Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 134 of 214
Found at i:40691450 original size:47 final size:48
Alignment explanation
Indices: 40691380--40691475 Score: 149
Period size: 47 Copynumber: 2.0 Consensus size: 48
40691370 TTCAACACCC
*
40691380 TTACCACCTTTACTGCCAACAACCTCAACACCC-TCCCACCTAAACCT
1 TTACCACCTTCACTGCCAACAACCTCAACACCCTTCCCACCTAAACCT
* **
40691427 TTACCACCTTCACTGCCAGCAACCTCAACACCCTTCCCATTTAAACCT
1 TTACCACCTTCACTGCCAACAACCTCAACACCCTTCCCACCTAAACCT
40691475 T
1 T
40691476 CAACACCCTT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
47 31 0.70
48 13 0.30
ACGTcount: A:0.28, C:0.45, G:0.03, T:0.24
Consensus pattern (48 bp):
TTACCACCTTCACTGCCAACAACCTCAACACCCTTCCCACCTAAACCT
Found at i:40691512 original size:104 final size:104
Alignment explanation
Indices: 40691325--40691515 Score: 285
Period size: 104 Copynumber: 1.8 Consensus size: 104
40691315 CAACACCCTC
* * *
40691325 ACCACATTTACTGCCAGCAACCTCAGCACACTCTCCATTTAGACCTTCAACACCCTTACCACCTT
1 ACCACATTCACTGCCAGCAACCTCAACACACTCTCCATTTAAACCTTCAACACCCTTACCACCTT
40691390 TACTGCCAACAACCTCAACACCCTCCCACCTAAACCTTT
66 TACTGCCAACAACCTCAACACCCTCCCACCTAAACCTTT
* * *
40691429 ACCACCTTCACTGCCAGCAACCTCAACACCCT-TCCCATTTAAACCTTCAACACCCTTACCACTT
1 ACCACATTCACTGCCAGCAACCTCAACACACTCT-CCATTTAAACCTTCAACACCCTTACCACCT
* **
40691493 TTACTGCCAGCAATTTCAACACC
65 TTACTGCCAACAACCTCAACACC
40691516 TTCATTACCA
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
103 1 0.01
104 76 0.99
ACGTcount: A:0.29, C:0.43, G:0.05, T:0.24
Consensus pattern (104 bp):
ACCACATTCACTGCCAGCAACCTCAACACACTCTCCATTTAAACCTTCAACACCCTTACCACCTT
TACTGCCAACAACCTCAACACCCTCCCACCTAAACCTTT
Found at i:40698494 original size:44 final size:44
Alignment explanation
Indices: 40698377--40698495 Score: 166
Period size: 44 Copynumber: 2.7 Consensus size: 44
40698367 TCGACTTCAA
* * *
40698377 TCTGCTCCACTGCAACCTCAGGGAGATAAAATTTGTTTTCTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTTTCTCAG
* ** *
40698421 TCTGCCCCACTGTGACTTCAGGGGGATAAGACTTGTTTTCTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTTTCTCAG
*
40698465 TCTGCTCCGCTGCAACTTCAGGGAGATAAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA
40698496 TCGAATGCGA
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 63 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTTTCTCAG
Found at i:40698612 original size:87 final size:87
Alignment explanation
Indices: 40698506--40698668 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 87
40698496 TCGAATGCGA
* * * *
40698506 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTATTGTTTTAATCCGCTCCATTGTAACTTCAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTATTGCTTTAATCCACTCCACTGCAACTTCAGG
*
40698571 GAGATAGGATTGATTTCTTCTG
66 GACATAGGATTGATTTCTTCTG
40698593 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTATTGCTTTAATCCACTCCACTGCAACTTCAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTATTGCTTTAATCCACTCCACTGCAACTTCAGG
40698658 GACATAGGATT
66 GACATAGGATT
40698669 ATCGGCTTCA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.34
Consensus pattern (87 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATCTATTGCTTTAATCCACTCCACTGCAACTTCAGG
GACATAGGATTGATTTCTTCTG
Found at i:40698644 original size:43 final size:43
Alignment explanation
Indices: 40698509--40698646 Score: 138
Period size: 43 Copynumber: 3.2 Consensus size: 43
40698499 AATGCGATCT
*
40698509 GCTCCACTACTGCTTAGGGAGATAAGATCTATTGTTTTAATCC
1 GCTCCACTACTGCTTAGGGAGATAAGATCTATTGCTTTAATCC
** * * * * *
40698552 GCTCCA-TTGTAACTTCAGGGAGATAGGAT-TGATTTCTTCT-GTCT
1 GCTCCACTACT-GCTT-AGGGAGATAAGATCT-ATTGCTT-TAATCC
40698596 GCTCCACTACTGCTTAGGGAGATAAGATCTATTGCTTTAATCC
1 GCTCCACTACTGCTTAGGGAGATAAGATCTATTGCTTTAATCC
*
40698639 ACTCCACT
1 GCTCCACT
40698647 GCAACTTCAG
Statistics
Matches: 72, Mismatches: 16, Indels: 14
0.71 0.16 0.14
Matches are distributed among these distances:
42 3 0.04
43 37 0.51
44 29 0.40
45 3 0.04
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (43 bp):
GCTCCACTACTGCTTAGGGAGATAAGATCTATTGCTTTAATCC
Found at i:40698884 original size:131 final size:131
Alignment explanation
Indices: 40698593--40699415 Score: 940
Period size: 131 Copynumber: 6.3 Consensus size: 131
40698583 ATTTCTTCTG
* ***
40698593 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTATTGC--TTT--AATCC-ACTCCACTGCAACT
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATC---TGCAATTTCCAA-CCTATTCCACTGC-TGG
* * * * * *
40698653 TCAGGGACATAGGA-TTATCGGCTTCAATCTGCTTCCTTAC-ACT--TGAAGATAAGATTCGCCG
61 TCAGGGACATAGGACTTGT-GGCTTAAATCTGTTTCCCTACTTCTGGGGAAGATAAGATTCGCCG
40698714 TCTTCGA
125 TCTTCGA
* *
40698721 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTCCAACCTATTCCACTACTAGTCAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTCCAACCTATTCCACTGCTGGTCAGG
*
40698786 GACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTTCTGGGGAAGATAAGATTCGCCGTCTTTG
66 GACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTTCTGGGGAAGATAAGATTCGCCGTCTTCG
40698851 A
131 A
*
40698852 TCTGCTCCACTATTGCTTAGGGAGATAAGATCTGCAATTTCCAACCTATTCCACTGCTGGTCAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTCCAACCTATTCCACTGCTGGTCAGG
* *
40698917 GACATAGGACTTGTGGCTCAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCG
66 GACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTTCTGGGGAAGATAAGATTCGCCGTCTTCG
40698982 A
131 A
* * * * *
40698983 ACTGCTCCACTACTACTTAGGAAGATAAGATCTGCAATTTCCAACCTATCCCACTGCTGGTCAAG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTCCAACCTATTCCACTGCTGGTCAGG
* ** *
40699048 GACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTGCTGAAGATAAAATTCGCCGTCTTCG
66 GACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTTCTGGGGAAGATAAGATTCGCCGTCTTCG
40699113 A
131 A
* * * * *
40699114 TCTGCTCTATTATTGCTTAGGGAGATAAGATCTGTAATTTCCAACCTATTCCACTGCTGGTCAAG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTCCAACCTATTCCACTGCTGGTCAGG
* * * * * *
40699179 GACATAGGACTCGGTGGGC-TAAATCTGCTTCCC-ACTATCTTGGAAATATAAGATTTGCCGTCT
66 GACATAGGACT-TGT-GGCTTAAATCTGTTTCCCTACT-TCTGGGGAAGATAAGATTCGCCGTCT
*
40699242 TTGA
128 TCGA
* * * * *
40699246 TCTGCTCCACTACTACTTAGGGAGATAAGATCTACAATCTT-CAACCTGCTT-CGCTGCTGCTCA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAAT-TTCCAACCT-ATTCCACTGCTGGTCA
* * * * * *
40699309 GGGAGACA-AGG-CTCGATGGCCTAAATCTGCTTCCC-ACTATCTTGGAAAGATAAGATTTGCCG
64 -GG-GACATAGGACTTG-TGGCTTAAATCTGTTTCCCTACT-TCTGGGGAAGATAAGATTCGCCG
*
40699371 TCTTTGA
125 TCTTCGA
* *
40699378 TCTGCTCCACTACTGCTTAGGAAGATAAGATCTACAAT
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAAT
40699416 ATTCACTGAT
Statistics
Matches: 616, Mismatches: 61, Indels: 32
0.87 0.09 0.05
Matches are distributed among these distances:
125 3 0.00
127 3 0.00
128 66 0.11
129 15 0.02
131 344 0.56
132 170 0.28
133 11 0.02
134 4 0.01
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (131 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTCCAACCTATTCCACTGCTGGTCAGG
GACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTTCTGGGGAAGATAAGATTCGCCGTCTTCG
A
Found at i:40701686 original size:30 final size:30
Alignment explanation
Indices: 40701650--40701709 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
40701640 CAATGTTTTT
40701650 ATAGATAAGATTTCTCACTTTCATCTTGTA
1 ATAGATAAGATTTCTCACTTTCATCTTGTA
40701680 ATAGATAAGATTTCTCACTTTCATCTTGTA
1 ATAGATAAGATTTCTCACTTTCATCTTGTA
40701710 TGCGAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.43
Consensus pattern (30 bp):
ATAGATAAGATTTCTCACTTTCATCTTGTA
Found at i:40707264 original size:29 final size:26
Alignment explanation
Indices: 40707229--40707282 Score: 72
Period size: 29 Copynumber: 2.0 Consensus size: 26
40707219 AAAATCTCTT
*
40707229 CTGCTATTTCTGTTATTTATTTTCTTTTC
1 CTGCTATTT-TGTT-TTT-TTCTCTTTTC
40707258 CTGCTATTTTGTTTTTTTCTCTTTT
1 CTGCTATTTTGTTTTTTTCTCTTTT
40707283 TCTCTTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 8 0.33
27 3 0.12
28 4 0.17
29 9 0.38
ACGTcount: A:0.07, C:0.17, G:0.07, T:0.69
Consensus pattern (26 bp):
CTGCTATTTTGTTTTTTTCTCTTTTC
Found at i:40708627 original size:27 final size:26
Alignment explanation
Indices: 40708597--40708653 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
40708587 CTAAGACCTA
40708597 AAATTATAAACTATTTTAATATAATT-T
1 AAATTAT-AA-TATTTTAATATAATTAT
* **
40708624 AAATTCTAATATTTTTTTATAATTAT
1 AAATTATAATATTTTAATATAATTAT
40708650 AAAT
1 AAAT
40708654 GTTCTCGTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 13 0.50
26 7 0.27
27 6 0.23
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (26 bp):
AAATTATAATATTTTAATATAATTAT
Found at i:40711214 original size:18 final size:18
Alignment explanation
Indices: 40711193--40711323 Score: 103
Period size: 18 Copynumber: 7.4 Consensus size: 18
40711183 CTTCTCACCA
*
40711193 TCTTTCTTGGTTTCATCT
1 TCTTTCTTGGCTTCATCT
** *
40711211 TCTTTCTTACCTTCTTCT
1 TCTTTCTTGGCTTCATCT
40711229 TCCTTT-TTGGCTTCATCT
1 T-CTTTCTTGGCTTCATCT
40711247 T-TCTT-TT-G-TTCATCT
1 TCT-TTCTTGGCTTCATCT
* * *
40711262 TCCTTCTTGGGTTCACCT
1 TCTTTCTTGGCTTCATCT
*
40711280 TCTTTCTTTTG-TTCATCT
1 TCTTTC-TTGGCTTCATCT
* *
40711298 TCTTTTTTGGCTTCACCT
1 TCTTTCTTGGCTTCATCT
40711316 TCTTTCTT
1 TCTTTCTT
40711324 TGGTTCCTCT
Statistics
Matches: 89, Mismatches: 16, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
15 10 0.11
16 4 0.04
17 8 0.09
18 60 0.67
19 7 0.08
ACGTcount: A:0.05, C:0.27, G:0.08, T:0.60
Consensus pattern (18 bp):
TCTTTCTTGGCTTCATCT
Found at i:40711258 original size:15 final size:15
Alignment explanation
Indices: 40711240--40711303 Score: 58
Period size: 15 Copynumber: 3.9 Consensus size: 15
40711230 CCTTTTTGGC
40711240 TTCATCTTTCTTTTG
1 TTCATCTTTCTTTTG
*
40711255 TTCATCTTCCTTCTTGGG
1 TTCATCTTTCTT-TT--G
40711273 TTCACCTTCTTTCTTTTG
1 TTCA---TCTTTCTTTTG
40711291 TTCATC-TTCTTTT
1 TTCATCTTTCTTTT
40711304 TTGGCTTCAC
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
14 7 0.17
15 13 0.32
16 2 0.05
18 10 0.24
20 2 0.05
21 7 0.17
ACGTcount: A:0.06, C:0.25, G:0.08, T:0.61
Consensus pattern (15 bp):
TTCATCTTTCTTTTG
Found at i:40711286 original size:69 final size:70
Alignment explanation
Indices: 40711196--40711340 Score: 175
Period size: 69 Copynumber: 2.1 Consensus size: 70
40711186 CTCACCATCT
* * * *
40711196 TTCTTGGTTTCATCTTCTTTCTTACCTTCTTCTTCCTTTTTGGCTTCA-TCTTTCTTTTGTTCAT
1 TTCTTGGGTTCACCTTCTTTCTTACCTTCATCTTCCTTTTTGGCTTCACTCTTTCTTTGGTTCAT
40711260 CTTCC
66 CTTCC
*** *
40711265 TTCTTGGGTTCACCTTCTTTCTTTTGTTCATCTTCTTTTTTGGCTTCACCTTCTTTCTTTGGTTC
1 TTCTTGGGTTCACCTTCTTTCTTACCTTCATCTTCCTTTTTGGCTTCA-C-TCTTTCTTTGGTTC
* *
40711330 CTCTTTC
64 ATCTTCC
40711337 TTCT
1 TTCT
40711341 CTGGTTCTTT
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
69 41 0.65
72 22 0.35
ACGTcount: A:0.05, C:0.27, G:0.09, T:0.59
Consensus pattern (70 bp):
TTCTTGGGTTCACCTTCTTTCTTACCTTCATCTTCCTTTTTGGCTTCACTCTTTCTTTGGTTCAT
CTTCC
Found at i:40711324 original size:36 final size:36
Alignment explanation
Indices: 40711196--40711340 Score: 152
Period size: 36 Copynumber: 4.1 Consensus size: 36
40711186 CTCACCATCT
* * *** *
40711196 TTCTTGGTTTCATCTTCTTTCTTACCTTCTTCTTCC
1 TTCTTGGCTTCACCTTCTTTCTTTTGTTCATCTTCC
*
40711232 TTTTTGGCTTCA---TCTTTCTTTTGTTCATCTTCC
1 TTCTTGGCTTCACCTTCTTTCTTTTGTTCATCTTCC
* *
40711265 TTCTTGGGTTCACCTTCTTTCTTTTGTTCATCTTCT
1 TTCTTGGCTTCACCTTCTTTCTTTTGTTCATCTTCC
* * * *
40711301 TTTTTGGCTTCACCTTCTTTCTTTGGTTCCTCTTTC
1 TTCTTGGCTTCACCTTCTTTCTTTTGTTCATCTTCC
40711337 TTCT
1 TTCT
40711341 CTGGTTCTTT
Statistics
Matches: 90, Mismatches: 16, Indels: 6
0.80 0.14 0.05
Matches are distributed among these distances:
33 27 0.30
36 63 0.70
ACGTcount: A:0.05, C:0.27, G:0.09, T:0.59
Consensus pattern (36 bp):
TTCTTGGCTTCACCTTCTTTCTTTTGTTCATCTTCC
Found at i:40719702 original size:16 final size:16
Alignment explanation
Indices: 40719665--40719706 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
40719655 TTAATCACAT
*
40719665 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
40719681 TT-AAATATATTATAA
1 TTAAAATATATTATAA
40719696 TTAAAATATAT
1 TTAAAATATAT
40719707 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:40719713 original size:14 final size:15
Alignment explanation
Indices: 40719674--40719715 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
40719664 TTTAAACATA
*
40719674 ATTATTATTAAATAT
1 ATTATAATTAAATAT
40719689 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
40719703 A-TATAATTTAATA
1 ATTATAATTAAATA
40719716 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:40719833 original size:14 final size:15
Alignment explanation
Indices: 40719784--40719835 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
40719774 GTAAAATATA
40719784 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
40719799 TATTAAATATATTAT
1 AATTAAATATATTAT
40719814 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
40719827 AATTTAATA
1 AATTAAATA
40719836 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:40719953 original size:14 final size:15
Alignment explanation
Indices: 40719904--40719955 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
40719894 GTAAAATATA
40719904 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
40719919 TATTAAATATATTAT
1 AATTAAATATATTAT
40719934 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
40719947 AATTTAATA
1 AATTAAATA
40719956 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:40720091 original size:120 final size:120
Alignment explanation
Indices: 40719668--40720080 Score: 749
Period size: 120 Copynumber: 3.4 Consensus size: 120
40719658 ATCACATTTA
40719668 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
40719733 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
40719788 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
40719853 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
40719908 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* * *
40719973 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
* *
40720028 GAA-ATAATTGA-TATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 -AACATAATT-ATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
40720081 TAAAATAATT
Statistics
Matches: 286, Mismatches: 5, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
120 283 0.99
121 3 0.01
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:40720179 original size:47 final size:46
Alignment explanation
Indices: 40720128--40720271 Score: 106
Period size: 47 Copynumber: 3.1 Consensus size: 46
40720118 TTGTATAATT
40720128 TAAAATAATAATTATTACATATAATTTAATAATAATATATAATTTCA
1 TAAAATAATAATTATTA-ATATAATTTAATAATAATATATAATTTCA
* ** * *
40720175 TAAAAT--T-CTTGA-TAATA-AATTTTCTTATATGAATTTATACAATT--
1 TAAAATAATAATT-ATTAATATAA-TTTAATA-AT-AATATATA-ATTTCA
*
40720219 TAAAATAATTAA-TATTAAATATAATTTAATAATGATATATAATTTCA
1 TAAAATAA-TAATTATT-AATATAATTTAATAATAATATATAATTTCA
40720266 TAAAAT
1 TAAAAT
40720272 TCTTAATAAT
Statistics
Matches: 72, Mismatches: 11, Indels: 28
0.65 0.10 0.25
Matches are distributed among these distances:
42 2 0.03
43 8 0.11
44 12 0.17
45 12 0.17
46 10 0.14
47 17 0.24
48 9 0.12
49 2 0.03
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (46 bp):
TAAAATAATAATTATTAATATAATTTAATAATAATATATAATTTCA
Found at i:40720190 original size:101 final size:93
Alignment explanation
Indices: 40720021--40720303 Score: 290
Period size: 91 Copynumber: 3.0 Consensus size: 93
40720011 ACTATAAAAG
* * * * *
40720021 ATAATTTGAAATAATTGATATTAAATATATTTTAATTAA-AATATATGATTTAATAAAATT-TAA
1 ATAATTTAAAATAATTAATATTAAATATAATTTAA-TAATAATATATAATTTCATAAAATTCT--
* * *
40720084 AATAATTATAACTAATAAATTATATTTTATGAATTTGT
63 --T-A--ATAA-T-ATAAATTTTATTATATGAATTTAT
* *
40720122 ATAATTTAAAATAA-TAATTATTACATATAATTTAATAATAATATATAATTTCATAAAATTCTTG
1 ATAATTTAAAATAATTAA-TATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTA
*
40720186 AT-A-ATAAATTTTCTTATATGAATTTAT
65 ATAATATAAATTTTATTATATGAATTTAT
* *
40720213 ACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCATAAAATTCTTAA
1 ATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTAA
* *
40720278 TAATA-AAATGTTCTTATATGAATTTA
66 TAATATAAATTTTATTATATGAATTTA
40720304 CTAAAATCAA
Statistics
Matches: 160, Mismatches: 16, Indels: 21
0.81 0.08 0.11
Matches are distributed among these distances:
91 78 0.49
92 24 0.15
93 1 0.01
94 1 0.01
95 2 0.01
98 1 0.01
100 5 0.03
101 47 0.29
102 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (93 bp):
ATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTAA
TAATATAAATTTTATTATATGAATTTAT
Found at i:40720191 original size:91 final size:91
Alignment explanation
Indices: 40720096--40720303 Score: 294
Period size: 91 Copynumber: 2.3 Consensus size: 91
40720086 TAATTATAAC
* * * *
40720096 TAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATTTAATAA
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTTAATAA
*
40720160 TAATATATAATTTCATAAAATTCTTGA
65 TAATATATAATTTCATAAAATTCTTAA
* *
40720187 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
40720252 GATATATAATTTCATAAAATTCTTAA
66 AATATATAATTTCATAAAATTCTTAA
*
40720278 TAATAAAATGT-TCTTATATGAATTTA
1 TAAT-AAAT-TATATTATATGAATTTA
40720304 CTAAAATCAA
Statistics
Matches: 106, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
91 83 0.78
92 22 0.21
93 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (91 bp):
TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
AATATATAATTTCATAAAATTCTTAA
Found at i:40720263 original size:44 final size:43
Alignment explanation
Indices: 40720077--40720263 Score: 112
Period size: 44 Copynumber: 4.1 Consensus size: 43
40720067 GATTTAATAA
* * * *
40720077 AATTTAAAATAATTATAACTAATAAAT-TATATTTTATGAATTTGTAT
1 AATTTAAAATAA-T-TAA-TATTAAATATA-ATTTAAT-AATATATAT
*
40720124 AATTTAAAATAA-TAATTATTACATATAATTTAATAATAATATAT
1 AATTTAAAATAATTAA-TATTAAATATAATTTAATAAT-ATATAT
** * * * * *
40720168 AATTTCATAAAATTCTTGATAATAAAT-T-TTCTTATATGAATTTATAC
1 AA-TT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATATATAT
40720215 AATTTAAAATAATTAATATTAAATATAATTTAATAATGATATAT
1 AATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATATAT
40720259 AATTT
1 AATTT
40720264 CATAAAATTC
Statistics
Matches: 107, Mismatches: 21, Indels: 27
0.69 0.14 0.17
Matches are distributed among these distances:
43 6 0.06
44 48 0.45
45 9 0.08
46 7 0.07
47 32 0.30
48 5 0.05
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (43 bp):
AATTTAAAATAATTAATATTAAATATAATTTAATAATATATAT
Found at i:40720278 original size:47 final size:47
Alignment explanation
Indices: 40720146--40720284 Score: 137
Period size: 47 Copynumber: 3.0 Consensus size: 47
40720136 TAATTATTAC
* *
40720146 ATATAATTTAATAATAATATATAATTTCATAAAATTCTTGATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
* * * ** *
40720193 AT-T--TTCTTAT-ATGAATTTATACAATT--TAAAATAATTAATATTAA
1 ATATAATT-TAATAATG-ATATATA-ATTTCATAAAATTCTTAATAATAA
40720237 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
40720284 A
1 A
40720285 ATGTTCTTAT
Statistics
Matches: 69, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
44 20 0.29
45 13 0.19
46 13 0.19
47 23 0.33
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (47 bp):
ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
Found at i:40731173 original size:9 final size:9
Alignment explanation
Indices: 40731159--40731237 Score: 131
Period size: 9 Copynumber: 8.8 Consensus size: 9
40731149 TTTGGTTAAA
40731159 AATTACCCG
1 AATTACCCG
40731168 AATTACCCG
1 AATTACCCG
40731177 AATTACCCG
1 AATTACCCG
40731186 AATTACCCG
1 AATTACCCG
40731195 AATTACCCG
1 AATTACCCG
*
40731204 AATTAACCG
1 AATTACCCG
*
40731213 AATTAACCG
1 AATTACCCG
*
40731222 AATTAACCG
1 AATTACCCG
40731231 AATTACC
1 AATTACC
40731238 GAAAAATACC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 68 1.00
ACGTcount: A:0.38, C:0.29, G:0.10, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:40742391 original size:18 final size:18
Alignment explanation
Indices: 40742368--40742405 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
40742358 TGCCAGGTGC
* *
40742368 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
40742386 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
40742404 GT
1 GT
40742406 TTCTTTTTCC
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:40744549 original size:125 final size:124
Alignment explanation
Indices: 40744253--40744663 Score: 617
Period size: 125 Copynumber: 3.3 Consensus size: 124
40744243 CTCAAACATG
*
40744253 CTATTGTAGAAAAAGCGCGTCCACGTGGGAGCAATTTCAAAAATTCTTCTGATAAAGCATCCTGC
1 CTATTGTAGAAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
*
40744318 TTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTA-TTTTTCAGGAC
66 TTGAAGCTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
* * * *
40744376 CTATTGTAGTAAATGCGCATCCACGTGGGAACGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
1 CTATTGTAGAAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
*
40744441 TTGAAGCATTTTTTATAATATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
66 TTGAAGC-TTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
* * * * * * * *
40744501 CTACTGTAGCAAAAGCACGTCTACGTGGGAGCGATTTCAGAAATTCTTCTAATAAAGTATCCTAC
1 CTATTGTAGAAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
* * *
40744566 TTGAAGCGTTTTTTATACTATTTACTCAGAAATGTCAACTCGAAATTATTTTCTCAGGAC
66 TTGAAGC-TTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
* *
40744626 CTATTGTATAAAAAACGCGTCCACGTGGGAGCGATTTC
1 CTATTGTAGAAAAAGCGCGTCCACGTGGGAGCGATTTC
40744664 CTTAATAAAT
Statistics
Matches: 257, Mismatches: 29, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
123 67 0.26
124 38 0.15
125 152 0.59
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (124 bp):
CTATTGTAGAAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
TTGAAGCTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
Found at i:40744886 original size:21 final size:22
Alignment explanation
Indices: 40744848--40744888 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
40744838 TTAAAAATCT
*
40744848 TAAAAACCCTAAACCCTAACCC
1 TAAAAACCCTAAAACCTAACCC
40744870 TAAAAACCC-AAAACCTAAC
1 TAAAAACCCTAAAACCTAAC
40744889 GTGGGAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.51, C:0.37, G:0.00, T:0.12
Consensus pattern (22 bp):
TAAAAACCCTAAAACCTAACCC
Found at i:40747855 original size:31 final size:31
Alignment explanation
Indices: 40747819--40747887 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
40747809 TTGTCGCCGA
* *
40747819 GCAATCCGGGGCGGTTGGTCATCATTGTTAG
1 GCAATCCGGGGCGGTTGATCATCATCGTTAG
* * **
40747850 GCAATCTGGGGTGGTTGATCATTGTCGTTAG
1 GCAATCCGGGGCGGTTGATCATCATCGTTAG
40747881 GCAATCC
1 GCAATCC
40747888 AAGATGACAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.17, C:0.19, G:0.33, T:0.30
Consensus pattern (31 bp):
GCAATCCGGGGCGGTTGATCATCATCGTTAG
Found at i:40749769 original size:17 final size:16
Alignment explanation
Indices: 40749747--40749779 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
40749737 TATCAACCAA
40749747 TTCATATACAATATCAT
1 TTCATATACAA-ATCAT
40749764 TTCATATACAAATCAT
1 TTCATATACAAATCAT
40749780 GTTAATCTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (16 bp):
TTCATATACAAATCAT
Found at i:40751950 original size:50 final size:50
Alignment explanation
Indices: 40751891--40752083 Score: 260
Period size: 50 Copynumber: 3.8 Consensus size: 50
40751881 ATTTGGGTAA
* ** *
40751891 AGAGGTCCCATGTAAGACCATGTCTGGGGCATGAAATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
*
40751941 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
** *
40751991 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACTGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
* ** * *
40752041 TGAACATCCCATGTAAGACCATGTCTGAGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
40752084 TGTTATTATC
Statistics
Matches: 125, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 92 0.74
51 33 0.26
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
Found at i:40760900 original size:15 final size:15
Alignment explanation
Indices: 40760862--40760901 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
40760852 TGGGTTTTGA
40760862 ATTTCGATTTTTAAAG
1 ATTT-GATTTTTAAAG
*
40760878 ATTT-ATTTTTAGAG
1 ATTTGATTTTTAAAG
40760892 ATTTGATTTT
1 ATTTGATTTT
40760902 CAGGGTTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 13 0.59
15 5 0.23
16 4 0.18
ACGTcount: A:0.28, C:0.03, G:0.12, T:0.57
Consensus pattern (15 bp):
ATTTGATTTTTAAAG
Found at i:40770075 original size:23 final size:23
Alignment explanation
Indices: 40770049--40770094 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
40770039 AGTTAAATAT
*
40770049 TATTTTTTATTATTTTACTTAGA
1 TATTTATTATTATTTTACTTAGA
*
40770072 TATTTATTATTATTTTATTTAGA
1 TATTTATTATTATTTTACTTAGA
40770095 AAATGGTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.65
Consensus pattern (23 bp):
TATTTATTATTATTTTACTTAGA
Found at i:40780260 original size:124 final size:124
Alignment explanation
Indices: 40780040--40780288 Score: 489
Period size: 124 Copynumber: 2.0 Consensus size: 124
40780030 CTGTTTTTGC
40780040 CCCCCATCCTTTGACATCAACCCGGTATACCCCCAACATAACTCCATCCCAAATTAAATATTAAT
1 CCCCCATCCTTTGACATCAACCCGGTATACCCCCAACATAACTCCATCCCAAATTAAATATTAAT
40780105 TACTTACCATAAAACTGACCTGAAAAATTAAAGCTTTACTTCACTCCGACTCGATATGT
66 TACTTACCATAAAACTGACCTGAAAAATTAAAGCTTTACTTCACTCCGACTCGATATGT
*
40780164 CCCCCATCCTTTGACATCAACTCGGTATACCCCCAACATAACTCCATCCCAAATTAAATATTAAT
1 CCCCCATCCTTTGACATCAACCCGGTATACCCCCAACATAACTCCATCCCAAATTAAATATTAAT
40780229 TACTTACCATAAAACTGACCTGAAAAATTAAAGCTTTACTTCACTCCGACTCGATATGT
66 TACTTACCATAAAACTGACCTGAAAAATTAAAGCTTTACTTCACTCCGACTCGATATGT
40780288 C
1 C
40780289 ACAGTTTTTT
Statistics
Matches: 124, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
124 124 1.00
ACGTcount: A:0.35, C:0.31, G:0.07, T:0.28
Consensus pattern (124 bp):
CCCCCATCCTTTGACATCAACCCGGTATACCCCCAACATAACTCCATCCCAAATTAAATATTAAT
TACTTACCATAAAACTGACCTGAAAAATTAAAGCTTTACTTCACTCCGACTCGATATGT
Found at i:40781016 original size:33 final size:33
Alignment explanation
Indices: 40780955--40781017 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
40780945 ATGTATTTAC
*
40780955 TTTTTATTAATAATTATAGATTATTATATTAGT
1 TTTTTATTAAAAATTATAGATTATTATATTAGT
40780988 TTTTTA-TAAAAATTATTA-ATTATATATATT
1 TTTTTATTAAAAATTA-TAGATTAT-TATATT
40781018 TGAAATATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (33 bp):
TTTTTATTAAAAATTATAGATTATTATATTAGT
Found at i:40781223 original size:18 final size:17
Alignment explanation
Indices: 40781197--40781238 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
40781187 ACTAAGTAAC
*
40781197 TATAGTTTAGTTTAGTTT
1 TATATTTTAGTTTA-TTT
*
40781215 TATATTTTATTTTATTT
1 TATATTTTAGTTTATTT
40781232 TAT-TTTT
1 TATATTTT
40781239 GGCATAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 4 0.18
17 6 0.27
18 12 0.55
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (17 bp):
TATATTTTAGTTTATTT
Found at i:40790478 original size:48 final size:48
Alignment explanation
Indices: 40790403--40790555 Score: 191
Period size: 48 Copynumber: 3.2 Consensus size: 48
40790393 GCGTACCGAT
* *
40790403 AATCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCCACCAAT
1 AATCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAAGCCACCAAG
* * * *
40790451 AA-CTTGTTAAGATACAAGGGTGGCACGGACTATGTGCAAGCCACCGAG
1 AATC-TGTTATGACACAAGGGTGGCACGGACTGTGTGCAAGCCACCAAG
* * * *
40790499 AATCTGTTATTACACAAAGGTGGTACGGACAGTGTGCAAGCCACCAAG
1 AATCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAAGCCACCAAG
40790547 AAATCTGTT
1 -AATCTGTT
40790556 TTTATCCCTA
Statistics
Matches: 88, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
47 1 0.01
48 78 0.89
49 9 0.10
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.22
Consensus pattern (48 bp):
AATCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAAGCCACCAAG
Found at i:40804232 original size:44 final size:44
Alignment explanation
Indices: 40804165--40804680 Score: 295
Period size: 44 Copynumber: 11.7 Consensus size: 44
40804155 TGCCTCACTA
* * *
40804165 CCAATATAGAAAGACAGGATCTGCTATTTTCGATCTACTTCAAG
1 CCAATACAGGAAGACAAGATCTGCTATTTTCGATCTACTTCAAG
* * * *
40804209 CCAATACATGAAGATAATATCTGCT-TTCTTCGATCTACTTCGCCA-
1 CCAATACAGGAAGACAAGATCTGCTATT-TTCGATCTACTT--CAAG
*** * * * *
40804254 CCAATGTGGGAATACAAGATCTGC-ATCTTCGATCCACTTCCTA-
1 CCAATACAGGAAGACAAGATCTGCTATTTTCGATCTACTT-CAAG
* * * ** *
40804297 CCAATACAGGAAGACAGGATATGTTATCATCGATCTACTTCACG
1 CCAATACAGGAAGACAAGATCTGCTATTTTCGATCTACTTCAAG
* *
40804341 CCAATACAGGAAGACAAGCTCTGCT-TTCTTCGATCTACTTCACG
1 CCAATACAGGAAGACAAGATCTGCTATT-TTCGATCTACTTCAAG
** *
40804385 TTAATACATGAAGACAAGATCTGCT-TTCTTCGATCTACTTC--G
1 CCAATACAGGAAGACAAGATCTGCTATT-TTCGATCTACTTCAAG
** * * *
40804427 CCACCAGTATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTCGCTA-
1 CCA--A-TACAGGAAGACAAGATCTGCTATTTTCGATCTACTT--CAAG
* * * * *
40804474 CCAATATAGGAAGATAGGATCTGTTATCTTCGATCTACTTCAAG
1 CCAATACAGGAAGACAAGATCTGCTATTTTCGATCTACTTCAAG
* * * * * *
40804518 CAAATACATGAAGACAAGATTTCCTTTTTTCGATATACTTC--G
1 CCAATACAGGAAGACAAGATCTGCTATTTTCGATCTACTTCAAG
** * * * *
40804560 CCACCAGTATGGGAAGACAAGATATGC-ATCTTCGATCCACTTCGCTA-
1 CCA--A-TACAGGAAGACAAGATCTGCTATTTTCGATCTACTT--CAAG
* * * * *
40804607 CCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTCACG
1 CCAATACAGGAAGACAAGATCTGCTATTTTCGATCTACTTCAAG
* * *
40804651 CCAATATATGAAGACAAGATCTACTATTTT
1 CCAATACAGGAAGACAAGATCTGCTATTTT
40804681 TTAGCCTGCT
Statistics
Matches: 361, Mismatches: 85, Indels: 52
0.72 0.17 0.10
Matches are distributed among these distances:
42 5 0.01
43 26 0.07
44 239 0.66
45 81 0.22
46 4 0.01
47 6 0.02
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (44 bp):
CCAATACAGGAAGACAAGATCTGCTATTTTCGATCTACTTCAAG
Found at i:40804310 original size:88 final size:88
Alignment explanation
Indices: 40804164--40804672 Score: 365
Period size: 88 Copynumber: 5.8 Consensus size: 88
40804154 CTGCCTCACT
* * * * * * * * *
40804164 ACCAATATAGAAAGACAGGATCTGCTATTTTCGATCTACTTCAAGCCAATACATGAAGATAATAT
1 ACCAATATGGGAAGACAAGATCTGCTATCTTCGATCCACTTCTA-CCAATACAGGAAGACAAGAT
40804229 CTGCTT-TCTTCGATCTACTTCGCC
65 CTG-TTATCTTCGATCTACTTCGCC
* * *
40804253 ACCAATGTGGGAATACAAGATCTGC-ATCTTCGATCCACTTCCTACCAATACAGGAAGACAGGAT
1 ACCAATATGGGAAGACAAGATCTGCTATCTTCGATCCACTT-CTACCAATACAGGAAGACAAGAT
* * *
40804317 ATGTTATCATCGATCTACTTC-AC
65 CTGTTATCTTCGATCTACTTCGCC
* ** * * * * *
40804340 GCCAATACAGGAAGACAAGCTCTGCTTTCTTCGATCTACTTC-ACGTTAATACATGAAGACAAGA
1 ACCAATATGGGAAGACAAGATCTGCTATCTTCGATCCACTTCTAC--CAATACAGGAAGACAAGA
40804404 TCTGCTT-TCTTCGATCTACTTCGCC
64 TCTG-TTATCTTCGATCTACTTCGCC
* * * *
40804429 ACCAGTATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTCGCTACCAATATAGGAAGATAGGA
1 ACCAATATGGGAAGACAAGATCTGCTATCTTCGATCCACTT--CTACCAATACAGGAAGACAAGA
40804493 TCTGTTATCTTCGATCTACTTCAAG-C
64 TCTGTTATCTTCGATCTACTTC--GCC
*** * * * * ** * * **
40804519 A--AATACATGAAGACAAGATTTCCTTTTTTCGATATACTTCGCCACCAGTATGGGAAGACAAGA
1 ACCAATATGGGAAGACAAGATCTGCTATCTTCGATCCACTT--CTACCAATACAGGAAGACAAGA
* * * *
40804582 TATG-CATCTTCGATCCACTTCGCT
64 TCTGTTATCTTCGATCTACTTCGCC
* * * * * *
40804606 ACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTC-ACGCCAATATATGAAGACAAGA
1 ACCAATATGGGAAGACAAGATCTGCTATCTTCGATCCACTTCTA--CCAATACAGGAAGACAAGA
40804670 TCT
64 TCT
40804673 ACTATTTTTT
Statistics
Matches: 328, Mismatches: 73, Indels: 39
0.75 0.17 0.09
Matches are distributed among these distances:
86 4 0.01
87 25 0.08
88 154 0.47
89 139 0.42
90 3 0.01
91 3 0.01
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (88 bp):
ACCAATATGGGAAGACAAGATCTGCTATCTTCGATCCACTTCTACCAATACAGGAAGACAAGATC
TGTTATCTTCGATCTACTTCGCC
Found at i:40804524 original size:133 final size:133
Alignment explanation
Indices: 40804267--40804672 Score: 532
Period size: 133 Copynumber: 3.1 Consensus size: 133
40804257 ATGTGGGAAT
* * * * ** * * *
40804267 ACAAGATCTGC-ATCTTCGATCCACTTC-CTACCAATACAGGAAGACAGGATATGTTATCATCGA
1 ACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATATG-CATCTTCGA
* * * * * * **
40804330 TCTACTTCAC-GCCAATACAGGAAGACAAGCTCTGCTT-TCTTCGATCTACTTCACGTTAATACA
65 TCCACTTCGCTACCAATATAGGAAGACAGGATCTG-TTATCTTCGATCTACTTCACGCAAATACA
40804393 TGAAG
129 TGAAG
*
40804398 ACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGAT
1 ACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATATGCATCTTCGAT
* *
40804463 CCACTTCGCTACCAATATAGGAAGATAGGATCTGTTATCTTCGATCTACTTCAAGCAAATACATG
66 CCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTCACGCAAATACATG
40804528 AAG
131 AAG
* * * *
40804531 ACAAGATTTCCTTTTTTCGATATACTTCGCCACCAGTATGGGAAGACAAGATATGCATCTTCGAT
1 ACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATATGCATCTTCGAT
* *
40804596 CCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTCACGCCAATATATG
66 CCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTCACGCAAATACATG
40804661 AAG
131 AAG
40804664 ACAAGATCT
1 ACAAGATCT
40804673 ACTATTTTTT
Statistics
Matches: 241, Mismatches: 30, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
131 11 0.05
132 31 0.13
133 199 0.83
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (133 bp):
ACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATATGCATCTTCGAT
CCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTCACGCAAATACATG
AAG
Found at i:40804594 original size:177 final size:176
Alignment explanation
Indices: 40804175--40804666 Score: 533
Period size: 177 Copynumber: 2.8 Consensus size: 176
40804165 CCAATATAGA
* * * * * * * *
40804175 AAGACAGGATCTGCTATT-TTCGATCTACTTCA-AGCCAATACATGAAGATAATATCTGCTTTCT
1 AAGACAAGATCTCCT-TTCTTCGATATACTTCACA-CCAATACAGGAAGACAAGATATGCTATCT
* *
40804238 TCGATCTACTTCGCCACCAATGTGGGAATACAAGATCTGCATCTTCGATCCACTTCCTACCAATA
64 TCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATA
* * *
40804303 CAGGAAGACAGGATATGTTATCATCGATCTACTTCACGCCAATACAGG
129 TAGGAAGACAGGATATGTTATCATCGATCTACTTCAAGCAAATACAGG
* * * *** * * *
40804351 AAGACAAGCTCTGCTTTCTTCGATCTACTTCACGTTAATACATGAAGACAAGATCTGCTTTCTTC
1 AAGACAAGATCTCCTTTCTTCGATATACTTCACACCAATACAGGAAGACAAGATATGCTATCTTC
*
40804416 GATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATAT
66 GATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTC-CTACCAATAT
* * * *
40804481 AGGAAGATAGGATCTGTTATCTTCGATCTACTTCAAGCAAATACATG
130 AGGAAGACAGGATATGTTATCATCGATCTACTTCAAGCAAATACAGG
* * * * **
40804528 AAGACAAGATTTCCTTTTTTCGATATACTTCGCCACCAGTATGGGAAGACAAGATATGC-ATCTT
1 AAGACAAGATCTCCTTTCTTCGATATACTTC-ACACCAATACAGGAAGACAAGATATGCTATCTT
* * * * * * *
40804592 CGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTCAC-GCCAAT
65 CGATCTACTTCGCCACCAATATGGGAAGACAAGATCTG-CATCTTCGATCCACTTC-CTACCAAT
*
40804656 ATATGAAGACA
128 ATAGGAAGACA
40804667 AGATCTACTA
Statistics
Matches: 268, Mismatches: 43, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
175 2 0.01
176 105 0.39
177 127 0.47
178 34 0.13
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.29
Consensus pattern (176 bp):
AAGACAAGATCTCCTTTCTTCGATATACTTCACACCAATACAGGAAGACAAGATATGCTATCTTC
GATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATA
GGAAGACAGGATATGTTATCATCGATCTACTTCAAGCAAATACAGG
Found at i:40805525 original size:24 final size:26
Alignment explanation
Indices: 40805498--40805545 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
40805488 AGTGTCTTGA
40805498 AAAGAA-AAAGTATT-CAAGAACAGC
1 AAAGAATAAAGTATTACAAGAACAGC
40805522 AAAGAATAAAGTATTACAAGAACA
1 AAAGAATAAAGTATTACAAGAACA
40805546 AACAAATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 6 0.27
25 8 0.36
26 8 0.36
ACGTcount: A:0.60, C:0.10, G:0.15, T:0.15
Consensus pattern (26 bp):
AAAGAATAAAGTATTACAAGAACAGC
Found at i:40812065 original size:360 final size:360
Alignment explanation
Indices: 40811404--40812129 Score: 1443
Period size: 360 Copynumber: 2.0 Consensus size: 360
40811394 TTTAACAACG
40811404 CCCATACTTATGAGTCTTTCAACCAGCTTTTTGAACACCGTACAATGCTCTATGGAATACCCCAC
1 CCCATACTTATGAGTCTTTCAACCAGCTTTTTGAACACCGTACAATGCTCTATGGAATACCCCAC
*
40811469 GATTTTCGCATGATAATCGCATTGTGCTTTTGCATCGTACCACTTGAGGTACGAAGGCTGCAGAG
66 GATTTCCGCATGATAATCGCATTGTGCTTTTGCATCGTACCACTTGAGGTACGAAGGCTGCAGAG
40811534 GTTCTAAATAAAAAGGAGAAACTACGTGTGCATTGAATAACTTTTGATACAACTCCTTATACGAC
131 GTTCTAAATAAAAAGGAGAAACTACGTGTGCATTGAATAACTTTTGATACAACTCCTTATACGAC
40811599 ATTGGAATGGGCGTAAACTGGGGCTTTTCCTTGTTTTGCCTTGTGTTGGCTCCTTGTTTGTCAAC
196 ATTGGAATGGGCGTAAACTGGGGCTTTTCCTTGTTTTGCCTTGTGTTGGCTCCTTGTTTGTCAAC
40811664 AGCCACCTTTCTCGGCTGATTCACCGTAATCATCTTTGAATAACTGGCATTATTGACCTCGTTTT
261 AGCCACCTTTCTCGGCTGATTCACCGTAATCATCTTTGAATAACTGGCATTATTGACCTCGTTTT
40811729 CCTTTTTCTTCGAGGTTGACCTTCTACTACTTTCT
326 CCTTTTTCTTCGAGGTTGACCTTCTACTACTTTCT
40811764 CCCATACTTATGAGTCTTTCAACCAGCTTTTTGAACACCGTACAATGCTCTATGGAATACCCCAC
1 CCCATACTTATGAGTCTTTCAACCAGCTTTTTGAACACCGTACAATGCTCTATGGAATACCCCAC
40811829 GATTTCCGCATGATAATCGCATTGTGCTTTTGCATCGTACCACTTGAGGTACGAAGGCTGCAGAG
66 GATTTCCGCATGATAATCGCATTGTGCTTTTGCATCGTACCACTTGAGGTACGAAGGCTGCAGAG
40811894 GTTCTAAATAAAAAGGAGAAACTACGTGTGCATTGAATAACTTTTGATACAACTCCTTATACGAC
131 GTTCTAAATAAAAAGGAGAAACTACGTGTGCATTGAATAACTTTTGATACAACTCCTTATACGAC
40811959 ATTGGAATGGGCGTAAACTGGGGCTTTTCCTTGTTTTGCCTTGTGTTGGCTCCTTGTTTGTCAAC
196 ATTGGAATGGGCGTAAACTGGGGCTTTTCCTTGTTTTGCCTTGTGTTGGCTCCTTGTTTGTCAAC
40812024 AGCCACCTTTCTCGGCTGATTCACCGTAATCATCTTTGAATAACTGGCATTATTGACCTCGTTTT
261 AGCCACCTTTCTCGGCTGATTCACCGTAATCATCTTTGAATAACTGGCATTATTGACCTCGTTTT
40812089 CCTTTTTCTTCGAGGTTGACCTTCTACTACTTTCT
326 CCTTTTTCTTCGAGGTTGACCTTCTACTACTTTCT
40812124 CCCATA
1 CCCATA
40812130 TCTATCTTCC
Statistics
Matches: 365, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
360 365 1.00
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.35
Consensus pattern (360 bp):
CCCATACTTATGAGTCTTTCAACCAGCTTTTTGAACACCGTACAATGCTCTATGGAATACCCCAC
GATTTCCGCATGATAATCGCATTGTGCTTTTGCATCGTACCACTTGAGGTACGAAGGCTGCAGAG
GTTCTAAATAAAAAGGAGAAACTACGTGTGCATTGAATAACTTTTGATACAACTCCTTATACGAC
ATTGGAATGGGCGTAAACTGGGGCTTTTCCTTGTTTTGCCTTGTGTTGGCTCCTTGTTTGTCAAC
AGCCACCTTTCTCGGCTGATTCACCGTAATCATCTTTGAATAACTGGCATTATTGACCTCGTTTT
CCTTTTTCTTCGAGGTTGACCTTCTACTACTTTCT
Found at i:40817262 original size:16 final size:16
Alignment explanation
Indices: 40817237--40817267 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40817227 TCGTTAAAAT
40817237 ATGTAAATATATACAC
1 ATGTAAATATATACAC
*
40817253 ATGTACATATATACA
1 ATGTAAATATATACA
40817268 AATATATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.32
Consensus pattern (16 bp):
ATGTAAATATATACAC
Found at i:40822621 original size:9 final size:9
Alignment explanation
Indices: 40822607--40822637 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
40822597 TTTGGTTAAA
40822607 AATTAACCG
1 AATTAACCG
40822616 AATTAACCG
1 AATTAACCG
*
40822625 AATTACCCG
1 AATTAACCG
40822634 AATT
1 AATT
40822638 GAATCACTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:40822667 original size:17 final size:17
Alignment explanation
Indices: 40822645--40822707 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
40822635 ATTGAATCAC
40822645 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
** * *
40822662 TACATAAGTCTTTGAATCAC
1 TACATAA---TTAAAAACAT
40822682 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
40822699 TACATAATT
1 TACATAATT
40822708 CTTGAAATTA
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
17 22 0.63
20 13 0.37
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.33
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:40822683 original size:37 final size:37
Alignment explanation
Indices: 40822636--40822710 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
40822626 ATTACCCGAA
40822636 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
*
40822673 TTGAATCACTACATAATTAAAAACATTACATAATTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
40822710 T
1 T
40822711 GAAATTAACA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.35
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:40822724 original size:37 final size:37
Alignment explanation
Indices: 40822636--40822727 Score: 125
Period size: 37 Copynumber: 2.5 Consensus size: 37
40822626 ATTACCCGAA
*
40822636 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
1 TTGAATAACTACATAATTAAAAACATTACATAAGTCT
* *
40822673 TTGAATCACTACATAATTAAAAACATTACATAATTC-
1 TTGAATAACTACATAATTAAAAACATTACATAAGTCT
40822709 TTGAAATTAAC-ACATAATT
1 TTG-AA-TAACTACATAATT
40822728 GAAATGTAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
36 3 0.06
37 45 0.88
38 3 0.06
ACGTcount: A:0.47, C:0.15, G:0.04, T:0.34
Consensus pattern (37 bp):
TTGAATAACTACATAATTAAAAACATTACATAAGTCT
Found at i:40822884 original size:38 final size:39
Alignment explanation
Indices: 40822840--40822913 Score: 123
Period size: 38 Copynumber: 1.9 Consensus size: 39
40822830 GACTTAGAGT
* *
40822840 TAGACTTTAGTTTTATTTTTATTGGGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTCGGTTGGGTAATTGGG
40822878 TAGACTTTAGTTTTAGTTTTATTCGGTTGGGTAATT
1 TAGACTTTAGTTTTAGTTTTATTCGGTTGGGTAATT
40822914 CGGTTGGGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
38 26 0.79
39 7 0.21
ACGTcount: A:0.19, C:0.04, G:0.24, T:0.53
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTCGGTTGGGTAATTGGG
Found at i:40822916 original size:13 final size:13
Alignment explanation
Indices: 40822898--40822952 Score: 56
Period size: 13 Copynumber: 3.9 Consensus size: 13
40822888 TTTTAGTTTT
40822898 ATTCGGTTGGGTA
1 ATTCGGTTGGGTA
40822911 ATTCGGTTGGGTTGGTA
1 ATTCGGTT--G--GGTA
*
40822928 ATTGGGTTGGGTA
1 ATTCGGTTGGGTA
*
40822941 ATTAGGTTGGGT
1 ATTCGGTTGGGT
40822953 TAGATAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
13 23 0.64
15 2 0.06
17 11 0.31
ACGTcount: A:0.15, C:0.04, G:0.42, T:0.40
Consensus pattern (13 bp):
ATTCGGTTGGGTA
Found at i:40822929 original size:17 final size:18
Alignment explanation
Indices: 40822902--40822939 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
40822892 AGTTTTATTC
40822902 GGTTGGGTAATTCGGTTG
1 GGTTGGGTAATTCGGTTG
*
40822920 GGTT-GGTAATTGGGTTG
1 GGTTGGGTAATTCGGTTG
40822937 GGT
1 GGT
40822940 AATTAGGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.11, C:0.03, G:0.47, T:0.39
Consensus pattern (18 bp):
GGTTGGGTAATTCGGTTG
Found at i:40824586 original size:38 final size:37
Alignment explanation
Indices: 40824506--40824586 Score: 85
Period size: 38 Copynumber: 2.2 Consensus size: 37
40824496 TAATCACTTT
*
40824506 AATATTAAATTAATATAATATTTATCAAGATAAATAT
1 AATATTAAATTAATATAATATTTATCAAGATAAATAG
* * *
40824543 TATATTAAATTTAATATTAA-ATCTTATTAA-ATTAATAG
1 AATATTAAA-TTAATA-TAATAT-TTATCAAGATAAATAG
40824581 AATATT
1 AATATT
40824587 TTTTAACAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
37 8 0.22
38 19 0.53
39 9 0.25
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (37 bp):
AATATTAAATTAATATAATATTTATCAAGATAAATAG
Found at i:40824613 original size:62 final size:58
Alignment explanation
Indices: 40824508--40824634 Score: 191
Period size: 62 Copynumber: 2.1 Consensus size: 58
40824498 ATCACTTTAA
* * *
40824508 TATTAAATTAATATAATATTTATCAAGATAAATATTATATTAAATTTAATATTAAATC
1 TATTAAATTAATAGAATATTTAACAAGATAAATATTAAATTAAATTTAATATTAAATC
40824566 TTATTAAATTAATAGAATATTTTTTAACAAGATAAATATTAAATTAAATTTAATATTAAATC
1 -TATTAAATTAATAGAATA---TTTAACAAGATAAATATTAAATTAAATTTAATATTAAATC
40824628 TATTAAA
1 TATTAAA
40824635 ATATTATTAT
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
59 17 0.27
61 7 0.11
62 38 0.61
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.44
Consensus pattern (58 bp):
TATTAAATTAATAGAATATTTAACAAGATAAATATTAAATTAAATTTAATATTAAATC
Found at i:40829070 original size:20 final size:20
Alignment explanation
Indices: 40829045--40829082 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
40829035 CCTCAAACTT
*
40829045 TTATTCCTCAAAACTTTTTA
1 TTATTCCCCAAAACTTTTTA
40829065 TTATTCCCCAAAACTTTT
1 TTATTCCCCAAAACTTTT
40829083 ACTTCTCACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.47
Consensus pattern (20 bp):
TTATTCCCCAAAACTTTTTA
Found at i:40830541 original size:26 final size:26
Alignment explanation
Indices: 40830516--40830575 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
40830506 AGATAATAAT
*
40830516 TAAAAATAAT-TTAATTATATTTTAA
1 TAAAAATAATATTAAATATATTTTAA
* * **
40830541 TATAATTCTTATTAAATATATTTTAA
1 TAAAAATAATATTAAATATATTTTAA
40830567 TAAAAATAA
1 TAAAAATAA
40830576 AAATATATAA
Statistics
Matches: 25, Mismatches: 9, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
TAAAAATAATATTAAATATATTTTAA
Found at i:40832527 original size:19 final size:20
Alignment explanation
Indices: 40832503--40832540 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
40832493 TTTATAATTT
*
40832503 ATTCTGTTTTTA-TTTTTTA
1 ATTCTGTTATTACTTTTTTA
40832522 ATTCTGTTATTACTTTTTT
1 ATTCTGTTATTACTTTTTT
40832541 TTTTTGTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.16, C:0.08, G:0.05, T:0.71
Consensus pattern (20 bp):
ATTCTGTTATTACTTTTTTA
Found at i:40840475 original size:21 final size:20
Alignment explanation
Indices: 40840449--40840492 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
40840439 ATAATAGAAT
*
40840449 AAATAATTCATGAAGTTAAAA
1 AAATAACTC-TGAAGTTAAAA
* *
40840470 AAATAACTCTTAATTTAAAA
1 AAATAACTCTGAAGTTAAAA
40840490 AAA
1 AAA
40840493 ATAAATGTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.30
Consensus pattern (20 bp):
AAATAACTCTGAAGTTAAAA
Found at i:40841344 original size:22 final size:22
Alignment explanation
Indices: 40841319--40841366 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
40841309 GAAAGTATAG
*
40841319 TGAACCATGAAATGCTTATGAT
1 TGAACCATGAAATGCTTACGAT
*
40841341 TGAACCATGAAATTCTTACGAT
1 TGAACCATGAAATGCTTACGAT
40841363 TGAA
1 TGAA
40841367 TTGAATGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.31
Consensus pattern (22 bp):
TGAACCATGAAATGCTTACGAT
Found at i:40842697 original size:28 final size:27
Alignment explanation
Indices: 40842633--40842697 Score: 62
Period size: 28 Copynumber: 2.4 Consensus size: 27
40842623 AATAATTAAA
*
40842633 GAAATAAAATAATAAAAATGAAATATT
1 GAAATAAAATAATAAAAATGAAATATG
* *
40842660 GAAA-AGAAATAAATAAAGGATTAAAT-TG
1 GAAATA-AAAT-AATAAA-AATGAAATATG
40842688 GAAATAAAAT
1 GAAATAAAAT
40842698 GAAACTAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
26 1 0.03
27 8 0.26
28 15 0.48
29 7 0.23
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.23
Consensus pattern (27 bp):
GAAATAAAATAATAAAAATGAAATATG
Found at i:40844636 original size:45 final size:44
Alignment explanation
Indices: 40844384--40845180 Score: 729
Period size: 44 Copynumber: 17.8 Consensus size: 44
40844374 GTGCTTGCTG
* * * * * * *
40844384 CTTCAATCTACTCTACTGCAACTTTAGGGAGATTAGACTTGCAG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAT
* * ** *
40844428 CTTTAATCTGCTCTACTGCAACTTCAAAGAGATAAGACTTGTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAT
* * * *
40844472 CTTCAATCTACTCCATTGCAACTTCAAGGAGAT--GATTTGTAG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAT
* * *
40844514 CTTTAATCTGCTCCACTGCAATTTCAGGGAGATAAGATTCATAACTTGTAG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAG----AT---TTGTAT
* ** *
40844565 CTTTAATCTATTCCACTGCAACTTCAGGGAAATAAGATTTGCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAT
* *
40844610 CTTCAATCTGCTCCACTGCAATTTCAGGGAGATAAGATTTGTAA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAT
* * *
40844654 CTTCAATCTGCTCCACTACAACTTCCGGGAGATAAGATTTGTAA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAT
** * * *
40844698 CTTCAATCTATTCCACTGCAACTTCAAGGAGATAAGACTTGTAA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAT
* * * * * **
40844742 CTTTAATCTGTTCTACTGCAATTTCAGGGAAATAAGATTCACTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-TGTAT
* * *
40844787 CTTCAATCTACTCCACTGCAACTTCAGAGAAATAAGATTCAT-TAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT--TGTAT
* * **
40844832 CTTCAATCTGTTCTACTGCAACTTCAGGGAGATAAGATTCACTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-TGTAT
* * * *
40844877 CTTCAATTTGCTCCACTACAACTTCAGAGAGATAAGATTTGGAGT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTA-T
* * * * * * *
40844922 -TTTAATCTGCTCTATTGTAACTTTAGAGAGATAAGATTTACTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTT-GTAT
* * *
40844966 CTTCAATTTGCTCCACTGCAACTTCAGGAAGTTAAGATTTGCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAT
**
40845011 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAT
* * * * *
40845055 CTTTAATTTACTCCACTACAACTTCAGGGAGACAAGATTTGCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAT
* * * **
40845100 CTTCAATCTGCTCTATTCCAACTTCAGGGAGATAAGATTTGTGG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAT
* * * *
40845144 CTTTAATATGCTTCACTGCAACTTCAGGGGGATAAGA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA
40845181 ATCGCTATGA
Statistics
Matches: 615, Mismatches: 120, Indels: 36
0.80 0.16 0.05
Matches are distributed among these distances:
42 35 0.06
44 283 0.46
45 255 0.41
47 2 0.00
48 2 0.00
51 38 0.06
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (44 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAT
Found at i:40844676 original size:89 final size:89
Alignment explanation
Indices: 40844384--40845180 Score: 748
Period size: 89 Copynumber: 8.9 Consensus size: 89
40844374 GTGCTTGCTG
* * * * * *
40844384 CTTCAATCTACTCTACTGCAACTTTAGGGAGATTAGACTTGC-AGCTTTAATCTGCTCTACTGCA
1 CTTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGATTTGCTAGCTTCAATCTGCTCCACTGCA
** *
40844448 ACTTCAAAGAGATAAGACTTGTAT
66 ACTTCAGGGAGATAAGATTTGTAT
* * * * *
40844472 CTTCAATCTACTCCATTGCAACTTCAAGGAGAT--GATTTG-TAGCTTTAATCTGCTCCACTGCA
1 CTTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGATTTGCTAGCTTCAATCTGCTCCACTGCA
* *
40844534 ATTTCAGGGAGATAAGATTCATAACTTGTAG
66 ACTTCAGGGAGATAAG----AT---TTGTAT
* ** * * *
40844565 CTTTAATCTATTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAATCTGCTCCACTGCA
1 CTTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGATTTGCTAGCTTCAATCTGCTCCACTGCA
* *
40844630 ATTTCAGGGAGATAAGATTTGTAA
66 ACTTCAGGGAGATAAGATTTGTAT
* * * * **
40844654 CTTCAATCTGCTCCACTACAACTTCCGGGAGATAAGATTTG-TAACTTCAATCTATTCCACTGCA
1 CTTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGATTTGCTAGCTTCAATCTGCTCCACTGCA
* * *
40844718 ACTTCAAGGAGATAAGACTTGTAA
66 ACTTCAGGGAGATAAGATTTGTAT
* * * * ** * *
40844742 CTTTAATCTGTTCTACTGCAATTTCAGGGAAATAAGATTCACTATCTTCAATCTACTCCACTGCA
1 CTTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGATTTGCTAGCTTCAATCTGCTCCACTGCA
* *
40844807 ACTTCAGAGAAATAAGATTCAT-TAT
66 ACTTCAGGGAGATAAGATT--TGTAT
* ** * * *
40844832 CTTCAATCTGTTCTACTGCAACTTCAGGGAGATAAGATTCACTATCTTCAATTTGCTCCACTACA
1 CTTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGATTTGCTAGCTTCAATCTGCTCCACTGCA
* *
40844897 ACTTCAGAGAGATAAGATTTGGAGT
66 ACTTCAGGGAGATAAGATTTGTA-T
* * * * * * * *
40844922 -TTTAATCTGCTCTATTGTAACTTTAGAGAGATAAGATTTACTATCTTCAATTTGCTCCACTGCA
1 CTTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGATTTGCTAGCTTCAATCTGCTCCACTGCA
* *
40844986 ACTTCAGGAAGTTAAGATTTGCTAT
66 ACTTCAGGGAGATAAGATTTG-TAT
* * * * * *
40845011 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TGGCTTTAATTTACTCCACTACA
1 CTTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGATTTGCTAGCTTCAATCTGCTCCACTGCA
*
40845075 ACTTCAGGGAGACAAGATTTGCTAT
66 ACTTCAGGGAGATAAGATTTG-TAT
* * * * * *
40845100 CTTCAATCTGCTCTATTCCAACTTCAGGGAGATAAGATTTG-TGGCTTTAATATGCTTCACTGCA
1 CTTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGATTTGCTAGCTTCAATCTGCTCCACTGCA
*
40845164 ACTTCAGGGGGATAAGA
66 ACTTCAGGGAGATAAGA
40845181 ATCGCTATGA
Statistics
Matches: 600, Mismatches: 91, Indels: 35
0.83 0.13 0.05
Matches are distributed among these distances:
86 39 0.06
88 103 0.17
89 264 0.44
90 115 0.19
91 1 0.00
92 2 0.00
93 33 0.05
95 6 0.01
96 37 0.06
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (89 bp):
CTTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGATTTGCTAGCTTCAATCTGCTCCACTGCA
ACTTCAGGGAGATAAGATTTGTAT
Found at i:40865700 original size:9 final size:9
Alignment explanation
Indices: 40865686--40865756 Score: 61
Period size: 9 Copynumber: 7.6 Consensus size: 9
40865676 TTTTGCCGAA
40865686 AAATATTAT
1 AAATATTAT
40865695 AAATATTAT
1 AAATATTAT
*
40865704 AAAAATTAT
1 AAATATTAT
*
40865713 AAAATATAAT
1 -AAATATTAT
*
40865723 AAATTATTAG
1 AAA-TATTAT
* *
40865733 AAATTTTAAA
1 AAATATT-AT
*
40865743 AAATATTAA
1 AAATATTAT
40865752 AAATA
1 AAATA
40865757 CCAAATAATT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
9 30 0.59
10 21 0.41
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (9 bp):
AAATATTAT
Found at i:40865717 original size:19 final size:19
Alignment explanation
Indices: 40865685--40865756 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
40865675 ATTTTGCCGA
*
40865685 AAAATATTATAAATATTAT
1 AAAATATTATAAATATAAT
40865704 AAAA-ATTATAAAATATAAT
1 AAAATATTAT-AAATATAAT
* * *
40865723 AAATTATTAGAAATTTTAA-
1 AAAATATTATAAA-TATAAT
*
40865742 AAAATATTAAAAATA
1 AAAATATTATAAATA
40865757 CCAAATAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
18 6 0.14
19 29 0.67
20 8 0.19
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (19 bp):
AAAATATTATAAATATAAT
Found at i:40865736 original size:10 final size:10
Alignment explanation
Indices: 40865684--40865824 Score: 57
Period size: 10 Copynumber: 14.3 Consensus size: 10
40865674 AATTTTGCCG
40865684 AAAAA-TATT
1 AAAAATTATT
40865693 ATAAATATTA-T
1 A-AAA-ATTATT
40865704 AAAAATTA-T
1 AAAAATTATT
40865713 -AAAA-TA-T
1 AAAAATTATT
40865720 AATAAATTATT
1 AA-AAATTATT
*
40865731 AGAAATT-TT
1 AAAAATTATT
*
40865740 AAAAAATATT
1 AAAAATTATT
**
40865750 AAAAA-TACC
1 AAAAATTATT
*
40865759 AAATAATTATAAA
1 AAA-AATTAT--T
*
40865772 AAAAATT-TG
1 AAAAATTATT
40865781 AAAAATTATT
1 AAAAATTATT
* * *
40865791 AAAATTTGTA
1 AAAAATTATT
*
40865801 AAAAGATTAGT
1 AAAA-ATTATT
*
40865812 AAAGATTATT
1 AAAAATTATT
40865822 AAA
1 AAA
40865825 GAAATATGTG
Statistics
Matches: 100, Mismatches: 18, Indels: 27
0.69 0.12 0.19
Matches are distributed among these distances:
7 3 0.03
8 5 0.05
9 28 0.28
10 42 0.42
11 13 0.13
12 6 0.06
13 3 0.03
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.34
Consensus pattern (10 bp):
AAAAATTATT
Found at i:40865745 original size:29 final size:28
Alignment explanation
Indices: 40865684--40865756 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 28
40865674 AATTTTGCCG
* *
40865684 AAAAATATTATAAATATTATAAAAATTA
1 AAAAATATAATAAATATTAGAAAAATTA
* **
40865712 TAAAATATAATAAATTATTAGAAATTTTA
1 AAAAATATAATAAA-TATTAGAAAAATTA
40865741 AAAAATATTAA-AAATA
1 AAAAATA-TAATAAATA
40865757 CCAAATAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
28 14 0.38
29 20 0.54
30 3 0.08
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (28 bp):
AAAAATATAATAAATATTAGAAAAATTA
Found at i:40867073 original size:21 final size:22
Alignment explanation
Indices: 40867048--40867103 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
40867038 AGTCAATTTT
*
40867048 CACACGGGCGTGTGTTC-TGGA
1 CACACGGGCGTGTGCTCGTGGA
* *
40867069 CACACGGTCGTGT-CTCGTGGG
1 CACACGGGCGTGTGCTCGTGGA
*
40867090 CACACAGGCGTGTG
1 CACACGGGCGTGTG
40867104 AGGCTTCCAC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.14, C:0.27, G:0.38, T:0.21
Consensus pattern (22 bp):
CACACGGGCGTGTGCTCGTGGA
Found at i:40872114 original size:20 final size:19
Alignment explanation
Indices: 40872089--40872127 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
40872079 CAGGGTACGA
*
40872089 AAGTGCATACATGAGCATCG
1 AAGTGCAAACATGA-CATCG
40872109 AAGTGCAAACATGACATCG
1 AAGTGCAAACATGACATCG
40872128 GAGTACATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (19 bp):
AAGTGCAAACATGACATCG
Found at i:40874119 original size:18 final size:17
Alignment explanation
Indices: 40874096--40874129 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40874086 GTTGGGTCGA
40874096 AATGGGTCGTGTGGGCCC
1 AATGGG-CGTGTGGGCCC
*
40874114 AATGGGCTTGTGGGCC
1 AATGGGCGTGTGGGCC
40874130 TCACATAGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.12, C:0.21, G:0.44, T:0.24
Consensus pattern (17 bp):
AATGGGCGTGTGGGCCC
Found at i:40877007 original size:37 final size:38
Alignment explanation
Indices: 40876932--40877029 Score: 117
Period size: 37 Copynumber: 2.6 Consensus size: 38
40876922 GGCTTAGACC
* **
40876932 CACTATTGTGCTGTGTAGGGTGGACGAGCATATTATAG
1 CACTATTGTGGTGTGTAGGGTGGACGAGCATACCATAG
* * *
40876970 C-CTATTGTGGTGTGCAGGGTGGACGGGCCTACCATAG
1 CACTATTGTGGTGTGTAGGGTGGACGAGCATACCATAG
* *
40877007 CACAATTGTGGTATGTAGGGTGG
1 CACTATTGTGGTGTGTAGGGTGG
40877030 TCGGAGTGGT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
37 31 0.62
38 19 0.38
ACGTcount: A:0.20, C:0.15, G:0.36, T:0.29
Consensus pattern (38 bp):
CACTATTGTGGTGTGTAGGGTGGACGAGCATACCATAG
Found at i:40878554 original size:18 final size:18
Alignment explanation
Indices: 40878533--40878571 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
40878523 TTGATTTTCG
40878533 AATTCGAAT-AACTCGAAT
1 AATTCGAATAAAC-CGAAT
40878551 AATTCGAATAAACCGAAT
1 AATTCGAATAAACCGAAT
40878569 AAT
1 AAT
40878572 AAACTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.26
Consensus pattern (18 bp):
AATTCGAATAAACCGAAT
Found at i:40880782 original size:6 final size:6
Alignment explanation
Indices: 40880771--40880796 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
40880761 AGTTGTAAAG
40880771 TTTTAT TTTTAT TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TT
40880797 ATTTATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:40889644 original size:41 final size:39
Alignment explanation
Indices: 40889556--40889644 Score: 88
Period size: 41 Copynumber: 2.2 Consensus size: 39
40889546 TTTAAACAGA
* * * *
40889556 TTCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATTT
1 TTCATCGGCACTTAGCCTGCTAGACATAAAGCCTGATGT
* *
40889595 TGTACATCGGCACTTAGCCTGCTAGACATATAGTCTGAAATGT
1 T-T-CATCGGCACTTAGCCTGCTAGACATAAAGCCTG--ATGT
40889638 TTCATCG
1 TTCATCG
40889645 ACATCAAGCT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
39 1 0.03
40 1 0.03
41 33 0.82
42 1 0.03
43 4 0.10
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (39 bp):
TTCATCGGCACTTAGCCTGCTAGACATAAAGCCTGATGT
Found at i:40889703 original size:15 final size:15
Alignment explanation
Indices: 40889683--40889711 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40889673 AATTATTTCA
40889683 CTGACAATAAACCTG
1 CTGACAATAAACCTG
40889698 CTGACAATAAACCT
1 CTGACAATAAACCT
40889712 AATAGGCACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.28, G:0.10, T:0.21
Consensus pattern (15 bp):
CTGACAATAAACCTG
Found at i:40889973 original size:91 final size:91
Alignment explanation
Indices: 40889818--40889999 Score: 355
Period size: 91 Copynumber: 2.0 Consensus size: 91
40889808 ATAATTTATT
40889818 AACTATATCTTTAAACCACATAGATATATAAAGATCAAATACCAAATTCAGCTAAATAATTTAAT
1 AACTATATCTTTAAACCACATAGATATATAAAGATCAAATACCAAATTCAGCTAAATAATTTAAT
40889883 TATACATCCGAACACTCACATATATA
66 TATACATCCGAACACTCACATATATA
*
40889909 AACTATATCTTTAAACCACATAGATATGTAAAGATCAAATACCAAATTCAGCTAAATAATTTAAT
1 AACTATATCTTTAAACCACATAGATATATAAAGATCAAATACCAAATTCAGCTAAATAATTTAAT
40889974 TATACATCCGAACACTCACATATATA
66 TATACATCCGAACACTCACATATATA
40890000 TATATAACTT
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 90 1.00
ACGTcount: A:0.47, C:0.19, G:0.05, T:0.30
Consensus pattern (91 bp):
AACTATATCTTTAAACCACATAGATATATAAAGATCAAATACCAAATTCAGCTAAATAATTTAAT
TATACATCCGAACACTCACATATATA
Found at i:40890304 original size:76 final size:77
Alignment explanation
Indices: 40890209--40890351 Score: 191
Period size: 76 Copynumber: 1.9 Consensus size: 77
40890199 CAATACAAAA
* *
40890209 ACTTATACATGTATATACATACATATTCGAAATTACATATAC-ATACATAACATTCATACCTTTA
1 ACTTATACATGTATATACATACATATTCCAAATCACATATACAATACATAACATTCATACCTTTA
40890273 AATATATTCAAG
66 AATATATTCAAG
* * * * *
40890285 ACTTATTCATG-AGTATACATATATGTTCCAACTCACATATACATATATATAACATTCATACCTT
1 ACTTATACATGTA-TATACATACATATTCCAAATCACATATACA-ATACATAACATTCATACCTT
40890349 TAA
64 TAA
40890352 CCACGTCCAA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
75 1 0.02
76 34 0.60
78 22 0.39
ACGTcount: A:0.41, C:0.18, G:0.04, T:0.36
Consensus pattern (77 bp):
ACTTATACATGTATATACATACATATTCCAAATCACATATACAATACATAACATTCATACCTTTA
AATATATTCAAG
Found at i:40891826 original size:34 final size:34
Alignment explanation
Indices: 40891783--40891852 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
40891773 TTTCATGAAC
40891783 AAATAAGATGCTTAAAACAATATGTAACCCATGT
1 AAATAAGATGCTTAAAACAATATGTAACCCATGT
* *
40891817 AAATGAGATGCTTAAAACAATATGTAACTCATGT
1 AAATAAGATGCTTAAAACAATATGTAACCCATGT
40891851 AA
1 AA
40891853 TCAAAACTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (34 bp):
AAATAAGATGCTTAAAACAATATGTAACCCATGT
Found at i:40894942 original size:3 final size:3
Alignment explanation
Indices: 40894934--40894963 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
40894924 TTGGTTGAGG
*
40894934 GAA GAA GAA GAA GAA GAA AAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
40894964 CGGGGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:40899958 original size:15 final size:17
Alignment explanation
Indices: 40899932--40899964 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
40899922 TTACAATAAT
40899932 AATTAGTATAGTA-ACA
1 AATTAGTATAGTATACA
40899948 AATTA-TATAGTATACA
1 AATTAGTATAGTATACA
40899964 A
1 A
40899965 GTCCTACCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (17 bp):
AATTAGTATAGTATACA
Found at i:40909361 original size:6 final size:6
Alignment explanation
Indices: 40909344--40909378 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
40909334 AATTCCAACC
40909344 AAAATT -AAATT AAAATT AAAATT AAAATT AAAATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT
40909379 TTAAATAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
AAAATT
Found at i:40911407 original size:27 final size:27
Alignment explanation
Indices: 40911372--40911624 Score: 287
Period size: 27 Copynumber: 9.4 Consensus size: 27
40911362 CCCTAAAATA
* * *
40911372 GGTATAATGACCGTAATGCCCTTATAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
* *
40911399 GGTAAAATGACCGTAATGTCCTTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
**
40911426 GGTAAAATGAATGTAATGCCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
* *
40911453 GGTAAAAAGACCATAATGCCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
* * *
40911480 GATAAAATGACTGTAATACCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
* * *
40911507 GATAAAATGACCGTAATACTCCC-ATAG
1 GGTAAAATGACCGTAATGC-CCCTGTAG
* *
40911534 GATAAAATGATCGTAATGCCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
* * *
40911561 GGTAAAATGACTGTAATGCCCCTATTG
1 GGTAAAATGACCGTAATGCCCCTGTAG
40911588 GGTAAAATGACCGTAATGCCCCTAG-AG
1 GGTAAAATGACCGTAATGCCCCT-GTAG
40911615 GGT-AAATGAC
1 GGTAAAATGAC
40911625 TATTTTGCCC
Statistics
Matches: 194, Mismatches: 29, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
26 10 0.05
27 181 0.93
28 3 0.02
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.25
Consensus pattern (27 bp):
GGTAAAATGACCGTAATGCCCCTGTAG
Found at i:40911657 original size:26 final size:25
Alignment explanation
Indices: 40911604--40911681 Score: 70
Period size: 26 Copynumber: 3.1 Consensus size: 25
40911594 ATGACCGTAA
*
40911604 TGCCCCTAGAGGGTAAATGACTATTT
1 TGCCCCT-GAGTGTAAATGACTATTT
*
40911630 TGCCCCTCGAGTGTAAATGATTGA-TT
1 TGCCCCT-GAGTGTAAATGACT-ATTT
* * *
40911656 TGTCCATGA-TGTAAATGACTAATT
1 TGCCCCTGAGTGTAAATGACTATTT
40911680 TG
1 TG
40911682 TCTGTGATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
23 1 0.02
24 14 0.32
25 2 0.05
26 26 0.59
27 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.35
Consensus pattern (25 bp):
TGCCCCTGAGTGTAAATGACTATTT
Found at i:40911689 original size:24 final size:24
Alignment explanation
Indices: 40911616--40911683 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
40911606 CCCCTAGAGG
* * *
40911616 GTAAATGACTATTTTGCCCCTCGAGT
1 GTAAATGACTAATTTGTCCAT-GA-T
* *
40911642 GTAAATGATTGATTTGTCCATGAT
1 GTAAATGACTAATTTGTCCATGAT
40911666 GTAAATGACTAATTTGTC
1 GTAAATGACTAATTTGTC
40911684 TGTGATTTGT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
24 17 0.49
25 2 0.06
26 16 0.46
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (24 bp):
GTAAATGACTAATTTGTCCATGAT
Found at i:40911805 original size:27 final size:27
Alignment explanation
Indices: 40911767--40911831 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
40911757 ATGGAGGAAG
40911767 TACTG-TACTGGTGGCTCCGCCACA-A
1 TACTGTTACTGGTGGCTCCGCCACATA
**
40911792 TCACTGTTACTGGTGGCTTGGCCACATA
1 T-ACTGTTACTGGTGGCTCCGCCACATA
*
40911820 TACTATTACTGG
1 TACTGTTACTGG
40911832 CAGCTTTGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 1 0.03
26 4 0.12
27 27 0.79
28 2 0.06
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (27 bp):
TACTGTTACTGGTGGCTCCGCCACATA
Found at i:40911837 original size:27 final size:27
Alignment explanation
Indices: 40911785--40911837 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
40911775 TGGTGGCTCC
* **
40911785 GCCACAATCACTGTTACTGGTGGCTTG
1 GCCACAATCACTATTACTGGCAGCTTG
40911812 GCCACATAT-ACTATTACTGGCAGCTT
1 GCCACA-ATCACTATTACTGGCAGCTT
40911838 TGCTGGGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (27 bp):
GCCACAATCACTATTACTGGCAGCTTG
Found at i:40911918 original size:32 final size:32
Alignment explanation
Indices: 40911873--40912045 Score: 222
Period size: 32 Copynumber: 5.4 Consensus size: 32
40911863 TTACTACGAT
40911873 GTTACTGATGGCTTTGTGCCGATCATATTACC
1 GTTACTGATGGCTTTGTGCCGATCATATTACC
* * * *
40911905 GTTACTGACGGCTTTGTGCTGGTCATATTATC
1 GTTACTGATGGCTTTGTGCCGATCATATTACC
40911937 GTTACTGATGGCTTTGTGCCGATCATATTACC
1 GTTACTGATGGCTTTGTGCCGATCATATTACC
* * * * *
40911969 GATACTGATGGCTATGTGCCGATCACATCACT
1 GTTACTGATGGCTTTGTGCCGATCATATTACC
* * *
40912001 GCTACTGATGGCTTTGTGCCAATCATATTACT
1 GTTACTGATGGCTTTGTGCCGATCATATTACC
*
40912033 G-TACTTATGGCTT
1 GTTACTGATGGCTT
40912046 GTAGCCATCT
Statistics
Matches: 122, Mismatches: 19, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
31 11 0.09
32 111 0.91
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (32 bp):
GTTACTGATGGCTTTGTGCCGATCATATTACC
Found at i:40916202 original size:27 final size:27
Alignment explanation
Indices: 40916164--40916218 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
40916154 AAAGAAAAGA
40916164 AAGTTTCTTTCTTTCTTTTCTCTTCAT
1 AAGTTTCTTTCTTTCTTTTCTCTTCAT
40916191 AAGTTTCTTTCTTTCTTTTCTCTTCAT
1 AAGTTTCTTTCTTTCTTTTCTCTTCAT
40916218 A
1 A
40916219 TGTTGGAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.13, C:0.22, G:0.04, T:0.62
Consensus pattern (27 bp):
AAGTTTCTTTCTTTCTTTTCTCTTCAT
Found at i:40918526 original size:23 final size:23
Alignment explanation
Indices: 40918494--40918592 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
40918484 AGTGTTATTG
*
40918494 ATCAGAGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
40918517 ATCAATGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
40918540 TTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
40918563 ATCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
40918586 ATCAGTG
1 ATCAGTG
40918593 TGGCACTTAT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 68 1.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:40919979 original size:23 final size:23
Alignment explanation
Indices: 40919945--40920019 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 23
40919935 ACATAACTGC
40919945 TAAATT-AGGAGCACCAAAATGG
1 TAAATTCAGGAGCACCAAAATGG
** * *
40919967 TAGTTTCAGGAGCACCAAAGTGT
1 TAAATTCAGGAGCACCAAAATGG
* * *
40919990 TAAATTCAGGAGCACCGAAGTGC
1 TAAATTCAGGAGCACCAAAATGG
40920013 TAAATTC
1 TAAATTC
40920020 TCAAGTGCTA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 4 0.09
23 40 0.91
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (23 bp):
TAAATTCAGGAGCACCAAAATGG
Found at i:40926414 original size:28 final size:27
Alignment explanation
Indices: 40926381--40926479 Score: 110
Period size: 28 Copynumber: 3.6 Consensus size: 27
40926371 TAATGAGATT
*
40926381 AGCACTAAGTGTGAGAGTTTAATTGAA
1 AGCACTAAGTGTGCGAGTTTAATTGAA
* **
40926408 ATGCACTAAGTGTGCGAGTATAAGGGTAA
1 A-GCACTAAGTGTGCGAGTTTAATTG-AA
*
40926437 AGCACTAAGTGTGCGAGTTTGATT-ATTA
1 AGCACTAAGTGTGCGAGTTTAATTGA--A
40926465 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
40926480 TGCTTATTAA
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 55 0.92
29 3 0.05
ACGTcount: A:0.32, C:0.11, G:0.28, T:0.28
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTTAATTGAA
Found at i:40927436 original size:22 final size:22
Alignment explanation
Indices: 40927411--40927532 Score: 86
Period size: 22 Copynumber: 5.3 Consensus size: 22
40927401 TTTGTGTTAT
40927411 AAATTTAATGTATAATGCTGTC
1 AAATTTAATGTATAATGCTGTC
40927433 AAATTTTAA-GTATATTGATGCTGTC
1 AAA-TTTAATGTATA---ATGCTGTC
* *
40927458 CATTTTAATGTATAATGCTGTCC
1 AAATTTAATGTATAATGCTGT-C
* * *
40927481 AATTTTGA-GTATATTGATGTTGTC
1 AAATTTAATGTATA---ATGCTGTC
* *
40927505 CATTTTAATGTATAATGCTGTC
1 AAATTTAATGTATAATGCTGTC
*
40927527 CAATTT
1 AAATTT
40927533 TGAGTATATT
Statistics
Matches: 81, Mismatches: 9, Indels: 20
0.74 0.08 0.18
Matches are distributed among these distances:
22 32 0.40
23 12 0.15
24 12 0.15
25 25 0.31
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.45
Consensus pattern (22 bp):
AAATTTAATGTATAATGCTGTC
Found at i:40927485 original size:47 final size:47
Alignment explanation
Indices: 40927414--40927599 Score: 234
Period size: 47 Copynumber: 4.0 Consensus size: 47
40927404 GTGTTATAAA
*
40927414 TTTAATGTATAATGCTGTCAAATTTTAAGTATATTGATGCTGTCCAT
1 TTTAATGTATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCCAT
* *
40927461 TTTAATGTATAATGCTGTCCAATTTTGAGTATATTGATGTTGTCCAT
1 TTTAATGTATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCCAT
* * * * *
40927508 TTTAATGTATAATGCTGTCCAATTTTGAGTATATTTAAGCTGTCTAA
1 TTTAATGTATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCCAT
** *
40927555 TTCGATGTATAATGCTGTCC-A-TTTAGAGCATATT-ATTGCTGTCCA
1 TTTAATGTATAATGCTGTCCAATTTTA-AGTATATTGA-TGCTGTCCA
40927600 AAACAGGGTT
Statistics
Matches: 123, Mismatches: 14, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
45 4 0.03
46 15 0.12
47 104 0.85
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.44
Consensus pattern (47 bp):
TTTAATGTATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCCAT
Found at i:40928644 original size:93 final size:93
Alignment explanation
Indices: 40928485--40928670 Score: 363
Period size: 93 Copynumber: 2.0 Consensus size: 93
40928475 AAATAACACA
40928485 ATCATACAAAACTATGCTTCGCATAATATTCATCACAAAGATTAGTTAAGTGTATAATCTTCCAA
1 ATCATACAAAACTATGCTTCGCATAATATTCATCACAAAGATTAGTTAAGTGTATAATCTTCCAA
40928550 AGTCATACTATCATAGTTTACCGAAACT
66 AGTCATACTATCATAGTTTACCGAAACT
*
40928578 ATCATACAAAACTGTGCTTCGCATAATATTCATCACAAAGATTAGTTAAGTGTATAATCTTCCAA
1 ATCATACAAAACTATGCTTCGCATAATATTCATCACAAAGATTAGTTAAGTGTATAATCTTCCAA
40928643 AGTCATACTATCATAGTTTACCGAAACT
66 AGTCATACTATCATAGTTTACCGAAACT
40928671 CCTAACGTAA
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.32
Consensus pattern (93 bp):
ATCATACAAAACTATGCTTCGCATAATATTCATCACAAAGATTAGTTAAGTGTATAATCTTCCAA
AGTCATACTATCATAGTTTACCGAAACT
Found at i:40938086 original size:29 final size:29
Alignment explanation
Indices: 40938054--40938113 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
40938044 AACATTTTCA
40938054 TACTCAAATAATCAAAATAGACATGAAAC
1 TACTCAAATAATCAAAATAGACATGAAAC
40938083 TACTCAAATAATCAAAATAGACATGAAAC
1 TACTCAAATAATCAAAATAGACATGAAAC
40938112 TA
1 TA
40938114 TTACTAAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.55, C:0.17, G:0.07, T:0.22
Consensus pattern (29 bp):
TACTCAAATAATCAAAATAGACATGAAAC
Found at i:40944378 original size:42 final size:42
Alignment explanation
Indices: 40944331--40944419 Score: 153
Period size: 42 Copynumber: 2.1 Consensus size: 42
40944321 TTATGAGGAA
*
40944331 GTTGAAAATTTGCAGAATGATGATGATCTCAAGAGTAC-GTTG
1 GTTGAAAATTTGCAGAATGATGATGATCTAAAGAGTACAG-TG
40944373 GTTGAAAATTTGCAGAATGATGATGATCTAAAGAGTACAGTG
1 GTTGAAAATTTGCAGAATGATGATGATCTAAAGAGTACAGTG
40944415 GTTGA
1 GTTGA
40944420 TTCGGAGTGT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
42 44 0.98
43 1 0.02
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.30
Consensus pattern (42 bp):
GTTGAAAATTTGCAGAATGATGATGATCTAAAGAGTACAGTG
Found at i:40946015 original size:31 final size:31
Alignment explanation
Indices: 40945980--40946041 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
40945970 GTAGAGAGAA
40945980 TAAAATCAATAATGAACTTTGTTGTATGGAT
1 TAAAATCAATAATGAACTTTGTTGTATGGAT
40946011 TAAAATCAATAATGAACTTTGTTGTATGGAT
1 TAAAATCAATAATGAACTTTGTTGTATGGAT
40946042 GCAAACATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (31 bp):
TAAAATCAATAATGAACTTTGTTGTATGGAT
Found at i:40946178 original size:22 final size:22
Alignment explanation
Indices: 40946153--40946196 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
40946143 TATATGGGTG
40946153 ACAAAAAAATTCTTATGCTTCA
1 ACAAAAAAATTCTTATGCTTCA
40946175 ACAAAAAAATTCTTATGCTTCA
1 ACAAAAAAATTCTTATGCTTCA
40946197 TACATATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (22 bp):
ACAAAAAAATTCTTATGCTTCA
Found at i:40946514 original size:20 final size:19
Alignment explanation
Indices: 40946486--40946566 Score: 83
Period size: 20 Copynumber: 4.1 Consensus size: 19
40946476 ATTATAAAAT
40946486 AATTCAAAATAATTTTCAAA
1 AATTCAAAATAATTTT-AAA
* * *
40946506 AATTTAAAATGATTTTTAA
1 AATTCAAAATAATTTTAAA
40946525 AATTCAAAAT-ATTTATAAA
1 AATTCAAAATAATTT-TAAA
*
40946544 AATTTCAAAATAAATTCTAAA
1 AA-TTCAAAAT-AATTTTAAA
40946565 AA
1 AA
40946567 ATATATGAAG
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
18 4 0.08
19 16 0.31
20 22 0.43
21 6 0.12
22 3 0.06
ACGTcount: A:0.56, C:0.06, G:0.01, T:0.37
Consensus pattern (19 bp):
AATTCAAAATAATTTTAAA
Found at i:40946528 original size:19 final size:19
Alignment explanation
Indices: 40946503--40946555 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
40946493 AATAATTTTC
40946503 AAAAATTTAAAATGATTT-T
1 AAAAATTTAAAAT-ATTTAT
* *
40946522 TAAAATTCAAAATATTTAT
1 AAAAATTTAAAATATTTAT
40946541 AAAAATTTCAAAATA
1 AAAAATTT-AAAATA
40946556 AATTCTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 4 0.14
19 18 0.64
20 6 0.21
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (19 bp):
AAAAATTTAAAATATTTAT
Found at i:40946565 original size:39 final size:39
Alignment explanation
Indices: 40946486--40946565 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 39
40946476 ATTATAAAAT
* * *
40946486 AATTCAAAATAATTTTCAAAAATTTAAAATGATTTTTAA
1 AATTCAAAATAATTTTCAAAAATTTAAAATAAATTCTAA
40946525 AATTCAAAAT-ATTTAT-AAAAATTTCAAAATAAATTCTAA
1 AATTCAAAATAATTT-TCAAAAATTT-AAAATAAATTCTAA
40946564 AA
1 AA
40946566 AATATATGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 12 0.33
39 24 0.67
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.38
Consensus pattern (39 bp):
AATTCAAAATAATTTTCAAAAATTTAAAATAAATTCTAA
Found at i:40947999 original size:16 final size:15
Alignment explanation
Indices: 40947978--40948007 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
40947968 AAATGATTCA
40947978 TATATAAACTTTTTTT
1 TATATAAA-TTTTTTT
40947994 TATATAAATTTTTT
1 TATATAAATTTTTT
40948008 ACCCAATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (15 bp):
TATATAAATTTTTTT
Found at i:40951323 original size:24 final size:25
Alignment explanation
Indices: 40951273--40951323 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
40951263 GACTCAAATT
* **
40951273 AAAATTTTTATTTATTTATTTTATA
1 AAAATTTTAATTTATTTATAATATA
*
40951298 AAAATTTTAATTT-TTTATAATGTA
1 AAAATTTTAATTTATTTATAATATA
40951322 AA
1 AA
40951324 CATAAATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
AAAATTTTAATTTATTTATAATATA
Found at i:40954817 original size:21 final size:21
Alignment explanation
Indices: 40954793--40954832 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
40954783 CTGTGCGGAG
40954793 GAGGCACACGA-CCGTGTGGAT
1 GAGGCACAC-ACCCGTGTGGAT
40954814 GAGGCACACACCCGTGTGG
1 GAGGCACACACCCGTGTGG
40954833 GATAGGGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.23, C:0.28, G:0.38, T:0.12
Consensus pattern (21 bp):
GAGGCACACACCCGTGTGGAT
Found at i:40956677 original size:25 final size:24
Alignment explanation
Indices: 40956640--40956686 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
40956630 GTGTTCACGC
*
40956640 TATATGTTATAAAAATAATATACT
1 TATATATTATAAAAATAATATACT
*
40956664 TATATATTCATAAAAATATTATA
1 TATATATT-ATAAAAATAATATA
40956687 ATTTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (24 bp):
TATATATTATAAAAATAATATACT
Found at i:40957327 original size:43 final size:43
Alignment explanation
Indices: 40957261--40957419 Score: 210
Period size: 43 Copynumber: 3.7 Consensus size: 43
40957251 TTTATGTGGA
* ** *
40957261 AAACACCGCTATAGAACATGATCTTTAGCAACGCTTTCCCTAC
1 AAACGCCGCTATAGAACATGATCTTTAGCGGCGCTTTTCCTAC
* * *
40957304 AAATGCCGCTATAGAACATGATCTTTCGCGGTGCTTTTCCTAC
1 AAACGCCGCTATAGAACATGATCTTTAGCGGCGCTTTTCCTAC
* * *
40957347 AAACACCGCTATAGAACATGATTTTTAGCGGCACTTTTCCTAC
1 AAACGCCGCTATAGAACATGATCTTTAGCGGCGCTTTTCCTAC
* *
40957390 AAACGCCACTATAGAACATGATATTTAGCG
1 AAACGCCGCTATAGAACATGATCTTTAGCG
40957420 AGACTTTTAT
Statistics
Matches: 100, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 100 1.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (43 bp):
AAACGCCGCTATAGAACATGATCTTTAGCGGCGCTTTTCCTAC
Found at i:40957426 original size:43 final size:43
Alignment explanation
Indices: 40957261--40957440 Score: 209
Period size: 43 Copynumber: 4.2 Consensus size: 43
40957251 TTTATGTGGA
* ** * *
40957261 AAACACCGCTATAGAACATGATCTTTAGCAACGCTTTCCCTAC
1 AAACGCCGCTATAGAACATGATCTTTAGCGGCACTTTTCCTAC
* * **
40957304 AAATGCCGCTATAGAACATGATCTTTCGCGGTGCTTTTCCTAC
1 AAACGCCGCTATAGAACATGATCTTTAGCGGCACTTTTCCTAC
* *
40957347 AAACACCGCTATAGAACATGATTTTTAGCGGCACTTTTCCTAC
1 AAACGCCGCTATAGAACATGATCTTTAGCGGCACTTTTCCTAC
* * **
40957390 AAACGCCACTATAGAACATGATATTTAGCGAG-ACTTTTATTAC
1 AAACGCCGCTATAGAACATGATCTTTAGCG-GCACTTTTCCTAC
40957433 AAACGCCG
1 AAACGCCG
40957441 AAAGAATATG
Statistics
Matches: 117, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
43 116 0.99
44 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (43 bp):
AAACGCCGCTATAGAACATGATCTTTAGCGGCACTTTTCCTAC
Found at i:40957427 original size:86 final size:86
Alignment explanation
Indices: 40957261--40957467 Score: 233
Period size: 86 Copynumber: 2.4 Consensus size: 86
40957251 TTTATGTGGA
* ** * * * *
40957261 AAACACCGCTATAGAACATGATCTTTAGCAACGCTTTCCCTACAAATGCCGCTATAGAACATGAT
1 AAACACCGCTATAGAACATGATTTTTAGCGGCACTTTTCCTACAAACGCCACTATAGAACATGAT
* * * *
40957326 CTTTCGCGGTGCTTTTCCTAC
66 ATTTAGCGGTACTTTTACTAC
40957347 AAACACCGCTATAGAACATGATTTTTAGCGGCACTTTTCCTACAAACGCCACTATAGAACATGAT
1 AAACACCGCTATAGAACATGATTTTTAGCGGCACTTTTCCTACAAACGCCACTATAGAACATGAT
*
40957412 ATTTAGCGAG-ACTTTTATTAC
66 ATTTAGCG-GTACTTTTACTAC
* * * *
40957433 AAACGCCG--AAAGAATATG-TTTTTAGCGGCATTTTT
1 AAACACCGCTATAGAACATGATTTTTAGCGGCACTTTT
40957468 TTTACAAGTG
Statistics
Matches: 104, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
83 16 0.15
84 8 0.08
86 79 0.76
87 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.30
Consensus pattern (86 bp):
AAACACCGCTATAGAACATGATTTTTAGCGGCACTTTTCCTACAAACGCCACTATAGAACATGAT
ATTTAGCGGTACTTTTACTAC
Found at i:40957898 original size:21 final size:21
Alignment explanation
Indices: 40957872--40957918 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
40957862 TTTTCTTGTT
* *
40957872 GCCTCTGCTACCCTTGCTGCC
1 GCCTCTACTACCCTCGCTGCC
* *
40957893 GCCTCTACTTCCCTCGCTGCT
1 GCCTCTACTACCCTCGCTGCC
40957914 GCCTC
1 GCCTC
40957919 CACTTTAAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.04, C:0.49, G:0.17, T:0.30
Consensus pattern (21 bp):
GCCTCTACTACCCTCGCTGCC
Found at i:40957923 original size:21 final size:21
Alignment explanation
Indices: 40957882--40957923 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40957872 GCCTCTGCTA
* *
40957882 CCCTTGCTGCCGCCTCTACTT
1 CCCTCGCTGCCGCCTCCACTT
*
40957903 CCCTCGCTGCTGCCTCCACTT
1 CCCTCGCTGCCGCCTCCACTT
40957924 TAAGTTGTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.05, C:0.50, G:0.14, T:0.31
Consensus pattern (21 bp):
CCCTCGCTGCCGCCTCCACTT
Found at i:40966743 original size:39 final size:40
Alignment explanation
Indices: 40966574--40966742 Score: 205
Period size: 40 Copynumber: 4.2 Consensus size: 40
40966564 GGACTAAGAT
* * *
40966574 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* * *
40966614 CCGAGGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
** *
40966654 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTACGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* * * * *
40966694 CCGAAGGCA-TGGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
40966733 CCGAAGGCAT
1 CCGAAGGCAT
40966743 GTGAACGAGG
Statistics
Matches: 111, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
39 32 0.29
40 79 0.71
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
Found at i:40966763 original size:79 final size:80
Alignment explanation
Indices: 40966574--40966778 Score: 204
Period size: 79 Copynumber: 2.6 Consensus size: 80
40966564 GGACTAAGAT
* * * * *
40966574 CCGAAGGCCTTTGTGCGA-GATACTAAATCCGGGTTAAGTCCCGAGGGCATTCGTGCGAGTTATT
1 CCGAAGGCATTCGTGCGAGGA-GCTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACT
* *
40966638 AAAGCCGGGTTAAGTC
65 AAAACCGGGCTAAGTC
** * * * *
40966654 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTACGTCCCGAAGGCA-TGGTGTGAGTTACTA
1 CCGAAGGCATTCGTGCGAGGAGCTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTA
*
40966718 AAACCGGGCTATGTC
66 AAACCGGGCTAAGTC
* *
40966733 CCGAAGGCA-T-GTGAACGAGGAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGAAGGCATTCGTG--CGAGGAGCTAAATCCGGGTTAAGTCCCGAAGG
40966779 TACGTGAATT
Statistics
Matches: 102, Mismatches: 20, Indels: 8
0.78 0.15 0.06
Matches are distributed among these distances:
77 3 0.03
78 15 0.15
79 44 0.43
80 40 0.39
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.23
Consensus pattern (80 bp):
CCGAAGGCATTCGTGCGAGGAGCTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTA
AAACCGGGCTAAGTC
Found at i:40974500 original size:40 final size:39
Alignment explanation
Indices: 40974470--40974639 Score: 216
Period size: 40 Copynumber: 4.3 Consensus size: 39
40974460 GGACTAAGAT
* * *
40974470 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTA-TAAATCCGGGTTAAGTC
*
40974510 CCGAAGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTA-TAAATCCGGGTTAAGTC
*
40974550 CCGAAGGCATTCGTGCGAGTTGATAAATCCGGGTTACGTC
1 CCGAAGGCATTCGTGCGAGTT-ATAAATCCGGGTTAAGTC
* * * *
40974590 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTA-TAAATCCGGGTTAAGTC
40974629 CCGAAGGCATT
1 CCGAAGGCATT
40974640 TGAACGAGGA
Statistics
Matches: 117, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
38 1 0.01
39 33 0.28
40 82 0.70
41 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.25
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGTTATAAATCCGGGTTAAGTC
Found at i:40974566 original size:80 final size:79
Alignment explanation
Indices: 40974417--40974639 Score: 234
Period size: 80 Copynumber: 2.8 Consensus size: 79
40974407 TTGAATGCTG
* * * ** * * * * *
40974417 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGCGAATATATCCGGACTAAGAT-CCGAAGGCCTT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAAACCGGGCTAAG-TCCCGAAGGCATT
*
40974481 TGTGCGAGAT-ACTAAA
64 CGTGCGAGATGA-TAAA
* * *
40974497 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
40974562 GTGCGAGTTGATAAA
65 GTGCGAGATGATAAA
* * *
40974577 TCCGGGTTACGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
40974640 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
79 35 0.29
80 81 0.67
81 5 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCG
TGCGAGATGATAAA
Found at i:40974659 original size:79 final size:80
Alignment explanation
Indices: 40974493--40974674 Score: 224
Period size: 79 Copynumber: 2.3 Consensus size: 80
40974483 TGCGAGATAC
* * *
40974493 TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTCCCGAAGGC
1 TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGC
** **
40974558 ATTCGTGCGAGTTGA
66 ATTCGAACGAGGAGA
* * *
40974573 TAAATCCGGGTTACGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGC
1 TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGC
* *
40974637 ATTTGAACGAGGAGC
66 ATTCGAACGAGGAGA
* *
40974652 TATATCC-GGTTAAATCCCGAAGG
1 TAAATCCGGGTTAAGTCCCGAAGG
40974675 TACGTGATTT
Statistics
Matches: 87, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
78 14 0.16
79 46 0.53
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (80 bp):
TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGC
ATTCGAACGAGGAGA
Found at i:40984245 original size:19 final size:20
Alignment explanation
Indices: 40984205--40984247 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
40984195 CGTGTTGATT
*
40984205 TCGTACTTTGGCCCATTTTC
1 TCGTACTTTGGCCCAGTTTC
*
40984225 TCGTATTTTGGCCC-GTTTC
1 TCGTACTTTGGCCCAGTTTC
40984244 TCGT
1 TCGT
40984248 TCCTTTTGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.07, C:0.28, G:0.19, T:0.47
Consensus pattern (20 bp):
TCGTACTTTGGCCCAGTTTC
Found at i:41001137 original size:51 final size:51
Alignment explanation
Indices: 41001077--41001176 Score: 155
Period size: 51 Copynumber: 2.0 Consensus size: 51
41001067 CTTCTTTAGC
* * * *
41001077 CCGCACATCCCAGGCACCAAGTTGCCGATGGTGTCCGAGGCTCCCGCACCT
1 CCGCACATCCCAGCCACCAAGGTACCGATGGTGCCCGAGGCTCCCGCACCT
*
41001128 CCGCACATCCGAGCCACCAAGGTACCGATGGTGCCCGAGGCTCCCGCAC
1 CCGCACATCCCAGCCACCAAGGTACCGATGGTGCCCGAGGCTCCCGCAC
41001177 GACCAAGGGC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.19, C:0.42, G:0.26, T:0.13
Consensus pattern (51 bp):
CCGCACATCCCAGCCACCAAGGTACCGATGGTGCCCGAGGCTCCCGCACCT
Found at i:41001259 original size:43 final size:43
Alignment explanation
Indices: 41001152--41001644 Score: 405
Period size: 43 Copynumber: 11.6 Consensus size: 43
41001142 CACCAAGGTA
*
41001152 CCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCGAGG-TG
1 CCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTG
** * * * ** *
41001194 CCGATGGTGGTCAAGGCCCCCGCATGACCAAGGGCCTATTTTA
1 CCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTG
* *
41001237 CCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCTTAGTTTG
1 CCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTG
* * * *
41001280 CCGATAGTGCCCGAGCCTCTCGCACGACCAAGGGCCTAGGCTG
1 CCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTG
** * * ** *
41001323 CCGATGGTGTGCGAGGTTCTCGCAC-ATCCAAGCACCAAGG-TG
1 CCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGGGCCTAGGTTG
* *
41001365 CCGATGGTGCTCGAGGCTCCCGTACGACCAAGGGCCTAGGTTG
1 CCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTG
** * *
41001408 CCGACAGTGTCCGAGGCTCCCGCAC-ATCATA--GCACTGAGG-TG
1 CCGATGGTGCCCGAGGCTCCCGCACGACCA-AGGGC-CT-AGGTTG
* * *
41001450 CTGATGGTGCCCGAGGCTCTCGCACGACCAAGGGCCTAGATTG
1 CCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTG
** *
41001493 CCGATGGTGCCCGAGGCTCCCGCAC-ACCGAAGCACCGAGG-TG
1 CCGATGGTGCCCGAGGCTCCCGCACGACC-AAGGGCCTAGGTTG
* * * * ** *
41001535 CCGATGGCGCCCGAGGCTCTCGTAC-ATCGAAGCACCGAGG-TG
1 CCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGGGCCTAGGTTG
** * * * *
41001577 CCGATGGCACCCGAGGCTCCTGCATGACCAAGGGCTTAGTTTG
1 CCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTG
* * *
41001620 CCGATGGTGTCCGGGGCTCCTGCAC
1 CCGATGGTGCCCGAGGCTCCCGCAC
41001645 ATCCTAGCAC
Statistics
Matches: 358, Mismatches: 78, Indels: 29
0.77 0.17 0.06
Matches are distributed among these distances:
41 2 0.01
42 163 0.46
43 191 0.53
44 2 0.01
ACGTcount: A:0.18, C:0.33, G:0.32, T:0.17
Consensus pattern (43 bp):
CCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTG
Found at i:41001312 original size:128 final size:127
Alignment explanation
Indices: 41001152--41001644 Score: 397
Period size: 128 Copynumber: 3.9 Consensus size: 127
41001142 CACCAAGGTA
* * * *
41001152 CCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCGAGGTGCCGATGGTGGTCAAGGCCCCCGC
1 CCGATAGTGCCCGAGGCTCCCGCACGACCAAGGGCCGAGGTGCCGATGGTGGTCGAGGCTCTCGC
** * * *
41001217 ATGACCAAGGGCCTATTTTACCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCTTAGTTTG
66 A-GACCAAGGGCCTAAATTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTG
* * * *
41001280 CCGATAGTGCCCGAGCCTCTCGCACGACCAAGGGCCTAGGCTGCCGATGGT-GTGCGAGGTTCTC
1 CCGATAGTGCCCGAGGCTCCCGCACGACCAAGGGCCGAGG-TGCCGATGGTGGT-CGAGGCTCTC
* ** ** * *
41001344 GCACATCCAAGCACC-AAGGTGCCGATGGTGCTCGAGGCTCCCGTACGACCAAGGGCCTAGGTTG
64 GCAGA-CCAAGGGCCTAAATTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTG
* * * ** * * **
41001408 CCGACAGTGTCCGAGGCTCCCGCAC-ATCATAGCACTGAGGTGCTGATGGTGCCCGAGGCTCTCG
1 CCGATAGTGCCCGAGGCTCCCGCACGACCA-AGGGCCGAGGTGCCGATGGTGGTCGAGGCTCTCG
* ** *
41001472 CACGACCAAGGGCCTAGATTGCCGATGGTGCCCGAGGCTCCCGCAC-ACCGAAGCACCGAGG-TG
65 CA-GACCAAGGGCCTAAATTGCCGATGGTGCCCGAGGCTCCCGCACGACC-AAGGGCCTAGGTTG
* * * * * ** ****
41001535 CCGATGGCGCCCGAGGCTCTCGTAC-ATCGAAGCACCGAGGTGCCGATGGCACCCGAGGCTC-CT
1 CCGATAGTGCCCGAGGCTCCCGCACGA-CCAAGGGCCGAGGTGCCGATGGTGGTCGAGGCTCTC-
* ** * * *
41001598 GCATGACCAAGGGCTTAGTTTGCCGATGGTGTCCGGGGCTCCTGCAC
64 GCA-GACCAAGGGCCTAAATTGCCGATGGTGCCCGAGGCTCCCGCAC
41001645 ATCCTAGCAC
Statistics
Matches: 294, Mismatches: 61, Indels: 21
0.78 0.16 0.06
Matches are distributed among these distances:
126 1 0.00
127 124 0.42
128 143 0.49
129 26 0.09
ACGTcount: A:0.18, C:0.33, G:0.32, T:0.17
Consensus pattern (127 bp):
CCGATAGTGCCCGAGGCTCCCGCACGACCAAGGGCCGAGGTGCCGATGGTGGTCGAGGCTCTCGC
AGACCAAGGGCCTAAATTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTG
Found at i:41001552 original size:85 final size:84
Alignment explanation
Indices: 41001152--41001556 Score: 441
Period size: 85 Copynumber: 4.8 Consensus size: 84
41001142 CACCAAGGTA
** ** * * *
41001152 CCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCGAGGTGCCGATGGTGGTCAAGGCCCCCGC
1 CCGATGGTGCCCGAGGCTCCCGCAC-ACCAAGCACCGAGGTGCCGATGGTGCCCGAGGCTCTCGC
* ** *
41001217 ATGACCAAGGGCCTATTTTA
65 ACGACCAAGGGCCTAGGTTG
** ** * * *
41001237 CCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCTTAGTTTGCCGATAGTGCCCGAGCCTCTCG
1 CCGATGGTGCCCGAGGCTCCCGCAC-ACCAAGCACCGAG-GTGCCGATGGTGCCCGAGGCTCTCG
*
41001302 CACGACCAAGGGCCTAGGCTG
64 CACGACCAAGGGCCTAGGTTG
** * * * * * *
41001323 CCGATGGTGTGCGAGGTTCTCGCACATCCAAGCACCAAGGTGCCGATGGTGCTCGAGGCTCCCGT
1 CCGATGGTGCCCGAGGCTCCCGCACA-CCAAGCACCGAGGTGCCGATGGTGCCCGAGGCTCTCGC
41001388 ACGACCAAGGGCCTAGGTTG
65 ACGACCAAGGGCCTAGGTTG
** * * * *
41001408 CCGACAGTGTCCGAGGCTCCCGCACATCATAGCACTGAGGTGCTGATGGTGCCCGAGGCTCTCGC
1 CCGATGGTGCCCGAGGCTCCCGCACACCA-AGCACCGAGGTGCCGATGGTGCCCGAGGCTCTCGC
*
41001473 ACGACCAAGGGCCTAGATTG
65 ACGACCAAGGGCCTAGGTTG
*
41001493 CCGATGGTGCCCGAGGCTCCCGCACACCGAAGCACCGAGGTGCCGATGGCGCCCGAGGCTCTCG
1 CCGATGGTGCCCGAGGCTCCCGCACACC-AAGCACCGAGGTGCCGATGGTGCCCGAGGCTCTCG
41001557 TACATCGAAG
Statistics
Matches: 266, Mismatches: 50, Indels: 8
0.82 0.15 0.02
Matches are distributed among these distances:
84 2 0.01
85 201 0.76
86 63 0.24
ACGTcount: A:0.18, C:0.33, G:0.32, T:0.16
Consensus pattern (84 bp):
CCGATGGTGCCCGAGGCTCCCGCACACCAAGCACCGAGGTGCCGATGGTGCCCGAGGCTCTCGCA
CGACCAAGGGCCTAGGTTG
Found at i:41001628 original size:170 final size:170
Alignment explanation
Indices: 41001152--41001638 Score: 462
Period size: 170 Copynumber: 2.9 Consensus size: 170
41001142 CACCAAGGTA
** * * ** * *
41001152 CCGATGGTGCCCGAGGCTCCCGCACGA-CCAAGGGCCGAGGTGCCGATGGTGGTCAAGGCCCCCG
1 CCGATGGTGCCCGAGGCTCCCGCAC-ATCCAAGCACCAAGGTGCCGATGGCGCCCGAGGCTCCCG
* * ** * ** *
41001216 CATGACCAAGGGCCTATTTTACCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCTTAGTTTGC
65 TACGACCAAGCACCGAGGTTGCCGATGGTGCCCGAGGCTCCCGCA-GACCAAGGGCTTAGTTTGC
* * *
41001281 CGATAGTGCCCGAGCCTCTCGCACGACCAAGGGCCTAGGCTG
129 CGATGGTGCCCGAGGCTCTCGCACGACCAAGGGCCTAGACTG
** * * * *
41001323 CCGATGGTGTGCGAGGTTCTCGCACATCCAAGCACCAAGGTGCCGATGGTGCTCGAGGCTCCCGT
1 CCGATGGTGCCCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGATGGCGCCCGAGGCTCCCGT
** * ** * * * ** * * *
41001388 ACGACCAAGGGCCTAGGTTGCCGACAGTGTCCGAGGCTCCCGCACATCATAGCACTGAG-GTGCT
66 ACGACCAAGCACCGAGGTTGCCGATGGTGCCCGAGGCTCCCGCAGACCA-AGGGCTTAGTTTGCC
*
41001452 GATGGTGCCCGAGGCTCTCGCACGACCAAGGGCCTAGATTG
130 GATGGTGCCCGAGGCTCTCGCACGACCAAGGGCCTAGACTG
* *
41001493 CCGATGGTGCCCGAGGCTCCCGCACA-CCGAAGCACCGAGGTGCCGATGGCGCCCGAGGCTCTCG
1 CCGATGGTGCCCGAGGCTCCCGCACATCC-AAGCACCAAGGTGCCGATGGCGCCCGAGGCTCCCG
* ** *
41001557 TAC-ATCGAAGCACCGAGG-TGCCGATGGCACCCGAGGCTCCTGCATGACCAAGGGCTTAGTTTG
65 TACGA-CCAAGCACCGAGGTTGCCGATGGTGCCCGAGGCTCCCGCA-GACCAAGGGCTTAGTTTG
* *
41001620 CCGATGGTGTCCGGGGCTC
128 CCGATGGTGCCCGAGGCTC
41001639 CTGCACATCC
Statistics
Matches: 254, Mismatches: 56, Indels: 13
0.79 0.17 0.04
Matches are distributed among these distances:
169 29 0.11
170 130 0.51
171 95 0.37
ACGTcount: A:0.18, C:0.33, G:0.32, T:0.17
Consensus pattern (170 bp):
CCGATGGTGCCCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGATGGCGCCCGAGGCTCCCGT
ACGACCAAGCACCGAGGTTGCCGATGGTGCCCGAGGCTCCCGCAGACCAAGGGCTTAGTTTGCCG
ATGGTGCCCGAGGCTCTCGCACGACCAAGGGCCTAGACTG
Found at i:41001728 original size:24 final size:24
Alignment explanation
Indices: 41001701--41001767 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
41001691 TGCTACCGGA
* * *
41001701 ACGGTTTGCTGGAGCACCGACGGG
1 ACGGTTCGCCGGAGCACCGACAGG
*
41001725 ACGGTTCGCCGGAGCACCGCCAGG
1 ACGGTTCGCCGGAGCACCGACAGG
*
41001749 ACGGATCGCCGGAGCACCG
1 ACGGTTCGCCGGAGCACCG
41001768 CTGGGAACCT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.18, C:0.33, G:0.39, T:0.10
Consensus pattern (24 bp):
ACGGTTCGCCGGAGCACCGACAGG
Found at i:41007125 original size:42 final size:42
Alignment explanation
Indices: 41007047--41007380 Score: 306
Period size: 42 Copynumber: 7.9 Consensus size: 42
41007037 ACTTTAGCTT
* * *
41007047 TGGTGCTCAAGGCTCCCG-TCATCCATGCACCAAGGTGCCGA
1 TGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
41007088 TGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
1 TGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
** * *
41007130 TGGTGCTCGAGGCTCCCGCACGA-CCAAGGGCCTAGGTTGCTGA
1 TGGTGCTCGAGGCTCCCGCAC-ATCCAAGCACCAAGG-TGCCGA
** *
41007173 CAGTG-TCCGAGGCTCCCGCACAT-CATAGCACCGAGGTGCCGA
1 TGGTGCT-CGAGGCTCCCGCACATCCA-AGCACCAAGGTGCCGA
* ** * *
41007215 TGGT-CTCCGAGGCTCCC-CACAACCAAGGGCCTAGTTTGCCGA
1 TGGTGCT-CGAGGCTCCCGCACATCCAAGCACCAAG-GTGCCGA
* * *
41007257 TCGTG-TCCGATGCTCCCGCACATCCATGCACCAAGGTGCCGA
1 TGGTGCT-CGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
* * *
41007299 TGGTGCTCGAGGCTCCCGCACATCCAAGCATCATGGTTACCGA
1 TGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGG-TGCCGA
* * *
41007342 TGGTG-TCTGAGGCTCCCACACATTCGAGCCACCAAGGTG
1 TGGTGCTC-GAGGCTCCCGCACATCCAAG-CACCAAGGTG
41007381 ATAGAGGCTC
Statistics
Matches: 238, Mismatches: 40, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
41 27 0.11
42 134 0.56
43 71 0.30
44 6 0.03
ACGTcount: A:0.20, C:0.34, G:0.28, T:0.18
Consensus pattern (42 bp):
TGGTGCTCGAGGCTCCCGCACATCCAAGCACCAAGGTGCCGA
Done.