Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007768.1 Hibiscus syriacus cultivar Beakdansim tig00110044_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: 2539099
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 11
Found at i:2363516 original size:31 final size:30
Alignment explanation
Indices: 2363463--2363523 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
2363453 GTAAGTCACA
*
2363463 TTTGATTTTTATATTAAGTATAAATAGTTT
1 TTTGATTTGTATATTAAGTATAAATAGTTT
* * *
2363493 TTTGAATTTGTATTTTAATTATAAATTGTTT
1 TTTG-ATTTGTATATTAAGTATAAATAGTTT
2363524 ATGACTTTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (30 bp):
TTTGATTTGTATATTAAGTATAAATAGTTT
Found at i:2369673 original size:19 final size:19
Alignment explanation
Indices: 2369651--2369695 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
2369641 TTATGCATCA
2369651 ATGCACTCTTTGTGCACCG
1 ATGCACTCTTTGTGCACCG
2369670 ATGCACTCTTTGTGCACCG
1 ATGCACTCTTTGTGCACCG
2369689 ATGCACT
1 ATGCACT
2369696 AAGGGTCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.18, C:0.31, G:0.20, T:0.31
Consensus pattern (19 bp):
ATGCACTCTTTGTGCACCG
Found at i:2373113 original size:20 final size:20
Alignment explanation
Indices: 2373088--2373128 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2373078 CGTTAGACAT
2373088 GGGGGAATCGGTACCCACTG
1 GGGGGAATCGGTACCCACTG
* *
2373108 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCGGTACCCACTG
2373128 G
1 G
2373129 ACATTCTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.27, G:0.39, T:0.17
Consensus pattern (20 bp):
GGGGGAATCGGTACCCACTG
Found at i:2376397 original size:20 final size:20
Alignment explanation
Indices: 2376372--2376418 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
2376362 AATCGTATAT
2376372 AGCCGTTGGGGATGTTTTGG
1 AGCCGTTGGGGATGTTTTGG
2376392 AGCCGTTGGGGATGTTTTGG
1 AGCCGTTGGGGATGTTTTGG
2376412 AGCCGTT
1 AGCCGTT
2376419 TGGAGATGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.11, C:0.13, G:0.43, T:0.34
Consensus pattern (20 bp):
AGCCGTTGGGGATGTTTTGG
Found at i:2376541 original size:20 final size:20
Alignment explanation
Indices: 2376504--2376542 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2376494 CCGTTAGATA
* *
2376504 GGGGGAATCGGTATCCCCTG
1 GGGGGAATCGATACCCCCTG
*
2376524 GGGGGAATCTATACCCCCT
1 GGGGGAATCGATACCCCCT
2376543 TGACATTCTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.28, G:0.33, T:0.21
Consensus pattern (20 bp):
GGGGGAATCGATACCCCCTG
Found at i:2379817 original size:31 final size:31
Alignment explanation
Indices: 2379781--2379839 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2379771 AACTTAAAAG
* *
2379781 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
2379812 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
2379840 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:2379890 original size:22 final size:22
Alignment explanation
Indices: 2379864--2379906 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2379854 TAATAAATTA
2379864 TTTAAAATAAATCAACCCATAT
1 TTTAAAATAAATCAACCCATAT
*
2379886 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAACCCATA
2379907 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (22 bp):
TTTAAAATAAATCAACCCATAT
Found at i:2379915 original size:22 final size:22
Alignment explanation
Indices: 2379866--2379914 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2379856 ATAAATTATT
**
2379866 TAAAATAAATCAACCCATATTT
1 TAAAATAAATCAACCCATATAA
*
2379888 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAACCCATA-TAA
2379911 TAAA
1 TAAA
2379915 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAATAAATCAACCCATATAA
Found at i:2379953 original size:26 final size:26
Alignment explanation
Indices: 2379923--2380044 Score: 83
Period size: 26 Copynumber: 4.6 Consensus size: 26
2379913 AATTATTTAA
2379923 AATAAATCAATCCATACAACTACAAT
1 AATAAATCAATCCATACAACTACAAT
* * **
2379949 AATAAATCAAACCAT---ATTTTAA-
1 AATAAATCAATCCATACAACTACAAT
* *
2379971 AATAAATCAATTCATACTAA-TAAATTATTT
1 AATAAATCAATCCATAC-AACTACA--A--T
*
2380001 AAAATAAATCAATCTATACAACTACAAT
1 --AATAAATCAATCCATACAACTACAAT
2380029 AATAAATCAATCCATA
1 AATAAATCAATCCATA
2380045 TTTTAAAATA
Statistics
Matches: 72, Mismatches: 12, Indels: 24
0.67 0.11 0.22
Matches are distributed among these distances:
22 13 0.18
23 4 0.06
25 2 0.03
26 30 0.42
27 1 0.01
28 1 0.01
30 1 0.01
31 2 0.03
32 18 0.25
ACGTcount: A:0.54, C:0.16, G:0.00, T:0.30
Consensus pattern (26 bp):
AATAAATCAATCCATACAACTACAAT
Found at i:2379964 original size:80 final size:80
Alignment explanation
Indices: 2379869--2380096 Score: 397
Period size: 80 Copynumber: 2.9 Consensus size: 80
2379859 AATTATTTAA
*
2379869 AATAAATCAACCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAAACCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
2379934 CCATACAACTACAAT
66 CCATACAACTACAAT
*
2379949 AATAAATCAAACCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAAACCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
*
2380014 CTATACAACTACAAT
66 CCATACAACTACAAT
* *
2380029 AATAAATCAATCCATATTTTAAAATAAATCAATCCGTACTAAT-AATTATTTAAAAT-AATCAAT
1 AATAAATCAAACCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
2380092 CCATA
66 CCATA
2380097 TTTTAAAATA
Statistics
Matches: 141, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
78 11 0.08
79 13 0.09
80 117 0.83
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.32
Consensus pattern (80 bp):
AATAAATCAAACCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAAT
Found at i:2380101 original size:52 final size:54
Alignment explanation
Indices: 2379854--2380207 Score: 349
Period size: 52 Copynumber: 6.6 Consensus size: 54
2379844 ACAACTACAA
*
2379854 TAATAAATTATTTAAAATAAATCAACCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*** * * *
2379908 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT-AATAAAT-CAAAC
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCCATAC
* * ** * *
2379961 -CAT--A-T-TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAA--A--T-AAATCAATCCATAC
* * *
2380015 T-ATACAACTA--CAATAATAAATCAATCCATATTTTAAAATAAATCAATCCGTAC
1 TAATA-AATTATTTAA-AATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
2380068 TAAT-AATTATTTAAAAT-AATCAATCCATATTTTAAAATAAATC-ATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
2380119 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAAT--A--AATCAATCCATAC
2380177 TAATAAATTATTTAAAATAAATCAATCCATA
1 TAATAAATTATTTAAAATAAATCAATCCATA
2380208 CAACTACAAT
Statistics
Matches: 250, Mismatches: 24, Indels: 48
0.78 0.07 0.15
Matches are distributed among these distances:
48 25 0.10
49 1 0.00
50 2 0.01
51 11 0.04
52 55 0.22
53 31 0.12
54 50 0.20
55 8 0.03
57 12 0.05
58 55 0.22
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:2380102 original size:21 final size:21
Alignment explanation
Indices: 2380077--2380117 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2380067 CTAATAATTA
2380077 TTTAAAAT-AATCAATCCATAT
1 TTTAAAATAAATC-ATCCATAT
2380098 TTTAAAATAAATCATCCATA
1 TTTAAAATAAATCATCCATA
2380118 CTAATAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.37
Consensus pattern (21 bp):
TTTAAAATAAATCATCCATAT
Found at i:2380125 original size:22 final size:21
Alignment explanation
Indices: 2380079--2380125 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
2380069 AATAATTATT
**
2380079 TAAAATAATCAATCCATATTT
1 TAAAATAATCAATCCATATAA
2380100 TAAAATAAATC-ATCCATACTAA
1 TAAAAT-AATCAATCCATA-TAA
2380122 TAAA
1 TAAA
2380126 TTATTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (21 bp):
TAAAATAATCAATCCATATAA
Found at i:2380196 original size:189 final size:189
Alignment explanation
Indices: 2379949--2380385 Score: 708
Period size: 189 Copynumber: 2.3 Consensus size: 189
2379939 CAACTACAAT
*
2379949 AATAAATCAAACCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
* *
2380014 CTATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCGTACTAAT-AATTAT
66 CCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
2380078 TTAAAAT-AATCAATCCATATTTTAAAATAAATC-ATCCATACTAATAAATTA-TTTAA
131 TTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTTAA
2380134 AATAAATCAATCCATATTTTAAAATAAATCAATCAATCCATACTAATAAATTATTTAAAATAAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAAT---T-CATACTAATAAATTATTTAAAATAAAT
*
2380199 CAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCATTCCATACTAATAAA
62 CAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAA
2380264 TTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTTAA
127 TTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTTAA
* * * *
2380327 AATAAATCAATCTATATTTTATAATAAAT-TATT-TTA-TAATAAATTATTTTAAAATAAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTA-TTTAAAATAAAT
2380386 AACCTTATTA
Statistics
Matches: 235, Mismatches: 8, Indels: 16
0.91 0.03 0.06
Matches are distributed among these distances:
185 32 0.14
186 10 0.04
187 14 0.06
188 1 0.00
189 87 0.37
190 13 0.06
191 26 0.11
192 20 0.09
193 32 0.14
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (189 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
TTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTTAA
Found at i:2380226 original size:58 final size:56
Alignment explanation
Indices: 2379854--2380233 Score: 278
Period size: 58 Copynumber: 7.0 Consensus size: 56
2379844 ACAACTACAA
* **
2379854 TAATAAATTATTTAAAATAAATCAACCCAT-ATTTTAA-AATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATAATTAAAATAATAAATCAATCCATAC
* * *
2379908 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAAACCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT--AATTAAAATAATAAATCAATCCATAC
** * ** * ** ** * * *
2379965 TTTTAAAATAAAT-CAATTCATACTAATAAATTATT-TAA-AATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAATTAAAATAATAAATCAATCCATAC
* ** *
2380020 -AACTACA--A--T--AATAAATCAATCCAT-ATTTTAA-AATAAATCAATCCGTAC
1 TAA-TAAATTATTTAAAATAAATCAATCCATAATTAAAATAATAAATCAATCCATAC
**
2380068 TAAT-AATTATTTAAAAT-AATCAATCCAT-ATTTTAA-AATAAATC-ATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATAATTAAAATAATAAATCAATCCATAC
* *
2380119 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATA-ATTAAAAT-AATAAATCAATCCATAC
* *
2380177 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATA
1 TAATAAATTATTTAAAATAAATCAATCCAT--AATTAAAATAATAAATCAATCCATA
2380234 TTTTAAAATA
Statistics
Matches: 262, Mismatches: 39, Indels: 46
0.76 0.11 0.13
Matches are distributed among these distances:
47 4 0.02
48 24 0.09
49 4 0.02
50 5 0.02
51 13 0.05
52 39 0.15
53 15 0.06
54 43 0.16
55 9 0.03
56 7 0.03
57 20 0.08
58 73 0.28
59 5 0.02
60 1 0.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (56 bp):
TAATAAATTATTTAAAATAAATCAATCCATAATTAAAATAATAAATCAATCCATAC
Found at i:2380275 original size:80 final size:82
Alignment explanation
Indices: 2380134--2380287 Score: 276
Period size: 80 Copynumber: 1.9 Consensus size: 82
2380124 AATTATTTAA
2380134 AATAAATCAATCCATATTTTAAAATAAATCAATCAATCCATACTAATAAATTATTTAAAATAAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAAT--ATCCATACTAATAAATTATTTAAAATAAAT
2380199 CAATCCATACAACTACAAT
64 CAATCCATACAACTACAAT
2380218 AATAAATCAATCCATATTTTAAAATAAATC-AT-TCCATACTAATAAATTATTTAAAATAAATCA
1 AATAAATCAATCCATATTTTAAAATAAATCAATATCCATACTAATAAATTATTTAAAATAAATCA
2380281 ATCCATA
66 ATCCATA
2380288 TTTTAAAATA
Statistics
Matches: 70, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
80 38 0.54
83 2 0.03
84 30 0.43
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (82 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATATCCATACTAATAAATTATTTAAAATAAATCA
ATCCATACAACTACAAT
Found at i:2380283 original size:54 final size:55
Alignment explanation
Indices: 2380218--2380385 Score: 263
Period size: 54 Copynumber: 3.1 Consensus size: 55
2380208 CAACTACAAT
2380218 AATAAATCAATCCATATTTTAAAATAAATCATTCCATACTAATAAATTA-TTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCATTCCATACTAATAAATTATTTTAA
*
2380272 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCATTCCATACTAATAAATTATTTTAA
* * * *
2380327 AATAAATCAATCTATATTTTATAATAAATTATT--TTA-TAATAAATTATTTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCATTCCATACTAATAAATTATTTTAA
2380379 AATAAAT
1 AATAAAT
2380386 AACCTTATTA
Statistics
Matches: 107, Mismatches: 6, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
52 23 0.21
53 2 0.02
54 48 0.45
55 34 0.32
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.40
Consensus pattern (55 bp):
AATAAATCAATCCATATTTTAAAATAAATCATTCCATACTAATAAATTATTTTAA
Found at i:2380293 original size:22 final size:22
Alignment explanation
Indices: 2380267--2380309 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2380257 TAATAAATTA
2380267 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
2380289 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
2380310 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:2380318 original size:22 final size:22
Alignment explanation
Indices: 2380269--2380317 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2380259 ATAAATTATT
**
2380269 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
2380291 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
2380314 TAAA
1 TAAA
2380318 TTATTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:2380325 original size:33 final size:34
Alignment explanation
Indices: 2380286--2380370 Score: 109
Period size: 33 Copynumber: 2.4 Consensus size: 34
2380276 AATCAATCCA
*
2380286 TATTTTAAAATAAATCAATCCATA-CTAATAAAT
1 TATTTTAAAATAAATCAATCCATATATAATAAAT
*
2380319 TATTTTAAAATAAATCAATCTATATTTTATAATAAAT
1 TATTTTAAAATAAATCAATCCATA---TATAATAAAT
*
2380356 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
2380371 TATTTTAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
33 23 0.51
37 22 0.49
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (34 bp):
TATTTTAAAATAAATCAATCCATATATAATAAAT
Found at i:2380332 original size:15 final size:15
Alignment explanation
Indices: 2380312--2380385 Score: 67
Period size: 15 Copynumber: 4.5 Consensus size: 15
2380302 AATCCATACT
2380312 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
2380327 AATAAATCAATCTATATTTTAT
1 AAT--A--AAT-TAT--TTTAA
*
2380349 AATAAATTATTTTAT
1 AATAAATTATTTTAA
2380364 AATAAATTATTTTAA
1 AATAAATTATTTTAA
2380379 AATAAAT
1 AATAAAT
2380386 AACCTTATTA
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
15 29 0.58
17 4 0.08
18 3 0.06
19 3 0.06
20 4 0.08
22 7 0.14
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:2380989 original size:23 final size:22
Alignment explanation
Indices: 2380912--2380989 Score: 68
Period size: 21 Copynumber: 3.5 Consensus size: 22
2380902 ACACTTAACA
**
2380912 GTGCATCGATGTATCCCTTTGAAT
1 GTGCATCGATACAT-CC-TTGAAT
* *
2380936 GTGCATCGATACA-CCATGAAG
1 GTGCATCGATACATCCTTGAAT
* *
2380957 GTGTACCGATACATGCCTTGAAT
1 GTGCATCGATACAT-CCTTGAAT
2380980 GTGCATCGAT
1 GTGCATCGAT
2380990 GCACACTACC
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
21 15 0.36
22 2 0.05
23 14 0.33
24 11 0.26
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (22 bp):
GTGCATCGATACATCCTTGAAT
Found at i:2383726 original size:63 final size:65
Alignment explanation
Indices: 2383575--2383732 Score: 180
Period size: 65 Copynumber: 2.5 Consensus size: 65
2383565 GAATAAATTG
* * * *
2383575 AACATCGAATGCATTTCATGCATCGATACACATACTATGCATTGATGCACTCAGAGTTTTATGAA
1 AACATCGAATGCATTTCATGCATCGATGCAAATACTATGCATCGATGCACTCAGACTTTTATGAA
* * * *
2383640 AACATTGAATGCATTTGATGCATCGATGCAAAGT-C-ATGCATCGATGTACTCAGTCTATTT-TG
1 AACATCGAATGCATTTCATGCATCGATGCAAA-TACTATGCATCGATGCACTCAGACT-TTTATG
2383702 -A
64 AA
* *
2383703 AATATCGAATGCATTTTATGCATCGATGCA
1 AACATCGAATGCATTTCATGCATCGATGCA
2383733 CTCTTCGTGC
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
63 28 0.35
64 19 0.24
65 32 0.40
66 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCAAATACTATGCATCGATGCACTCAGACTTTTATGAA
Found at i:2386263 original size:29 final size:30
Alignment explanation
Indices: 2386173--2386255 Score: 116
Period size: 30 Copynumber: 2.8 Consensus size: 30
2386163 AATAAAAATA
* *
2386173 TGTCAAATTTTGAAATCATGCACTATTCGG
1 TGTCAAACTTTGAAATCATGCACCATTCGG
*
2386203 TG-CTAAACTTTGAAACCATGCACCATTCGG
1 TGTC-AAACTTTGAAATCATGCACCATTCGG
2386233 TGTCAAACTTTG-AATCATGCACC
1 TGTCAAACTTTGAAATCATGCACC
2386256 GAACGGTGCA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
29 11 0.23
30 35 0.74
31 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (30 bp):
TGTCAAACTTTGAAATCATGCACCATTCGG
Found at i:2389193 original size:23 final size:23
Alignment explanation
Indices: 2389142--2389187 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
2389132 ATTATTTTAC
2389142 AAAAA-AAT-AATTTTATAAATT
1 AAAAATAATGAATTTTATAAATT
2389163 AAAAATAATGAATTTTATAATATT
1 AAAAATAATGAATTTTATAA-ATT
2389187 A
1 A
2389188 TTATAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.23
22 3 0.14
23 10 0.45
24 4 0.18
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
AAAAATAATGAATTTTATAAATT
Found at i:2392690 original size:21 final size:20
Alignment explanation
Indices: 2392604--2392760 Score: 93
Period size: 20 Copynumber: 7.8 Consensus size: 20
2392594 AAATGACCAA
**
2392604 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
2392623 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
2392643 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
2392663 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
2392684 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
2392704 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
2392724 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
2392745 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
2392761 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 9
0.73 0.20 0.06
Matches are distributed among these distances:
19 16 0.15
20 56 0.54
21 32 0.31
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:2392713 original size:41 final size:41
Alignment explanation
Indices: 2392604--2392760 Score: 126
Period size: 41 Copynumber: 3.9 Consensus size: 41
2392594 AAATGACCAA
* **
2392604 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGA-TCCC
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
* ** * *
2392643 CAGAATCGCAAATC-AGTTTCCAAAATCGCAACGCGATTCTT-
1 CAAAATCGCAACGCGAATAT-CAAAATCGCAACGCGATT-TTC
* * * **
2392684 GAAAATCGCAATGCG-ATAGTCAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGAATA-TCAAAATCGCAACGCGATTTTC
*
2392725 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGA
2392761 ACACATAAAT
Statistics
Matches: 87, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
38 1 0.01
39 12 0.14
40 17 0.20
41 53 0.61
42 4 0.05
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (41 bp):
CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
Found at i:2392789 original size:20 final size:20
Alignment explanation
Indices: 2392727--2392936 Score: 188
Period size: 20 Copynumber: 10.5 Consensus size: 20
2392717 CGATTTTCCA
** *
2392727 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
2392747 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
* *
2392767 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATCCGT
* * **
2392787 AAATCGCAACACGTATGGGT
1 AAATCGCAACGCGAATCCGT
**
2392807 AAATCGCAACGCGTTTCCGT
1 AAATCGCAACGCGAATCCGT
* * *
2392827 ATATCGCAACGCGTATTCGT
1 AAATCGCAACGCGAATCCGT
**
2392847 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
2392867 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
2392887 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
2392907 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
2392927 AAATCACAAC
1 AAATCGCAAC
2392937 ACTGAAATTT
Statistics
Matches: 158, Mismatches: 30, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
20 157 0.99
21 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:2393044 original size:22 final size:22
Alignment explanation
Indices: 2393019--2393088 Score: 99
Period size: 22 Copynumber: 3.3 Consensus size: 22
2393009 TATCACTCTC
2393019 TCCGGCGACATCCGTTCCTATA
1 TCCGGCGACATCCGTTCCTATA
2393041 TCCGGCGACATCCGTTCCTATA
1 TCCGGCGACATCCGTTCCTATA
** *
2393063 TCCAACGACATCC-TTCCCA-A
1 TCCGGCGACATCCGTTCCTATA
2393083 TCCGGC
1 TCCGGC
2393089 AACAGGTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
20 5 0.12
21 5 0.12
22 33 0.77
ACGTcount: A:0.20, C:0.40, G:0.16, T:0.24
Consensus pattern (22 bp):
TCCGGCGACATCCGTTCCTATA
Found at i:2393680 original size:24 final size:24
Alignment explanation
Indices: 2393641--2393687 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2393631 AAATTTGGTC
2393641 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
2393665 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
2393688 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:2393879 original size:12 final size:12
Alignment explanation
Indices: 2393862--2393886 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2393852 ATATAATCCT
2393862 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2393874 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2393886 G
1 G
2393887 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2396212 original size:33 final size:33
Alignment explanation
Indices: 2396166--2396487 Score: 155
Period size: 33 Copynumber: 9.5 Consensus size: 33
2396156 CGGAAATTAC
*
2396166 AATCGCAACGCGAAATGAAAATCCCAAC-ATGA-
1 AATCGCAATGCGAAATGAAAATCCCAACGA-GAG
*
2396198 ACATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 A-ATCGCAATGCGAAATGAAAATCCCAACGAGAG
* * *
2396232 AATCGCAATGCGAAATGAAAATCGCAATGCGA-
1 AATCGCAATGCGAAATGAAAATCCCAACGAGAG
* * * * * *
2396264 AAT-GAAAATCCCAACATGAAAATCGCAATGCGA-
1 AATCG-CAATGCGAA-ATGAAAATCCCAACGAGAG
* * * * *
2396297 AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCG-CAATGCGAAATGA-A-AATCCCAA--CG--A-GAG
*
2396336 AATCGCAATGCGAAATG-AAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCCCAACGAGAG
*
2396368 AATCGCAATGCGAAATGAAAATCGCAATGCG-GA-
1 AATCGCAATGCGAAATGAAAATCCCAA--CGAGAG
* * * * *
2396401 AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATG
1 AATCG-CAATGCGAAATGA-A-AATCCCAA--CGAGA-G
*
2396438 AAATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 -AATCGCAATGCGAAATGAAAATCCCAACGAGAG
2396472 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
2396488 TATAAACGCA
Statistics
Matches: 239, Mismatches: 24, Indels: 53
0.76 0.08 0.17
Matches are distributed among these distances:
31 4 0.02
32 39 0.16
33 124 0.52
34 17 0.07
35 10 0.04
37 16 0.07
38 10 0.04
39 13 0.05
40 6 0.03
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCCCAACGAGAG
Found at i:2396226 original size:52 final size:52
Alignment explanation
Indices: 2396166--2396310 Score: 152
Period size: 52 Copynumber: 2.8 Consensus size: 52
2396156 CGGAAATTAC
* *
2396166 AATCGCAACGCGA-AAT-GAAAATCCCAACATGAACATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCG-AAATCCCAA-ATGAAAATCGCAATGCGAAATGAA
* * *
2396218 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGAAATCCCAAATGAAAATCGCAATGCGAAATGAA
* * * * *
2396270 AATCCCAAC-ATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAACGA-GAGAATCGAAATCCCAAATGAAAATCGCAA
2396311 CGAGAGAATC
Statistics
Matches: 83, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
51 1 0.01
52 72 0.87
53 9 0.11
54 1 0.01
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.14
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGAAATCCCAAATGAAAATCGCAATGCGAAATGAA
Found at i:2396301 original size:85 final size:85
Alignment explanation
Indices: 2396166--2396394 Score: 399
Period size: 85 Copynumber: 2.7 Consensus size: 85
2396156 CGGAAATTAC
* *
2396166 AATCGCAACGCGAAATGAAAATCCCAACATGAACATCGCAATGCGAAATGAAAATCGCAACGAGA
1 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGA
2396231 GAATCGCAATGCGAAATGAA
66 GAATCGCAATGCGAAATGAA
2396251 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGA
1 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGA
2396316 GAATCGCAATGCGAAATGAA
66 GAATCGCAATGCGAAATGAA
* *
2396336 AATCGCAATGCGAAATG-AAATCGCAACGA-GAGAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGAAATGAAAATCGCAA
2396395 TGCGGAAATG
Statistics
Matches: 139, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
84 38 0.27
85 101 0.73
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.14
Consensus pattern (85 bp):
AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGA
GAATCGCAATGCGAAATGAA
Found at i:2396322 original size:14 final size:15
Alignment explanation
Indices: 2396303--2396484 Score: 66
Period size: 14 Copynumber: 10.8 Consensus size: 15
2396293 GCGAAATGAA
2396303 AATCGCAA-CGAGAG
1 AATCGCAAGCGAGAG
*
2396317 AATCGCAATGCGAAATGAA
1 AATCGCAA-GCG--A-GAG
*
2396336 AATCGCAATGCGAAATG
1 AATCGCAA-GCGAGA-G
2396353 AAATCGCAA-CGAGAG
1 -AATCGCAAGCGAGAG
*
2396368 AATCGCAATGCGAAATGAA
1 AATCGCAA-GCG--A-GAG
*
2396387 AATCGCAATGCGGAAATGAA
1 AATCGCAA-GC-G--A-GAG
2396407 AATCGCAA-CGAGAG
1 AATCGCAAGCGAGAG
*
2396421 AATCGCAATGCGAAATG
1 AATCGCAA-GCGAGA-G
*
2396438 AAATCGCAATGCGAAATGAA
1 -AATCGCAA-GCG--A-GAG
2396458 AATCGCAA-CGAGAG
1 AATCGCAAGCGAGAG
2396472 AATCGCAATGCGA
1 AATCGCAA-GCGA
2396485 AATTATAAAC
Statistics
Matches: 136, Mismatches: 10, Indels: 42
0.72 0.05 0.22
Matches are distributed among these distances:
14 36 0.26
15 3 0.02
16 16 0.12
17 5 0.04
18 23 0.17
19 35 0.26
20 17 0.12
21 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (15 bp):
AATCGCAAGCGAGAG
Found at i:2396377 original size:51 final size:52
Alignment explanation
Indices: 2396232--2396487 Score: 412
Period size: 51 Copynumber: 4.9 Consensus size: 52
2396222 GCAACGAGAG
* * * * *
2396232 AATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAATCCCAACATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAA-ATGAA
2396284 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
2396336 AATCGCAATGCGAAATG-AAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
2396387 AATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG-A
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
2396439 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
2396488 TATAAACGCA
Statistics
Matches: 195, Mismatches: 5, Indels: 9
0.93 0.02 0.04
Matches are distributed among these distances:
51 83 0.43
52 70 0.36
53 41 0.21
54 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:2396503 original size:104 final size:105
Alignment explanation
Indices: 2396232--2396487 Score: 414
Period size: 104 Copynumber: 2.5 Consensus size: 105
2396222 GCAACGAGAG
* * * * *
2396232 AATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAATCCCAACATGAAAATCGCAATGC
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAA-ATGAAAATCGCAATGC
2396295 -GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
64 GGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
2396336 AATCGCAATGCGAAATG-AAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGG
2396400 AAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG-A
66 AAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
2396439 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
2396488 TATAAACGCA
Statistics
Matches: 143, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
103 46 0.32
104 96 0.67
105 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (105 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGG
AAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:2396606 original size:52 final size:53
Alignment explanation
Indices: 2396494--2396609 Score: 216
Period size: 53 Copynumber: 2.2 Consensus size: 53
2396484 AAATTATAAA
*
2396494 CGCATTGCGGTTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
2396547 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
2396599 CGCATTGCGAT
1 CGCATTGCGAT
2396610 AGTCATTTTT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (53 bp):
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
Found at i:2396617 original size:19 final size:19
Alignment explanation
Indices: 2396512--2396609 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
2396502 GGTTCTCTCG
2396512 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2396532 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2396551 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2396565 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2396584 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2396603 TTGCGAT
1 TTGCGAT
2396610 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2396735 original size:14 final size:14
Alignment explanation
Indices: 2396716--2396752 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2396706 CATCAATTAC
2396716 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2396730 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2396744 ACAAATCAA
1 ACAAATCAA
2396753 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2398754 original size:14 final size:14
Alignment explanation
Indices: 2398735--2398791 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2398725 GCGAAATGAA
*
2398735 AATCGCAACGACAG
1 AATCGCAACGAAAG
2398749 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
2398766 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
2398782 AATCGCAACG
1 AATCGCAACG
2398792 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:2398762 original size:33 final size:33
Alignment explanation
Indices: 2398716--2398808 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
2398706 GCGAAACCAA
*
2398716 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
2398749 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
2398782 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
2398809 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:2398773 original size:19 final size:19
Alignment explanation
Indices: 2398679--2398813 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
2398669 TAGTTTACTT
* *
2398679 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
2398699 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
2398718 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2398737 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
2398751 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
2398770 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
2398784 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2398803 TCGCAATGCGA
1 TCGCAACGCGA
2398814 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2398831 original size:19 final size:19
Alignment explanation
Indices: 2398809--2398937 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
2398799 AAAATCGCAA
2398809 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2398828 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
2398842 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2398861 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
2398875 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
2398894 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
2398913 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
2398933 TGCGA
1 TGCGA
2398938 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:2398851 original size:33 final size:33
Alignment explanation
Indices: 2398809--2398900 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
2398799 AAAATCGCAA
2398809 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
2398842 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
2398875 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
2398901 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:2399101 original size:93 final size:93
Alignment explanation
Indices: 2398985--2399267 Score: 550
Period size: 93 Copynumber: 3.1 Consensus size: 93
2398975 ATGGATTGCA
2398985 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2399049 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2399077 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2399142 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2399170 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
2399235 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2399263 TTACT
1 TTACT
2399268 AAGCAATCTA
Statistics
Matches: 189, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
92 4 0.02
93 185 0.98
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:2400994 original size:14 final size:14
Alignment explanation
Indices: 2400975--2401064 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
2400965 TTGAAATGAA
2400975 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2400989 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
2401008 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2401022 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2401041 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2401055 AATCGTAACG
1 AATCGCAACG
2401065 CGAAATGAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
14 29 0.48
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 20 0.33
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2401012 original size:33 final size:33
Alignment explanation
Indices: 2400967--2401074 Score: 198
Period size: 33 Copynumber: 3.3 Consensus size: 33
2400957 TCTTTTGGTT
2400967 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
2401000 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
2401033 GAAATGAAAATCGCAACGAGAGAATCGTAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2401066 GAAATGAAA
1 GAAATGAAA
2401075 TCTAAGTGAA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 72 1.00
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2401013 original size:19 final size:19
Alignment explanation
Indices: 2400989--2401050 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
2400979 GCAACGAGAG
*
2400989 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
2401008 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
2401022 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
2401041 AATCGCAACG
1 AATCGCAACG
2401051 AGAGAATCGT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 10 0.28
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 20 0.56
ACGTcount: A:0.44, C:0.24, G:0.23, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:2401308 original size:22 final size:22
Alignment explanation
Indices: 2401256--2401310 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
2401246 TGGTTGTGAG
**
2401256 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
2401278 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
2401300 GGATTTCTTCG
1 GGATTTCTTCG
2401311 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:2401482 original size:20 final size:20
Alignment explanation
Indices: 2401457--2401650 Score: 203
Period size: 20 Copynumber: 9.7 Consensus size: 20
2401447 CTTTAAATAT
2401457 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2401477 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
2401499 -TCGTTGCGATTTACCGATA
1 CGCGTTGCGATTTACGGATA
*
2401518 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
2401538 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
2401558 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2401578 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
2401598 CGCATTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
2401618 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
2401638 CGCGTTGCGATTT
1 CGCGTTGCGATTT
2401651 TGGAAAATCG
Statistics
Matches: 143, Mismatches: 26, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
19 2 0.01
20 124 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2401622 original size:60 final size:60
Alignment explanation
Indices: 2401459--2401630 Score: 236
Period size: 60 Copynumber: 2.9 Consensus size: 60
2401449 TTAAATATCG
* ** *
2401459 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACCGATACG
1 CGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCGCGTTGCGATTTACCGATACA
* *** * *
2401520 CGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACCGATACA
*
2401580 CGTTGCGATTTACGGATACGCATTGCGATTTATGTGTTCGCGTTGCGATTT
1 CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTT
2401631 TCATATTCGC
Statistics
Matches: 95, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 69 0.73
61 26 0.27
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACCGATACA
Found at i:2401644 original size:60 final size:60
Alignment explanation
Indices: 2401456--2401771 Score: 232
Period size: 60 Copynumber: 5.2 Consensus size: 60
2401446 GCTTTAAATA
* ** * *
2401456 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACCGAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCGCGTTGCGATTTTCAGAT
* * *** * * *
2401517 ACGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCAGAT
* * * *
2401577 ACACGTTGCGATTTACGGATACGCATTGCGATTTATGTGTTCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCAGAT
* * * * * *
2401637 TCGCGTTGCGATTT-TGGAAAATCGCAATGCGAATT-TG-ACTATCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTACGG-ATA-CGCATTGCGATTTATGTA-T-TCGCGTTGCGATTTTC-AGAT
* * ** * * *
2401699 TCGCGTTGCGATTT-TGGAAACTG-ATTTGCGATTCTGGGGA-TCGCGTTGCGATTTTTA-TT
1 TCGCGTTGCGATTTACGGATAC-GCA-TTGCGATT-TATGTATTCGCGTTGCGATTTTCAGAT
2401758 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
2401772 TGTTTGGTCA
Statistics
Matches: 208, Mismatches: 37, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
59 16 0.08
60 92 0.44
61 78 0.38
62 20 0.10
63 1 0.00
64 1 0.00
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (60 bp):
TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCAGAT
Found at i:2401667 original size:21 final size:20
Alignment explanation
Indices: 2401617--2401714 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
2401607 ATTTATGTGT
* * * *
2401617 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTGAAAA
*
2401637 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * **
2401658 TCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTGAAAA
*
2401678 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
2401699 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
2401715 GAAACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.52
21 29 0.48
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:2401690 original size:61 final size:60
Alignment explanation
Indices: 2401617--2401773 Score: 176
Period size: 61 Copynumber: 2.6 Consensus size: 60
2401607 ATTTATGTGT
*
2401617 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATCGCA-ATGCGAATT-TGACTA
1 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAAT-G-ATATGCG-ATTCTGACGA
* * * * * **
2401678 TCGCATTGCGATTTTCAAGAATCGCGTTGCGATTTTGGAAACTGATTTGCGATTCTGGGGA
1 TCGCGTTGCGATTTTC-ATATTCGCGTTGCGATTTTGGAAAATGATATGCGATTCTGACGA
*
2401739 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTG
2401774 TTTGGTCATT
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
59 16 0.20
60 5 0.06
61 37 0.46
62 23 0.28
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (60 bp):
TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATGATATGCGATTCTGACGA
Found at i:2401709 original size:41 final size:41
Alignment explanation
Indices: 2401617--2401773 Score: 110
Period size: 41 Copynumber: 3.9 Consensus size: 41
2401607 ATTTATGTGT
* * *
2401617 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
2401658 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTGCAA-AA
* * * ***
2401699 TCGCGTTGCGATTTTGGAAACT-G-ATTTGCGATTCTG-GGGA
1 TCGCGTTGCGATTTT-GATATTCGCA-TTGCGATTTTGCAAAA
* *
2401739 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTG
2401774 TTTGGTCATT
Statistics
Matches: 89, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
38 1 0.01
39 12 0.13
40 19 0.21
41 52 0.58
42 5 0.06
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:2403821 original size:4 final size:4
Alignment explanation
Indices: 2403814--2403844 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
2403804 TATACATATA
*
2403814 TATG TATG TATG TATG TATG TATG CATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
2403845 ACAAACCCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:2407376 original size:16 final size:17
Alignment explanation
Indices: 2407355--2407386 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2407345 GTGCCTAAAC
2407355 ATTTTAAAAT-TTATAT
1 ATTTTAAAATATTATAT
2407371 ATTTTAAAATATTATA
1 ATTTTAAAATATTATA
2407387 ACGACAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTAAAATATTATAT
Found at i:2407576 original size:13 final size:13
Alignment explanation
Indices: 2407560--2407593 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
2407550 ATTAAATAAA
*
2407560 AATATTTCATCTT
1 AATATTTAATCTT
2407573 AATATTTAATCTT
1 AATATTTAATCTT
2407586 AATATTTA
1 AATATTTA
2407594 CTGAATTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (13 bp):
AATATTTAATCTT
Found at i:2408186 original size:2 final size:2
Alignment explanation
Indices: 2408106--2408170 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
2408096 TGTACGTGTG
2408106 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
2408148 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
2408171 CATTGCATGT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2411757 original size:29 final size:29
Alignment explanation
Indices: 2411724--2411797 Score: 148
Period size: 29 Copynumber: 2.6 Consensus size: 29
2411714 ACCGCAACCA
2411724 CACCGCAACCGCATCCAAGGTCACCACGT
1 CACCGCAACCGCATCCAAGGTCACCACGT
2411753 CACCGCAACCGCATCCAAGGTCACCACGT
1 CACCGCAACCGCATCCAAGGTCACCACGT
2411782 CACCGCAACCGCATCC
1 CACCGCAACCGCATCC
2411798 GAAAGTTATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.27, C:0.47, G:0.16, T:0.09
Consensus pattern (29 bp):
CACCGCAACCGCATCCAAGGTCACCACGT
Found at i:2416727 original size:96 final size:93
Alignment explanation
Indices: 2416450--2416811 Score: 503
Period size: 93 Copynumber: 3.9 Consensus size: 93
2416440 ATCTTGCAGT
* * * *
2416450 GCCTCCAGTTTCTAATAGAACAAGGTCTACTTTAATTTACGGTGATGAATTTCTTCAGGATAACT
1 GCCTTCAGTTTCTAAAAGAACAAGGTCTCCTTTAATTTACGATGATGAATTTCTTCAGGATAACT
* *
2416515 CCACTCCTATTGAAGTGCAAAACATTGC
66 CCACTCCTACTGAAGTGCAAAACATTGG
* **
2416543 GCCTTCAGTTTCTAAAAGAACGAGGTCTCCTCCAATTTACGATGATGAATTTCTTCAGGATAACT
1 GCCTTCAGTTTCTAAAAGAACAAGGTCTCCTTTAATTTACGATGATGAATTTCTTCAGGATAACT
2416608 CCACTCCTACTGAAGTGCAAAACATTGG
66 CCACTCCTACTGAAGTGCAAAACATTGG
* *
2416636 GCCTTCAGTTTCTAAAAGAACAAGGTCTCCTCCTTTAATTTATGATGATGAATTTCTTCAAGATA
1 GCCTTCAGTTTCTAAAAGAACAAGG--T-CTCCTTTAATTTACGATGATGAATTTCTTCAGGATA
* *
2416701 ACTCCACTCCTACTGAAGTGCGAAACA-TCG
63 ACTCCACTCCTACTGAAGTGCAAAACATTGG
* * *
2416731 GCCTTTCAGTTTCTAAAAGAACACGGTCTCCTTCAATTTACCG-TGATGAAGTTCTTCAGGATAA
1 GCC-TTCAGTTTCTAAAAGAACAAGGTCTCCTTTAATTTA-CGATGATGAATTTCTTCAGGATAA
* *
2416795 CTCCGCTCCTATTGAAG
64 CTCCACTCCTACTGAAG
2416812 ATGATACTGA
Statistics
Matches: 241, Mismatches: 23, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
93 154 0.64
94 2 0.01
95 6 0.02
96 79 0.33
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.31
Consensus pattern (93 bp):
GCCTTCAGTTTCTAAAAGAACAAGGTCTCCTTTAATTTACGATGATGAATTTCTTCAGGATAACT
CCACTCCTACTGAAGTGCAAAACATTGG
Found at i:2416780 original size:189 final size:186
Alignment explanation
Indices: 2416450--2416811 Score: 532
Period size: 189 Copynumber: 1.9 Consensus size: 186
2416440 ATCTTGCAGT
* * *
2416450 GCCTCCAGTTTCTAATAGAACAAGGTCTACTTTAATTTACGGTGATGAATTTCTTCAGGATAACT
1 GCCTCCAGTTTCTAAAAGAACAAGGTCTACTTTAATTTACGATGATGAATTTCTTCAAGATAACT
* *
2416515 CCACTCCTATTGAAGTGCAAAACATTGCGCCTTCAGTTTCTAAAAGAACGAGGTCTCCTCCAATT
66 CCACTCCTACTGAAGTGCAAAACATCGCGCCTTCAGTTTCTAAAAGAACGAGGTCTCCTCCAATT
*
2416580 TACGATGATGAATTTCTTCAGGATAACTCCACTCCTACTGAAGTGCAAAACATTGG
131 TACGATGATGAAGTTCTTCAGGATAACTCCACTCCTACTGAAGTGCAAAACATTGG
* * *
2416636 GCCTTCAGTTTCTAAAAGAACAAGGTCTCCTCCTTTAATTTATGATGATGAATTTCTTCAAGATA
1 GCCTCCAGTTTCTAAAAGAACAAGG--T-CTACTTTAATTTACGATGATGAATTTCTTCAAGATA
* *
2416701 ACTCCACTCCTACTGAAGTGCGAAACATCG-GCCTTTCAGTTTCTAAAAGAAC-ACGGTCTCCTT
63 ACTCCACTCCTACTGAAGTGCAAAACATCGCGCC-TTCAGTTTCTAAAAGAACGA-GGTCTCCTC
* *
2416764 CAATTTACCG-TGATGAAGTTCTTCAGGATAACTCCGCTCCTATTGAAG
126 CAATTTA-CGATGATGAAGTTCTTCAGGATAACTCCACTCCTACTGAAG
2416812 ATGATACTGA
Statistics
Matches: 157, Mismatches: 13, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
186 23 0.15
188 5 0.03
189 127 0.81
190 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.31
Consensus pattern (186 bp):
GCCTCCAGTTTCTAAAAGAACAAGGTCTACTTTAATTTACGATGATGAATTTCTTCAAGATAACT
CCACTCCTACTGAAGTGCAAAACATCGCGCCTTCAGTTTCTAAAAGAACGAGGTCTCCTCCAATT
TACGATGATGAAGTTCTTCAGGATAACTCCACTCCTACTGAAGTGCAAAACATTGG
Found at i:2428420 original size:33 final size:33
Alignment explanation
Indices: 2428378--2428460 Score: 148
Period size: 33 Copynumber: 2.5 Consensus size: 33
2428368 CTACTATACA
*
2428378 TTTAGTACCTAAACTATTATTATTTTTGTATGT
1 TTTAGTACCTAAACTATTATTATTTTTGTATAT
*
2428411 TTTAGTACCTAAACTATTATTTTTTTTGTATAT
1 TTTAGTACCTAAACTATTATTATTTTTGTATAT
2428444 TTTAGTACCTAAACTAT
1 TTTAGTACCTAAACTAT
2428461 CGGTTTTGAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.29, C:0.11, G:0.07, T:0.53
Consensus pattern (33 bp):
TTTAGTACCTAAACTATTATTATTTTTGTATAT
Found at i:2434062 original size:2 final size:2
Alignment explanation
Indices: 2434057--2434089 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2434047 TTTTTTATTT
2434057 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2434090 GAGTAAGTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2434945 original size:60 final size:59
Alignment explanation
Indices: 2434867--2434988 Score: 158
Period size: 60 Copynumber: 2.1 Consensus size: 59
2434857 AACATAATAA
* * *
2434867 ATAGTCGGATGACTATTTTGTAACTTTTAATAGTCGAA-AGACTTAACAAAATAACATTCT
1 ATAGTCGAATGACTATTTTGTAACTTTTAATAATC-AATAAAC-TAACAAAATAACATTCT
* *
2434927 ATAGTCGAATGA-TCATTTTGTAACTTTTAATAATCAATAAACTAATAAAATAATATTCT
1 ATAGTCGAATGACT-ATTTTGTAACTTTTAATAATCAATAAACTAACAAAATAACATTCT
2434986 ATA
1 ATA
2434989 ATTAAGAGAT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
59 21 0.38
60 34 0.62
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (59 bp):
ATAGTCGAATGACTATTTTGTAACTTTTAATAATCAATAAACTAACAAAATAACATTCT
Found at i:2435000 original size:59 final size:60
Alignment explanation
Indices: 2434881--2435008 Score: 145
Period size: 59 Copynumber: 2.1 Consensus size: 60
2434871 TCGGATGACT
* * * *
2434881 ATTTTGTAACTTTTAATAGTCGAAAGACTTAACAAAATAACATTCTATAGTCGAATGATC
1 ATTTTGTAACTTTTAATAATCGAAAAACTTAACAAAATAACATTCTATAATCGAAAGATC
* * *
2434941 ATTTTGTAACTTTTAATAATC-AATAAAC-TAATAAAATAATATTCTATAAT-TAAGAGATC
1 ATTTTGTAACTTTTAATAATCGAA-AAACTTAACAAAATAACATTCTATAATCGAA-AGATC
2435000 ATTTGTGTA
1 ATTT-TGTA
2435009 TTTTACCCTA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
58 2 0.03
59 29 0.50
60 27 0.47
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.38
Consensus pattern (60 bp):
ATTTTGTAACTTTTAATAATCGAAAAACTTAACAAAATAACATTCTATAATCGAAAGATC
Found at i:2441273 original size:17 final size:19
Alignment explanation
Indices: 2441251--2441285 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
2441241 TTAAATTAAT
2441251 ACAAAAAT-AT-AATAAAA
1 ACAAAAATGATAAATAAAA
2441268 ACAAAAATGATAAATAAA
1 ACAAAAATGATAAATAAA
2441286 GCCTATTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 2 0.12
19 6 0.38
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.17
Consensus pattern (19 bp):
ACAAAAATGATAAATAAAA
Found at i:2446191 original size:27 final size:28
Alignment explanation
Indices: 2446145--2446202 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
2446135 ATAGGATTCA
* *
2446145 TTATCTATTATTGTAGCACAT-TTTTTT
1 TTATCTATTATTATAACACATCTTTTTT
*
2446172 TTATCTATTCTTATAACACATCTTTTTT
1 TTATCTATTATTATAACACATCTTTTTT
2446200 TTA
1 TTA
2446203 ATTAAATTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 18 0.67
28 9 0.33
ACGTcount: A:0.24, C:0.14, G:0.03, T:0.59
Consensus pattern (28 bp):
TTATCTATTATTATAACACATCTTTTTT
Found at i:2453992 original size:30 final size:30
Alignment explanation
Indices: 2453945--2454002 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
2453935 AGTGATCACC
* * *
2453945 ATAGGTCTTCAGGAGCACATGGCGACCTTT
1 ATAGGTCTTCAGAAGCACACGACGACCTTT
2453975 ATAGGT-TTCCAGAAGCACACGACGACCT
1 ATAGGTCTT-CAGAAGCACACGACGACCT
2454003 ATGAAACTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (30 bp):
ATAGGTCTTCAGAAGCACACGACGACCTTT
Found at i:2454051 original size:19 final size:19
Alignment explanation
Indices: 2454027--2454068 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
2454017 GCGAGGGAAG
2454027 AGAGAAGAGTTGCTACAAC
1 AGAGAAGAGTTGCTACAAC
* *
2454046 AGAGAAGAGTTGTTGCAAC
1 AGAGAAGAGTTGCTACAAC
2454065 AGAG
1 AGAG
2454069 GAGACTTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.31, T:0.17
Consensus pattern (19 bp):
AGAGAAGAGTTGCTACAAC
Found at i:2454083 original size:20 final size:19
Alignment explanation
Indices: 2454027--2454083 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
2454017 GCGAGGGAAG
*
2454027 AGAGAAGAGTTG-CTACAAC
1 AGAGAAGAGTTGTC-GCAAC
*
2454046 AGAGAAGAGTTGTTGCAAC
1 AGAGAAGAGTTGTCGCAAC
* *
2454065 AGAGGAGACTTTGTCGCAA
1 AGAGAAGA-GTTGTCGCAA
2454084 GGAGCATTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 23 0.74
20 8 0.26
ACGTcount: A:0.37, C:0.14, G:0.30, T:0.19
Consensus pattern (19 bp):
AGAGAAGAGTTGTCGCAAC
Found at i:2460123 original size:23 final size:22
Alignment explanation
Indices: 2460079--2460128 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
2460069 TTTAATAAAA
**
2460079 TAATTAATAATGGAATTGTTTT
1 TAATTAATAATGGAATAATTTT
*
2460101 TAATATAATAATTGAATAATTTT
1 TAAT-TAATAATGGAATAATTTT
*
2460124 AAATT
1 TAATT
2460129 GTGGGCACGT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (22 bp):
TAATTAATAATGGAATAATTTT
Found at i:2481451 original size:12 final size:12
Alignment explanation
Indices: 2481434--2481512 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 12
2481424 GTTTAACATC
2481434 TATATTCGTCAA
1 TATATTCGTCAA
*
2481446 TATATTCGTTTAA
1 TATATTCG-TCAA
2481459 CGTCTATATTCGTCAA
1 ----TATATTCGTCAA
*
2481475 TATATTCGTTTAA
1 TATATTCG-TCAA
2481488 CGTCTATATTCGTCAA
1 ----TATATTCGTCAA
2481504 TATATTCGT
1 TATATTCGT
2481513 TTAACGTCGT
Statistics
Matches: 53, Mismatches: 4, Indels: 20
0.69 0.05 0.26
Matches are distributed among these distances:
12 25 0.47
13 6 0.11
16 6 0.11
17 16 0.30
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (12 bp):
TATATTCGTCAA
Found at i:2481457 original size:29 final size:29
Alignment explanation
Indices: 2481424--2481520 Score: 185
Period size: 29 Copynumber: 3.3 Consensus size: 29
2481414 GAATACGTTT
*
2481424 GTTTAACATCTATATTCGTCAATATATTC
1 GTTTAACGTCTATATTCGTCAATATATTC
2481453 GTTTAACGTCTATATTCGTCAATATATTC
1 GTTTAACGTCTATATTCGTCAATATATTC
2481482 GTTTAACGTCTATATTCGTCAATATATTC
1 GTTTAACGTCTATATTCGTCAATATATTC
2481511 GTTTAACGTC
1 GTTTAACGTC
2481521 GTCAATATAT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 67 1.00
ACGTcount: A:0.28, C:0.18, G:0.10, T:0.44
Consensus pattern (29 bp):
GTTTAACGTCTATATTCGTCAATATATTC
Found at i:2481468 original size:17 final size:17
Alignment explanation
Indices: 2481446--2481500 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
2481436 TATTCGTCAA
2481446 TATATTCGTTTAACGTC
1 TATATTCGTTTAACGTC
*
2481463 TATATTCG-TCAA----
1 TATATTCGTTTAACGTC
2481475 TATATTCGTTTAACGTC
1 TATATTCGTTTAACGTC
2481492 TATATTCGT
1 TATATTCGT
2481501 CAATATATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
12 8 0.26
13 3 0.10
16 3 0.10
17 17 0.55
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.47
Consensus pattern (17 bp):
TATATTCGTTTAACGTC
Found at i:2482101 original size:17 final size:17
Alignment explanation
Indices: 2482076--2482116 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
2482066 TTATGTTCGT
*
2482076 TCATGTATGTTCATTTA
1 TCATTTATGTTCATTTA
*
2482093 TCATTTATGTTCGTTTA
1 TCATTTATGTTCATTTA
2482110 TCATTTA
1 TCATTTA
2482117 ACAAGTGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.22, C:0.12, G:0.10, T:0.56
Consensus pattern (17 bp):
TCATTTATGTTCATTTA
Found at i:2484358 original size:35 final size:35
Alignment explanation
Indices: 2484319--2484393 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
2484309 TCTAAACCTT
*
2484319 AAATTGAGGTATTTTAGAATTTAGGGTTTAGAATA
1 AAATTGAAGTATTTTAGAATTTAGGGTTTAGAATA
* *
2484354 AAATTGAAGTATTTTAGAATTTGGGGTTTAGAATG
1 AAATTGAAGTATTTTAGAATTTAGGGTTTAGAATA
2484389 AAATT
1 AAATT
2484394 AAGGATTGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (35 bp):
AAATTGAAGTATTTTAGAATTTAGGGTTTAGAATA
Found at i:2487819 original size:19 final size:20
Alignment explanation
Indices: 2487795--2487843 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
2487785 GACCCAACTC
2487795 AAAATAATATATTTATT-AA
1 AAAATAATATATTTATTCAA
* *
2487814 AAAATATTATTTTTATTCAA
1 AAAATAATATATTTATTCAA
*
2487834 TAAA-AATATA
1 AAAATAATATA
2487844 GATTTAAATG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
AAAATAATATATTTATTCAA
Found at i:2509204 original size:17 final size:17
Alignment explanation
Indices: 2509182--2509214 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2509172 GATTAAGCGT
2509182 TGAATGATTCAATGGCC
1 TGAATGATTCAATGGCC
2509199 TGAATGATTCAATGGC
1 TGAATGATTCAATGGC
2509215 TCTGTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (17 bp):
TGAATGATTCAATGGCC
Found at i:2510330 original size:32 final size:31
Alignment explanation
Indices: 2510294--2510397 Score: 118
Period size: 31 Copynumber: 3.1 Consensus size: 31
2510284 TTCGGGTTTG
*
2510294 GGTCGAGGTTTTTTAAGTTTGATATTCGGGTC
1 GGTCG-GGTTTTTTAAGTGTGATATTCGGGTC
2510326 GGTCGGGTTTTTTAAGTGTGATATTCGGGTC
1 GGTCGGGTTTTTTAAGTGTGATATTCGGGTC
2510357 GGGTTCGGGTTGGGTTTTTTTAAGTGTGATATTCGGGTC
1 -GG-TC-----GGG-TTTTTTAAGTGTGATATTCGGGTC
2510396 GG
1 GG
2510398 GTCTCGGGTG
Statistics
Matches: 63, Mismatches: 1, Indels: 10
0.85 0.01 0.14
Matches are distributed among these distances:
31 25 0.40
32 7 0.11
33 2 0.03
38 5 0.08
39 24 0.38
ACGTcount: A:0.12, C:0.09, G:0.37, T:0.42
Consensus pattern (31 bp):
GGTCGGGTTTTTTAAGTGTGATATTCGGGTC
Found at i:2510335 original size:31 final size:32
Alignment explanation
Indices: 2510283--2510400 Score: 130
Period size: 39 Copynumber: 3.4 Consensus size: 32
2510273 TTTTTTTTAA
* *
2510283 ATTCGGGTTTGGGTCGAGGTTTTTTAAGTTTGAT
1 ATTCGGG-TCGGGTCG-GGTTTTTTAAGTGTGAT
2510317 ATTCGGGTC-GGTCGGGTTTTTTAAGTGTGAT
1 ATTCGGGTCGGGTCGGGTTTTTTAAGTGTGAT
2510348 ATTCGGGTCGGGTTCGGGTTGGGTTTTTTTAAGTGTGAT
1 ATTCGGGTCGGG-TC-----GGG-TTTTTTAAGTGTGAT
2510387 ATTCGGGTCGGGTC
1 ATTCGGGTCGGGTC
2510401 TCGGGTGGAG
Statistics
Matches: 74, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
31 25 0.34
32 7 0.09
33 3 0.04
34 7 0.09
38 5 0.07
39 27 0.36
ACGTcount: A:0.12, C:0.09, G:0.36, T:0.42
Consensus pattern (32 bp):
ATTCGGGTCGGGTCGGGTTTTTTAAGTGTGAT
Found at i:2517235 original size:11 final size:12
Alignment explanation
Indices: 2517208--2517234 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2517198 AACTTTTAAA
2517208 TTTTATGTATTT
1 TTTTATGTATTT
2517220 TTTTATGTATTT
1 TTTTATGTATTT
2517232 TTT
1 TTT
2517235 AAAAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (12 bp):
TTTTATGTATTT
Found at i:2517641 original size:36 final size:36
Alignment explanation
Indices: 2517595--2517665 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
2517585 TAAAGTCTAG
2517595 TTTTTGTTTCATTCAGTATTCCATTCAAAATTTGAT
1 TTTTTGTTTCATTCAGTATTCCATTCAAAATTTGAT
**
2517631 TTTTTGTTTCATTCAGTATTCTGTTCAAAATTTGA
1 TTTTTGTTTCATTCAGTATTCCATTCAAAATTTGA
2517666 CATTAACTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.24, C:0.13, G:0.10, T:0.54
Consensus pattern (36 bp):
TTTTTGTTTCATTCAGTATTCCATTCAAAATTTGAT
Found at i:2523694 original size:63 final size:64
Alignment explanation
Indices: 2523545--2523709 Score: 194
Period size: 63 Copynumber: 2.6 Consensus size: 64
2523535 ATTGTTTAAG
* * ** *
2523545 ATGCATCGATGCACATGCAGTGCATCGATGCATGATTTTAAATAGAAAACATCGAATAGGATTT
1 ATGCATCGATGCACAAGCAGTGCATCGATGCATCACATTAAATAGAAAACATCGAATAGCATTT
* * *
2523609 ATGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAA-A-AAAACATCGAAT-GCATTT
1 ATGCATCGATGCACAAGCAGTGCATCGATGCAT-CACATTAAATAGAAAACATCGAATAGCA-TT
2523671 T
64 T
* *
2523672 ATGCACCGATGCACAAGTAGTGCATCGATGCAT-ACATT
1 ATGCATCGATGCACAAGCAGTGCATCGATGCATCACATT
2523710 CATTGAAAGA
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
61 4 0.05
62 2 0.02
63 45 0.52
64 31 0.36
65 5 0.06
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (64 bp):
ATGCATCGATGCACAAGCAGTGCATCGATGCATCACATTAAATAGAAAACATCGAATAGCATTT
Found at i:2524417 original size:30 final size:30
Alignment explanation
Indices: 2524383--2524446 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
2524373 AAGGAATATA
*
2524383 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* * *
2524413 TGGATAGTTACCGGGGTTCTTTGTAACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
2524443 TGGA
1 TGGA
2524447 CAGGTCCTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:2527827 original size:64 final size:64
Alignment explanation
Indices: 2527741--2527901 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 64
2527731 ATTGTTTAAG
* * ** *
2527741 ATGCATCGATGCACATGCAGTGCATCGATGCAT-GATTTTAAATAGAAAACATCGAATAGGA-TT
1 ATGCATCGATGCACAAGCAGTGCATCGATGCATCCACATTAAATA-AAAACATCGAAT-GCATTT
2527804 T
64 T
* * *
2527805 ATGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAAAAACATCGAATGCATTTT
1 ATGCATCGATGCACAAGCAGTGCATCGATGCATCCACATTAAATAAAAACATCGAATGCATTTT
* *
2527869 ATGCACCGATGCACAAGTAGTGCATCGATGCAT
1 ATGCATCGATGCACAAGCAGTGCATCGATGCAT
2527902 ACATTCATTG
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
63 2 0.02
64 75 0.89
65 7 0.08
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (64 bp):
ATGCATCGATGCACAAGCAGTGCATCGATGCATCCACATTAAATAAAAACATCGAATGCATTTT
Found at i:2528610 original size:30 final size:30
Alignment explanation
Indices: 2528574--2528637 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
2528564 AAGGAACATA
* *
2528574 TGGATAGTTGCCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* * *
2528604 TGGATAGTTACCGGGGTTCTTTGTAACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
2528634 TGGA
1 TGGA
2528638 CAGGTCCTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:2532306 original size:12 final size:12
Alignment explanation
Indices: 2532289--2532313 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2532279 ACAAAGCACC
2532289 ATTTGGTGCCTA
1 ATTTGGTGCCTA
2532301 ATTTGGTGCCTA
1 ATTTGGTGCCTA
2532313 A
1 A
2532314 ATTATTTGAC
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:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (12 bp):
ATTTGGTGCCTA
Found at i:2535149 original size:22 final size:25
Alignment explanation
Indices: 2535110--2535159 Score: 70
Period size: 22 Copynumber: 2.1 Consensus size: 25
2535100 CAAACTTTGA
2535110 AAACATTTTCAAAGAAACATTTACC
1 AAACATTTTCAAAGAAACATTTACC
*
2535135 AAAC-TTTT-AAA-AAACATTTTCC
1 AAACATTTTCAAAGAAACATTTACC
2535157 AAA
1 AAA
2535160 GTTGGTTGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 13 0.54
23 3 0.12
24 4 0.17
25 4 0.17
ACGTcount: A:0.50, C:0.18, G:0.02, T:0.30
Consensus pattern (25 bp):
AAACATTTTCAAAGAAACATTTACC
Done.