
39 13 0.18
40 8 0.11
41 8 0.11
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.31
Consensus pattern (37 bp):
TTGTTTTGAGAAAAAAATGTCTCAAGCGAGACAAAGT
Found at i:4627101 original size:153 final size:155
Alignment explanation
Indices: 4626842--4627126 Score: 364
Period size: 153 Copynumber: 1.9 Consensus size: 155
4626832 GGAAATTAGC
* * * * * *
4626842 TCAAGCGAGATAAATTTTGGTTTTAAGAAAAACAATATGGAGTGAAATGAATATTCTTGTTTTGA
1 TCAAGCGAGACAAAGTATGGTTTTAAAAAAAACAATATGAAGTGAAATGAATATTATTGTTTTGA
* * *
4626907 GTAAAAAAATGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAATAAT-CTGTAGTGAAACGAAA
66 GTAAAAAAATGTCTCAAGCGAGACAAAGTTTATTTTAAGAAAAACAATATTG-AGTGAAACGAAA
4626971 TGTCTTGTTTTGAGAAAAAAAATGTT
130 TGTCTTGTTTTGAGAAAAAAAATGTT
* * *
4626997 TCAAGCGAGACAAAGTAT-GTTTTAAAAAAAACAATCTTAAGTGAAATGAA-ATGTATTTTTTTG
1 TCAAGCGAGACAAAGTATGGTTTTAAAAAAAACAATATGAAGTGAAATGAATAT-TATTGTTTTG
* * * *
4627060 AG-CAAAAACTGTCTCAAGTGAGACAAA-TCTTATTTTAAGAAAAACAATATTGAGTGAAATGAA
65 AGTAAAAAAATGTCTCAAGCGAGACAAAGT-TTATTTTAAGAAAAACAATATTGAGTGAAACGAA
4627123 ATGT
129 ATGT
4627127 ATTCTTTCGA
Statistics
Matches: 111, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
152 1 0.01
153 55 0.50
154 40 0.36
155 15 0.14
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.31
Consensus pattern (155 bp):
TCAAGCGAGACAAAGTATGGTTTTAAAAAAAACAATATGAAGTGAAATGAATATTATTGTTTTGA
GTAAAAAAATGTCTCAAGCGAGACAAAGTTTATTTTAAGAAAAACAATATTGAGTGAAACGAAAT
GTCTTGTTTTGAGAAAAAAAATGTT
Found at i:4627181 original size:76 final size:76
Alignment explanation
Indices: 4626841--4627174 Score: 361
Period size: 77 Copynumber: 4.4 Consensus size: 76
4626831 GGGAAATTAG
* * * *
4626841 CTCAAGCGAGATAAATTTTGGTTTTAAGAAAAACAATATGGAGTGAAATGAATAT-TCTTGTTTT
1 CTCAAGCGAGACAAAGTTT-GTTTTAAGAAAAACAATATTGAGTGAAATGAA-ATGTATTGTTTT
4626905 GAGTAAAAAAATGT
64 GAGT-AAAAAATGT
* * * *
4626919 CTCAAGCGAGACAAAGTTTGTTTTAAGAAAAATAAT-CTGTAGTGAAACGAAATGTCTTGTTTTG
1 CTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATATTG-AGTGAAATGAAATGTATTGTTTTG
*
4626983 AGAAAAAAAATGT
65 AG-TAAAAAATGT
* * * * * *
4626996 TTCAAGCGAGACAAAGTATGTTTTAAAAAAAACAATCTTAAGTGAAATGAAATGTATTTTTTTGA
1 CTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATATTGAGTGAAATGAAATGTATTGTTTTGA
* *
4627061 GCAAAAACTGT
66 GTAAAAAATGT
* * * *
4627072 CTCAAGTGAGACAAA-TCTTATTTTAAGAAAAACAATATTGAGTGAAATGAAATGTATTCTTTCG
1 CTCAAGCGAGACAAAGT-TTGTTTTAAGAAAAACAATATTGAGTGAAATGAAATGTATTGTTTTG
*
4627136 AGTAAAAATTGT
65 AGTAAAAAATGT
**
4627148 CTCAAATGAGACAAA-TCTTGTTTTAAG
1 CTCAAGCGAGACAAAGT-TTGTTTTAAG
4627175 GGAAACATAT
Statistics
Matches: 220, Mismatches: 31, Indels: 12
0.84 0.12 0.05
Matches are distributed among these distances:
75 1 0.00
76 99 0.45
77 102 0.46
78 18 0.08
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.32
Consensus pattern (76 bp):
CTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATATTGAGTGAAATGAAATGTATTGTTTTGA
GTAAAAAATGT
Found at i:4627311 original size:65 final size:67
Alignment explanation
Indices: 4627145--4627303 Score: 227
Period size: 65 Copynumber: 2.4 Consensus size: 67
4627135 GAGTAAAAAT
*
4627145 TGTCTCAA-ATGAGAC-AAATCTTGTTTTAAGGGAAACATATTTAAAGATTTTGTGTTTCAAGAG
1 TGTCTCAAGA-GAGACAAAAT-TTGTTTTAAGGGAAACATATTCAAAGATTTTGTGTTTCAAGAG
4627208 AAAC
64 AAAC
* * * *
4627212 TCTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACATATTCAAAGA-TTT-TGTTTCAAGAGGA
1 TGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAACATATTCAAAGATTTTGTGTTTCAAGAGAA
4627275 AC
66 AC
4627277 TGTCTCAAGAGAGACAAAATTTGTTTT
1 TGTCTCAAGAGAGACAAAATTTGTTTT
4627304 TTTGGAAAAC
Statistics
Matches: 82, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
65 38 0.46
66 3 0.04
67 37 0.45
68 4 0.05
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (67 bp):
TGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAACATATTCAAAGATTTTGTGTTTCAAGAGAA
AC
Found at i:4627504 original size:37 final size:36
Alignment explanation
Indices: 4627462--4627796 Score: 131
Period size: 37 Copynumber: 9.6 Consensus size: 36
4627452 GGTCTGAAGG
* *
4627462 AAAATATCTCCAGTGAGACGAAATTCGTTTTGAGAGA
1 AAAATATCTCAAGTGAGACGAAATT-GTTTTAAGAGA
*
4627499 AAAATATCTCAAGTGAGATGAAATTG-TTTAAGAGA
1 AAAATATCTCAAGTGAGACGAAATTGTTTTAAGAGA
* * *
4627534 AAAATGTCTCAAATGAGACAAAATTTGTTTCTAAGA-A
1 AAAATATCTCAAGTGAGACGAAA-TTGTTT-TAAGAGA
* * ** *
4627571 AAACA-A-CT----T----TGAAATTTTTGTTCCGAAGG
1 AAA-ATATCTCAAGTGAGACGAAATTGTT-TTAAG-AGA
* *
4627600 AAAATGTCTCAAGTGAGACGAAATATGTTCTAAGAGA
1 AAAATATCTCAAGTGAGACGAAAT-TGTTTTAAGAGA
* * * *
4627637 AAAATGTCTCAAATGAGACAAAATTTGTTTTTA-AGA
1 AAAATATCTCAAGTGAGACGAAA-TTGTTTTAAGAGA
* * * ** *
4627673 AAAA-A-CT----TTA-A--AATTTGTGTTCCGAAGG
1 AAAATATCTCAAGTGAGACGAAATTGTTTTAAG-AGA
* *
4627701 AAAATGTCTCAAGTGAGACGAAATTTATTTTAAGAGA
1 AAAATATCTCAAGTGAGACGAAA-TTGTTTTAAGAGA
* *
4627738 AAAATGTCTCAAGTGAGACAAAATTTGTTTTTAAGA-A
1 AAAATATCTCAAGTGAGACGAAA-TTG-TTTTAAGAGA
* *
4627775 AACAATATCTCTAGCGAGACGA
1 AA-AATATCTCAAGTGAGACGA
4627797 TATTTTATTT
Statistics
Matches: 219, Mismatches: 46, Indels: 65
0.66 0.14 0.20
Matches are distributed among these distances:
26 6 0.03
27 8 0.04
28 12 0.05
29 4 0.02
30 6 0.03
32 1 0.00
34 5 0.02
35 28 0.13
36 13 0.06
37 90 0.41
38 43 0.20
39 3 0.01
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (36 bp):
AAAATATCTCAAGTGAGACGAAATTGTTTTAAGAGA
Found at i:4627544 original size:35 final size:37
Alignment explanation
Indices: 4627462--4627573 Score: 131
Period size: 35 Copynumber: 3.1 Consensus size: 37
4627452 GGTCTGAAGG
* *
4627462 AAAATATCTCCAGTGAGACGAAATTCGTTTTGAGAGA
1 AAAATATCTCAAGTGAGACGAAATTCGTTTTAAGAGA
*
4627499 AAAATATCTCAAGTGAGATGAAATT-G-TTTAAGAGA
1 AAAATATCTCAAGTGAGACGAAATTCGTTTTAAGAGA
* * * *
4627534 AAAATGTCTCAAATGAGACAAAATTTGTTTCTAAGA-A
1 AAAATATCTCAAGTGAGACGAAATTCGTTT-TAAGAGA
4627571 AAA
1 AAA
4627574 CAACTTTGAA
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
35 29 0.45
36 2 0.03
37 29 0.45
38 5 0.08
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.28
Consensus pattern (37 bp):
AAAATATCTCAAGTGAGACGAAATTCGTTTTAAGAGA
Found at i:4627661 original size:138 final size:137
Alignment explanation
Indices: 4627359--4627666 Score: 388
Period size: 138 Copynumber: 2.2 Consensus size: 137
4627349 CAAAATTTTG
* ** * *
4627359 GAAAAATGTCTCAAGCGAGACAATTTTTGTTTTGAGAGAAATTGTCTCAATCGAGACAAAATTTG
1 GAAAAATGTCTCAAGTGAGACAA-AATTGTTTAGAGAGAAAATGTCTCAATCGAGACAAAATTTG
* * *
4627424 GTTCAAGTAAAACAACTTTGAAATTTTTGGTCTGAAGGAAAATATCTCCAGTGAGACGAAATTCG
65 GTTCAAGAAAAACAACTTTGAAATTTTTGGTCCGAAGGAAAATATCTCAAGTGAGACGAAATTCG
* *
4627489 TTTTGAGA
130 TTCTAAGA
* **
4627497 GAAAAATATCTCAAGTGAGATGAAATTGTTTA-AGAGAAAAATGTCTCAAAT-GAGACAAAATTT
1 GAAAAATGTCTCAAGTGAGACAAAATTGTTTAGAGAG-AAAATGTCTC-AATCGAGACAAAATTT
* * *
4627560 GTTTCTAAGAAAAACAACTTTGAAATTTTTGTTCCGAAGGAAAATGTCTCAAGTGAGACGAAATA
64 GGTTC-AAGAAAAACAACTTTGAAATTTTTGGTCCGAAGGAAAATATCTCAAGTGAGACGAAAT-
4627625 T-GTTCTAAGA
127 TCGTTCTAAGA
*
4627635 GAAAAATGTCTCAAATGAGACAAAATTTGTTT
1 GAAAAATGTCTCAAGTGAGACAAAA-TTGTTT
4627667 TTAAGAAAAA
Statistics
Matches: 145, Mismatches: 20, Indels: 9
0.83 0.11 0.05
Matches are distributed among these distances:
136 4 0.03
137 31 0.21
138 103 0.71
139 7 0.05
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (137 bp):
GAAAAATGTCTCAAGTGAGACAAAATTGTTTAGAGAGAAAATGTCTCAATCGAGACAAAATTTGG
TTCAAGAAAAACAACTTTGAAATTTTTGGTCCGAAGGAAAATATCTCAAGTGAGACGAAATTCGT
TCTAAGA
Found at i:4627676 original size:103 final size:103
Alignment explanation
Indices: 4627499--4628416 Score: 742
Period size: 101 Copynumber: 8.7 Consensus size: 103
4627489 TTTTGAGAGA
* *
4627499 AAAATATCTCAAGTGAGATGAAA-TTG-TTTAAGAGAAAAATGTCTCAAATGAGACAAAATTTGT
1 AAAATGTCTCAAGTGAGACGAAATTTGTTTTAAGAGAAAAATGTCTCAAATGAGACAAAATTTGT
* *
4627562 TTCTAAGAAAAACAACTTTGAAATTTTTGTTCCGAAGG
66 TTTTAAGAAAAACAACTTTGAAATTTGTGTTCCGAAGG
* *
4627600 AAAATGTCTCAAGTGAGACGAAATATGTTCTAAGAGAAAAATGTCTCAAATGAGACAAAATTTGT
1 AAAATGTCTCAAGTGAGACGAAATTTGTTTTAAGAGAAAAATGTCTCAAATGAGACAAAATTTGT
*
4627665 TTTTAAG-AAAA-AACTTTAAAATTTGTGTTCCGAAGG
66 TTTTAAGAAAAACAACTTTGAAATTTGTGTTCCGAAGG
* *
4627701 AAAATGTCTCAAGTGAGACGAAATTTATTTTAAGAGAAAAATGTCTCAAGTGAGACAAAATTTGT
1 AAAATGTCTCAAGTGAGACGAAATTTGTTTTAAGAGAAAAATGTCTCAAATGAGACAAAATTTGT
* * * **
4627766 TTTTAAG-AAAACAATATCTCTAGCGAGACGATATTTTATTTTG-AGAG
66 TTTTAAGAAAAAC-A-A-CT-T--TGA-A--AT-TTGTGTTCCGAAG-G
*** * * * * *
4627813 AAACAACACACAAG-GAGACAAAGAGTCTATTTGTTCCTTAACGTTGAGGAAATGTTTTCAGAA-
1 AAA-ATGTCTCAAGTGAGAC---GA---AATTTGTT--TTAA-G-AGA-AAAATG-TCTCA-AAT
* * * * * *** *** * * **
4627876 GA-TC-TAA-TTGTTAGCTTCAGAAGATTTA-TTTGTTCCTTTTACATATTTCAAAATTTTTGG
52 GAGACAAAATTTGTT--TTTAAGAAAAACAACTTTG--AAATTT--GT-GTTCCGAA-----GG
* * ** * * * **
4627936 AGAATGTCTCAAGTGATACGATGTTTGTTTTGAGAG-AAATTATCTCAAGCGAGACAAAATTTG-
1 AAAATGTCTCAAGTGAGACGAAATTTGTTTTAAGAGAAAAATGTCTCAAATGAGACAAAATTTGT
* * *
4627999 GTTCAAGTAAAACAACTTTGAAATTTGTGTTCCGAAGG
66 TTTTAAGAAAAACAACTTTGAAATTTGTGTTCCGAAGG
* * * * * * *
4628037 AAAATATCTCCAGTGAGACGAAATTCGTTTTGAA-AGAAAAATATCTCAAGTGAG---AATTTTT
1 AAAATGTCTCAAGTGAGACGAAATTTGTTTT-AAGAGAAAAATGTCTCAAATGAGACAAAATTTG
4628098 TTTTTAAGAAAAACAACTTTGAAATTTGTGTTCCGAAGG
65 TTTTTAAGAAAAACAACTTTGAAATTTGTGTTCCGAAGG
* * * *
4628137 AAAATATATCAAGTGAGACAAAATTTGTTTTAAGAGAAAAATGTCTCAAATGAAACAAAATTTGT
1 AAAATGTCTCAAGTGAGACGAAATTTGTTTTAAGAGAAAAATGTCTCAAATGAGACAAAATTTGT
* * *
4628202 TTCTAAGAAAAATAACTTTGAAATTTGTGTTCTGAAGG
66 TTTTAAGAAAAACAACTTTGAAATTTGTGTTCCGAAGG
* *
4628240 AAAATGTCTCAAGTGAGACGAAATTTGATTTAAGAGAAAAATGTCTCAAATGAAACAAAATTTGT
1 AAAATGTCTCAAGTGAGACGAAATTTGTTTTAAGAGAAAAATGTCTCAAATGAGACAAAATTTGT
4628305 TTTTAAG-AAAA-AACTTTGAAATTTGTGTTCCGAAGG
66 TTTTAAGAAAAACAACTTTGAAATTTGTGTTCCGAAGG
* * *
4628341 AAAATGTCTCAAGTGAGATGAAATTTGTTTTAAGAGAAAAATGTCTCAAGTGAGACAAATTTTGT
1 AAAATGTCTCAAGTGAGACGAAATTTGTTTTAAGAGAAAAATGTCTCAAATGAGACAAAATTTGT
4628406 TTTTAAGAAAA
66 TTTTAAGAAAA
4628417 CAATATCTCT
Statistics
Matches: 647, Mismatches: 114, Indels: 111
0.74 0.13 0.13
Matches are distributed among these distances:
99 7 0.01
100 79 0.12
101 235 0.36
102 29 0.04
103 151 0.23
104 1 0.00
105 2 0.00
106 6 0.01
107 1 0.00
108 1 0.00
109 5 0.01
110 12 0.02
111 12 0.02
112 17 0.03
113 10 0.02
114 1 0.00
115 7 0.01
116 1 0.00
117 9 0.01
118 8 0.01
119 2 0.00
120 7 0.01
121 6 0.01
122 11 0.02
123 17 0.03
124 9 0.01
125 1 0.00
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (103 bp):
AAAATGTCTCAAGTGAGACGAAATTTGTTTTAAGAGAAAAATGTCTCAAATGAGACAAAATTTGT
TTTTAAGAAAAACAACTTTGAAATTTGTGTTCCGAAGG
Found at i:4627794 original size:38 final size:37
Alignment explanation
Indices: 4627701--4627815 Score: 106
Period size: 38 Copynumber: 3.1 Consensus size: 37
4627691 GTTCCGAAGG
* * *
4627701 AAAATGTCTCAAGTGAGACGAAATTTATTTTAAGAGA
1 AAAATATCTCAAGCGAGACAAAATTTATTTTAAGAGA
* * *
4627738 AAAATGTCTCAAGTGAGACAAAATTTGTTTTTAAGA-A
1 AAAATATCTCAAGCGAGACAAAATTT-ATTTTAAGAGA
* * * *
4627775 AACAATATCTCTAGCGAGACGATATTTTATTTTGAGAGA
1 AA-AATATCTCAAGCGAGAC-AAAATTTATTTTAAGAGA
4627814 AA
1 AA
4627816 CAACACACAA
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
37 28 0.43
38 29 0.45
39 8 0.12
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (37 bp):
AAAATATCTCAAGCGAGACAAAATTTATTTTAAGAGA
Found at i:4628195 original size:37 final size:37
Alignment explanation
Indices: 4628145--4628317 Score: 129
Period size: 37 Copynumber: 4.9 Consensus size: 37
4628135 GGAAAATATA
* *
4628145 TCAAGTGAGACAAAATTTGTTTTAAGAGAAAAATGTC
1 TCAAATGAAACAAAATTTGTTTTAAGAGAAAAATGTC
**
4628182 TCAAATGAAACAAAATTTGTTTCT-A-AGAAAAATAAC
1 TCAAATGAAACAAAATTTGTTT-TAAGAGAAAAATGTC
*
4628218 T---TTG-----AAATTTGTGTTCTGAAG-G-AAAATGTC
1 TCAAATGAAACAAAATTTGT-TT-T-AAGAGAAAAATGTC
* * * *
4628248 TCAAGTGAGACGAAATTTGATTTAAGAGAAAAATGTC
1 TCAAATGAAACAAAATTTGTTTTAAGAGAAAAATGTC
4628285 TCAAATGAAACAAAATTTGTTTTTAAGA-AAAAA
1 TCAAATGAAACAAAATTTG-TTTTAAGAGAAAAA
4628318 CTTTGAAATT
Statistics
Matches: 107, Mismatches: 13, Indels: 32
0.70 0.09 0.21
Matches are distributed among these distances:
28 8 0.07
29 4 0.04
30 7 0.07
31 2 0.02
33 4 0.04
35 3 0.03
36 12 0.11
37 52 0.49
38 15 0.14
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.31
Consensus pattern (37 bp):
TCAAATGAAACAAAATTTGTTTTAAGAGAAAAATGTC
Found at i:4628329 original size:63 final size:64
Alignment explanation
Indices: 4628259--4628381 Score: 144
Period size: 64 Copynumber: 1.9 Consensus size: 64
4628249 CAAGTGAGAC
4628259 GAAATTTGAT-TTAAG-AGAAAAATGTCTCAAATGAAACAAAATTTGTTTTTAAGA-AAAAACTT
1 GAAATTTG-TGTTAAGAAGAAAAATGTCTCAAATGAAACAAAATTTG-TTTTAAGAGAAAAACTT
4628321 T
64 T
** * * * **
4628322 GAAATTTGTGTTCCGAAGGAAAATGTCTCAAGTGAGATGAAATTTGTTTTAAGAGAAAAA
1 GAAATTTGTGTTAAGAAGAAAAATGTCTCAAATGAAACAAAATTTGTTTTAAGAGAAAAA
4628382 TGTCTCAAGT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
62 1 0.02
63 19 0.38
64 30 0.60
ACGTcount: A:0.44, C:0.07, G:0.18, T:0.32
Consensus pattern (64 bp):
GAAATTTGTGTTAAGAAGAAAAATGTCTCAAATGAAACAAAATTTGTTTTAAGAGAAAAACTTT
Found at i:4628401 original size:36 final size:39
Alignment explanation
Indices: 4628341--4628413 Score: 116
Period size: 37 Copynumber: 1.9 Consensus size: 39
4628331 GTTCCGAAGG
*
4628341 AAAATGTCTCAAGTGAGATGAAA-TTTG-TTTTAAGAGA
1 AAAATGTCTCAAGTGAGATCAAATTTTGTTTTTAAGAGA
4628378 AAAATGTCTCAAGTGAGA-CAAATTTTGTTTTTAAGA
1 AAAATGTCTCAAGTGAGATCAAATTTTGTTTTTAAGA
4628414 AAACAATATC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
36 3 0.09
37 22 0.67
38 8 0.24
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.34
Consensus pattern (39 bp):
AAAATGTCTCAAGTGAGATCAAATTTTGTTTTTAAGAGA
Found at i:4628434 original size:38 final size:39
Alignment explanation
Indices: 4628347--4628460 Score: 119
Period size: 38 Copynumber: 3.0 Consensus size: 39
4628337 AAGGAAAATG
* * *
4628347 TCTCAAGTGAGATGAAA-TTTGTTTTAAGAGAAA-AATG
1 TCTCAAGCGAGACGAAATTTTGTTTTAAGAGAAACAATA
*
4628384 TCTCAAGTGAGAC-AAATTTTGTTTTTAAGA-AAACAATA
1 TCTCAAGCGAGACGAAATTTTG-TTTTAAGAGAAACAATA
* * * *
4628422 TCTCTAGCGAGACGATATTTTATTTTGAGAGAAACAATA
1 TCTCAAGCGAGACGAAATTTTGTTTTAAGAGAAACAATA
4628461 CCCAAGGAGA
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
36 3 0.05
37 19 0.29
38 29 0.45
39 14 0.22
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (39 bp):
TCTCAAGCGAGACGAAATTTTGTTTTAAGAGAAACAATA
Found at i:4629833 original size:2 final size:2
Alignment explanation
Indices: 4629826--4629856 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4629816 TATGTATGTG
4629826 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4629857 TCTGGGTATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4633713 original size:2 final size:2
Alignment explanation
Indices: 4633706--4633735 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4633696 TGAAATATGC
4633706 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
4633736 GAGACTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4635218 original size:3 final size:3
Alignment explanation
Indices: 4635204--4635237 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
4635194 ATGTAAAATG
*
4635204 TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
4635238 TTTGTAGACC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:4639123 original size:41 final size:41
Alignment explanation
Indices: 4639066--4639144 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
4639056 TTATATAGAC
*
4639066 ATATTGGAGTATTTTGGTTATGTTTCTTGACAATGTGATGA
1 ATATTGAAGTATTTTGGTTATGTTTCTTGACAATGTGATGA
4639107 ATATTGAAGTATTTTGGTTATGTTTCTTGACAATGTGA
1 ATATTGAAGTATTTTGGTTATGTTTCTTGACAATGTGA
4639145 GATAAAAGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.25, C:0.05, G:0.23, T:0.47
Consensus pattern (41 bp):
ATATTGAAGTATTTTGGTTATGTTTCTTGACAATGTGATGA
Found at i:4640843 original size:31 final size:31
Alignment explanation
Indices: 4640773--4640843 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
4640763 AGAGGTGAGC
* * * *
4640773 AAAATTTAACTCGACTCGATTTAAAAAATCT
1 AAAATTTTACTCGAATCGACTTAAAAAATCA
** *
4640804 AATTTTTTACTCGAATCGACTTGAAAAATCA
1 AAAATTTTACTCGAATCGACTTAAAAAATCA
4640835 AAAATTTTA
1 AAAATTTTA
4640844 AATTGATTCG
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (31 bp):
AAAATTTTACTCGAATCGACTTAAAAAATCA
Found at i:4641827 original size:31 final size:31
Alignment explanation
Indices: 4641773--4641831 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
4641763 AGTTTTAGTC
*
4641773 ACTTACGTTATTATTTGAGTAAGTTTTGATT
1 ACTTACGTTATCATTTGAGTAAGTTTTGATT
* * *
4641804 ACTTACGTTATCGTTTTATTAAGTTTTG
1 ACTTACGTTATCATTTGAGTAAGTTTTG
4641832 GTCACGTGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.24, C:0.08, G:0.15, T:0.53
Consensus pattern (31 bp):
ACTTACGTTATCATTTGAGTAAGTTTTGATT
Found at i:4641977 original size:14 final size:13
Alignment explanation
Indices: 4641921--4641978 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
4641911 ATTAAAAAAC
4641921 TAAAA-TATTTT-
1 TAAAATTATTTTA
4641932 TAAAATTATATTTA
1 TAAAATTAT-TTTA
* * *
4641946 TAAAACTAATATA
1 TAAAATTATTTTA
4641959 TAAAATTATTTTAA
1 TAAAATTATTTT-A
4641973 TAAAAT
1 TAAAAT
4641979 ATACTATTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
11 5 0.14
12 3 0.08
13 15 0.41
14 14 0.38
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (13 bp):
TAAAATTATTTTA
Found at i:4642026 original size:27 final size:27
Alignment explanation
Indices: 4641921--4642042 Score: 83
Period size: 27 Copynumber: 4.4 Consensus size: 27
4641911 ATTAAAAAAC
*
4641921 TAAAAT-ATTTTTAAAATTA-TATTTA
1 TAAAATAATATTTAAAATTATTATTTA
* *
4641946 TAAAACTAATATATAAAATTATT-TTAA
1 TAAAA-TAATATTTAAAATTATTATTTA
*
4641973 TAAAATATACTATTT-TAATATATTTATTTA
1 TAAAATA-A-TATTTAAAAT-TA-TTATTTA
* *
4642003 TAAAA-AATACTTTAATATTATTATTAA
1 TAAAATAATA-TTTAAAATTATTATTTA
*
4642030 CATAAATAATATT
1 TA-AAATAATATT
4642043 AATTAAATTA
Statistics
Matches: 75, Mismatches: 10, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
25 5 0.07
26 3 0.04
27 32 0.43
28 18 0.24
29 9 0.12
30 8 0.11
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (27 bp):
TAAAATAATATTTAAAATTATTATTTA
Found at i:4642080 original size:19 final size:19
Alignment explanation
Indices: 4642062--4642097 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
4642052 ATTGGAATAT
4642062 TTAAATAATATT-TTTATA
1 TTAAATAATATTATTTATA
*
4642080 TTGAATAATATTATTTAT
1 TTAAATAATATTATTTAT
4642098 TATATTTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
TTAAATAATATTATTTATA
Found at i:4642112 original size:23 final size:22
Alignment explanation
Indices: 4642065--4642119 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
4642055 GGAATATTTA
4642065 AATAATATTT-TTATATTGAAT
1 AATAATATTTATTATATTGAAT
*
4642086 AATATTATTTATTATATTTG-AT
1 AATAATATTTATTATA-TTGAAT
4642108 GAATAATATTTA
1 -AATAATATTTA
4642120 AAAAAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 9 0.31
22 7 0.24
23 13 0.45
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (22 bp):
AATAATATTTATTATATTGAAT
Found at i:4646485 original size:18 final size:18
Alignment explanation
Indices: 4646462--4646499 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
4646452 GTGATATTCG
*
4646462 AATATTTGAATAGAATAT
1 AATATTTAAATAGAATAT
*
4646480 AATATTTAAATCGAATAT
1 AATATTTAAATAGAATAT
4646498 AA
1 AA
4646500 AATCTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.37
Consensus pattern (18 bp):
AATATTTAAATAGAATAT
Found at i:4646719 original size:2 final size:2
Alignment explanation
Indices: 4646712--4646741 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4646702 ATAGCCAATT
4646712 TA 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 TA
4646742 GATGCTAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4646802 original size:13 final size:13
Alignment explanation
Indices: 4646784--4646808 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4646774 CATTAGTCCA
4646784 CATAATCAATATT
1 CATAATCAATATT
4646797 CATAATCAATAT
1 CATAATCAATAT
4646809 GCCATAGGAA
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:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
CATAATCAATATT
Found at i:4647806 original size:36 final size:37
Alignment explanation
Indices: 4647735--4647819 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 37
4647725 ATCCCATTAT
*
4647735 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
* *
4647771 TATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
4647807 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
4647820 TTGGTTACCA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 13 0.30
37 30 0.70
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.33
Consensus pattern (37 bp):
CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
Found at i:4651660 original size:3 final size:3
Alignment explanation
Indices: 4651654--4651714 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
4651644 TTATATAATA
* * * * *
4651654 ATT ATT ATT ATT ATA ATT ATA ATT ATA ATT ATA ATT ATA ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
4651702 AAT ATAT ATT ATT
1 ATT AT-T ATT ATT
4651715 TAATATTACA
Statistics
Matches: 45, Mismatches: 12, Indels: 2
0.76 0.20 0.03
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:4651665 original size:6 final size:6
Alignment explanation
Indices: 4651647--4651702 Score: 76
Period size: 6 Copynumber: 9.3 Consensus size: 6
4651637 ATGTTATTTA
* * *
4651647 TATAAT AATTAT TATTAT TATAAT TATAAT TATAAT TATAAT TATAAT
1 TATAAT TATAAT TATAAT TATAAT TATAAT TATAAT TATAAT TATAAT
*
4651695 TATTAT TA
1 TATAAT TA
4651703 ATATATATTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TATAAT
Done.