Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 26 of 187
Found at i:8555500 original size:7 final size:7
Alignment explanation
Indices: 8555488--8555517 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
8555478 AACATATACT
8555488 TTTTATA
1 TTTTATA
8555495 TTTTATA
1 TTTTATA
*
8555502 TTTCATA
1 TTTTATA
8555509 TTTTATA
1 TTTTATA
8555516 TT
1 TT
8555518 CTTTATATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTTATA
Found at i:8555642 original size:24 final size:22
Alignment explanation
Indices: 8555597--8555640 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
8555587 ATATACACAC
8555597 ATACTTACATTTTTATTTTATA
1 ATACTTACATTTTTATTTTATA
*
8555619 ATACTTACAGATTTT-TTTTATA
1 ATACTTACA-TTTTTATTTTATA
8555641 TATGTATGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.57
Consensus pattern (22 bp):
ATACTTACATTTTTATTTTATA
Found at i:8567569 original size:44 final size:44
Alignment explanation
Indices: 8567497--8567948 Score: 563
Period size: 44 Copynumber: 10.3 Consensus size: 44
8567487 GTTATTAAAC
* *
8567497 CAGATCTTGTCTTCATGCATTGGCGTGAAGTAGATCAAAGATAG
1 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAG
* * * * *
8567541 CAGGTCCTATCTTCATGTATTGGGGTGAAGTGGATCGAAGAT-G
1 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAG
*** * * *
8567584 CAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAG
1 CAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAG
*
8567629 TAGATCTTGTCTTCATGTATTGGCGTGAAGT-GAATCGAAGAT-G
1 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAG-ATCGAAGATAG
*** * * *
8567672 CAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAG
1 CAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAG
*
8567717 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAAATAG
1 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAG
* * * *
8567761 CAGGTCCTATCTTCATGTATTGGCGTGAAGTGGATCGAAGA-AG
1 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAG
* *
8567804 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAA
1 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAG
8567848 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAG
1 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAG
* * *
8567892 CAGGTCCTATCTTCATGTATTGGCGTGAAGTAGATCGAAGAT-G
1 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAG
*
8567935 CAGATTTTGTCTTC
1 CAGATCTTGTCTTC
8567949 CCATACTGGT
Statistics
Matches: 345, Mismatches: 56, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
43 89 0.26
44 214 0.62
45 42 0.12
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (44 bp):
CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAG
Found at i:8567974 original size:263 final size:264
Alignment explanation
Indices: 8567506--8567987 Score: 718
Period size: 263 Copynumber: 1.8 Consensus size: 264
8567496 CCAGATCTTG
* *
8567506 TCTTCATGCATTGGCGTGAAGTAGATCAAAGATAGCAGGTCCTATCTTCATGTATTGGGGTGAAG
1 TCTTCATGCATTGGCGTGAAGTAGATCAAAGATAGCAGATCCTATCTTCATGTATTGGCGTGAAG
* ** * * * *
8567571 TGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGTAGATCT
66 TAGATCGAAGAAACAGATCTTGTCTTCACATATTGGTCGCGAAGTAGATCGAAGAAAGCAGATCC
* *
8567636 TGTCTTCATGTATTGGCGTGAAGTGAATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGA
131 TATCTTCATGTATTGGCGTGAAGTGAATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGA
*
8567701 AGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAAATAGCAGGT
196 AGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAAATAGCAGGT
8567766 CCTA
261 CCTA
* * * * *
8567770 TCTTCATGTATTGGCGTGAAGTGGATCGAAGA-AGCAGATCTTGTCTTCATGTATTGGCGTGAAG
1 TCTTCATGCATTGGCGTGAAGTAGATCAAAGATAGCAGATCCTATCTTCATGTATTGGCGTGAAG
** * * *
8567834 TAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAGCAGGTC
66 TAGATCGAAG-AAACAGATCTTGTCTTCACATATTGGTCGCGAAGTAGATCGAAGAAAGCAGATC
*
8567898 CTATCTTCATGTATTGGCGTGAAGT-AGATCGAAGATGCAGATTTTGTCTTCCCATACTGGTGGC
130 CTATCTTCATGTATTGGCGTGAAGTGA-ATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGC
8567962 GAAGTAGATCGAAGAAAACAGATCTT
194 GAAGTAGATCGAAGAAAACAGATCTT
8567988 ATCTCCCTAA
Statistics
Matches: 193, Mismatches: 23, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
262 1 0.01
263 142 0.74
264 50 0.26
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (264 bp):
TCTTCATGCATTGGCGTGAAGTAGATCAAAGATAGCAGATCCTATCTTCATGTATTGGCGTGAAG
TAGATCGAAGAAACAGATCTTGTCTTCACATATTGGTCGCGAAGTAGATCGAAGAAAGCAGATCC
TATCTTCATGTATTGGCGTGAAGTGAATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGA
AGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAAATAGCAGGT
CCTA
Found at i:8568741 original size:9 final size:9
Alignment explanation
Indices: 8568729--8568762 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
8568719 CGTCTCTTTC
8568729 TATTTTATT
1 TATTTTATT
*
8568738 TATTTGATCT
1 TATTTTAT-T
8568748 TATTTTATT
1 TATTTTATT
8568757 TATTTT
1 TATTTT
8568763 TTTTCTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (9 bp):
TATTTTATT
Found at i:8569820 original size:7 final size:7
Alignment explanation
Indices: 8569808--8569837 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
8569798 AACATATACT
8569808 TTTTATA
1 TTTTATA
8569815 TTTTATA
1 TTTTATA
*
8569822 TTTCATA
1 TTTTATA
8569829 TTTTATA
1 TTTTATA
8569836 TT
1 TT
8569838 CTTTATATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTTATA
Found at i:8569962 original size:24 final size:22
Alignment explanation
Indices: 8569917--8569960 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
8569907 ATATACACAC
8569917 ATACTTACATTTTTATTTTATA
1 ATACTTACATTTTTATTTTATA
*
8569939 ATACTTACAGATTTT-TTTTATA
1 ATACTTACA-TTTTTATTTTATA
8569961 TATGTATGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.57
Consensus pattern (22 bp):
ATACTTACATTTTTATTTTATA
Found at i:8570873 original size:15 final size:15
Alignment explanation
Indices: 8570853--8570886 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
8570843 CAACAATTAC
8570853 TATTATTATTATCAT
1 TATTATTATTATCAT
*
8570868 TATTATTTTTATCAT
1 TATTATTATTATCAT
8570883 TATT
1 TATT
8570887 TTTTAAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTATTATTATCAT
Found at i:8572789 original size:31 final size:32
Alignment explanation
Indices: 8572724--8572790 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
8572714 CTCTTTTTAT
* * * *
8572724 GAGTTAAATTTGACTATTCAATATTTTAAAAA
1 GAGTCAAATTTGACCATTCAACATTTCAAAAA
*
8572756 GAGTCAAATTTGACCA-TCAACCTTTCAAAAA
1 GAGTCAAATTTGACCATTCAACATTTCAAAAA
8572787 GAGT
1 GAGT
8572791 TGAATTCATG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 16 0.53
32 14 0.47
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (32 bp):
GAGTCAAATTTGACCATTCAACATTTCAAAAA
Found at i:8580940 original size:25 final size:25
Alignment explanation
Indices: 8580799--8580941 Score: 144
Period size: 25 Copynumber: 5.8 Consensus size: 25
8580789 AGCATGTAAA
* * * *
8580799 CGGGAAGCTCTTCCGAGCTATATAA
1 CGGGAAGCTCATGCGAGCTAAATAT
* * *
8580824 CGGAAAGCTCATGTGAGCTAAATAA
1 CGGGAAGCTCATGCGAGCTAAATAT
* *
8580849 CAGGAAGCTCATGCGAGCTATATAT
1 CGGGAAGCTCATGCGAGCTAAATAT
** *
8580874 CGGGAAGCTCATAAGAGCTGAA-AT
1 CGGGAAGCTCATGCGAGCTAAATAT
8580898 CGGGAAGCTCATGCGAGCTAAATAT
1 CGGGAAGCTCATGCGAGCTAAATAT
* * *
8580923 TGGGAAGCTCTTGAGAGCT
1 CGGGAAGCTCATGCGAGCT
8580942 GTGGTGTGTT
Statistics
Matches: 96, Mismatches: 21, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
24 21 0.22
25 75 0.78
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.22
Consensus pattern (25 bp):
CGGGAAGCTCATGCGAGCTAAATAT
Found at i:8582109 original size:13 final size:13
Alignment explanation
Indices: 8582091--8582265 Score: 77
Period size: 13 Copynumber: 13.2 Consensus size: 13
8582081 TATTTATATC
8582091 CATATAAACATTT
1 CATATAAACATTT
8582104 CATATAAACATTT
1 CATATAAACATTT
8582117 CATAT-AACTATTT
1 CATATAAAC-ATTT
** *
8582130 CCATATAGCCGA-AT
1 -CATATAAAC-ATTT
8582144 CATATAAACATTT
1 CATATAAACATTT
***
8582157 CATATATTTATTT
1 CATATAAACATTT
* * *
8582170 CCATACAATCAATT
1 -CATATAAACATTT
* * *
8582184 CACATAACCATTC
1 CATATAAACATTT
*
8582197 CATAT-ATCTATTT
1 CATATAAAC-ATTT
*
8582210 CCATATAATCATTT
1 -CATATAAACATTT
* * **
8582224 CGTATATATGTTT
1 CATATAAACATTT
* *
8582237 CCATATAATCAATT
1 -CATATAAACATTT
*
8582251 CATATAACCATTT
1 CATATAAACATTT
8582264 CA
1 CA
8582266 AATATTCATT
Statistics
Matches: 118, Mismatches: 35, Indels: 18
0.69 0.20 0.11
Matches are distributed among these distances:
12 6 0.05
13 76 0.64
14 31 0.26
15 5 0.04
ACGTcount: A:0.38, C:0.20, G:0.02, T:0.39
Consensus pattern (13 bp):
CATATAAACATTT
Found at i:8582135 original size:40 final size:40
Alignment explanation
Indices: 8582080--8582229 Score: 158
Period size: 40 Copynumber: 3.8 Consensus size: 40
8582070 CACTTTTTAC
* * *
8582080 ATATTTATATCCATATAAACATTTCATATAAACATTTCAT
1 ATATCTATTTCCATATAATCATTTCATATAAACATTTCAT
* ** *
8582120 ATAACTATTTCCATATAGCCGA-ATCATATAAACATTTCAT
1 ATATCTATTTCCATATAATC-ATTTCATATAAACATTTCAT
* * * * * *
8582160 ATATTTATTTCCATACAATCAATTCACATAACCATTCCAT
1 ATATCTATTTCCATATAATCATTTCATATAAACATTTCAT
*
8582200 ATATCTATTTCCATATAATCATTTCGTATA
1 ATATCTATTTCCATATAATCATTTCATATA
8582230 TATGTTTCCA
Statistics
Matches: 88, Mismatches: 20, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
39 1 0.01
40 86 0.98
41 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.02, T:0.40
Consensus pattern (40 bp):
ATATCTATTTCCATATAATCATTTCATATAAACATTTCAT
Found at i:8582213 original size:14 final size:14
Alignment explanation
Indices: 8582194--8582243 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
8582184 CACATAACCA
8582194 TTCCATATATCTAT
1 TTCCATATATCTAT
8582208 TTCCATATAATC-AT
1 TTCCATAT-ATCTAT
* * *
8582222 TT-CGTATATATGT
1 TTCCATATATCTAT
8582235 TTCCATATA
1 TTCCATATA
8582244 ATCAATTCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
12 2 0.07
13 7 0.24
14 17 0.59
15 3 0.10
ACGTcount: A:0.30, C:0.18, G:0.04, T:0.48
Consensus pattern (14 bp):
TTCCATATATCTAT
Found at i:8582264 original size:27 final size:27
Alignment explanation
Indices: 8582091--8582264 Score: 81
Period size: 27 Copynumber: 6.5 Consensus size: 27
8582081 TATTTATATC
* * *
8582091 CATATAAACATTT-CATATAAACATTT
1 CATATAACCATTTCCATATAATCAATT
* **
8582117 CATATAACTATTTCCATATAGCCGAA-T
1 CATATAACCATTTCCATATAATC-AATT
* * * *
8582144 CATATAAACATTT-CATATATTTATTT
1 CATATAACCATTTCCATATAATCAATT
* * * * *
8582170 CCATACAATCAATT-CACATAA-CCATT
1 -CATATAACCATTTCCATATAATCAATT
* * *
8582196 CCATATATCTATTTCCATATAATCATTT
1 -CATATAACCATTTCCATATAATCAATT
* **
8582224 CGTATATA-TGTTTCCATATAATCAATT
1 CATATA-ACCATTTCCATATAATCAATT
8582251 CATATAACCATTTC
1 CATATAACCATTTC
8582265 AAATATTCAT
Statistics
Matches: 106, Mismatches: 34, Indels: 15
0.68 0.22 0.10
Matches are distributed among these distances:
25 1 0.01
26 30 0.28
27 71 0.67
28 4 0.04
ACGTcount: A:0.38, C:0.20, G:0.02, T:0.40
Consensus pattern (27 bp):
CATATAACCATTTCCATATAATCAATT
Found at i:8582407 original size:14 final size:14
Alignment explanation
Indices: 8582388--8582416 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
8582378 AGATGTTAAA
8582388 CTATTTCCATATAG
1 CTATTTCCATATAG
8582402 CTATTTCCATATAG
1 CTATTTCCATATAG
8582416 C
1 C
8582417 CAAATCATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.24, G:0.07, T:0.41
Consensus pattern (14 bp):
CTATTTCCATATAG
Found at i:8582479 original size:40 final size:40
Alignment explanation
Indices: 8582390--8582561 Score: 191
Period size: 40 Copynumber: 4.3 Consensus size: 40
8582380 ATGTTAAACT
* ** * *
8582390 ATTTCCATATAGCTATTTCCATATAGCCAAATCATATAAAC
1 ATTT-CATATATCTATTTCCATATAATCAATTCATATAACC
* * *
8582431 ATTTCATATATTTATTTCCATACAATCAATTCACATAACC
1 ATTTCATATATCTATTTCCATATAATCAATTCATATAACC
*
8582471 ATTCCATATATCTATTTCCATATAATCAATTCATATAACC
1 ATTTCATATATCTATTTCCATATAATCAATTCATATAACC
* * * * * *
8582511 ATTTCGTGTATATGTTTCCATAGAATAAATTCATATAACC
1 ATTTCATATATCTATTTCCATATAATCAATTCATATAACC
*
8582551 ATTTCAAATAT
1 ATTTCATATAT
8582562 TCATTTTCCA
Statistics
Matches: 109, Mismatches: 22, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
40 105 0.96
41 4 0.04
ACGTcount: A:0.38, C:0.20, G:0.03, T:0.39
Consensus pattern (40 bp):
ATTTCATATATCTATTTCCATATAATCAATTCATATAACC
Found at i:8582529 original size:80 final size:80
Alignment explanation
Indices: 8582392--8582553 Score: 216
Period size: 80 Copynumber: 2.0 Consensus size: 80
8582382 GTTAAACTAT
* *
8582392 TTCCATATAGCTATTTCCATATAGCCAAATCATATAAACATTTCATATATTTATTTCCATACAAT
1 TTCCATATAGCTATTTCCATATAACCAAATCATATAAACATTTCATATATATATTTCCATACAAT
*
8582457 CAATTCACATAACCA
66 AAATTCACATAACCA
* * * * * * * *
8582472 TTCCATATATCTATTTCCATATAATCAATTCATATAACCATTTCGTGTATATGTTTCCATAGAAT
1 TTCCATATAGCTATTTCCATATAACCAAATCATATAAACATTTCATATATATATTTCCATACAAT
*
8582537 AAATTCATATAACCA
66 AAATTCACATAACCA
8582552 TT
1 TT
8582554 TCAAATATTC
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
80 70 1.00
ACGTcount: A:0.37, C:0.20, G:0.04, T:0.39
Consensus pattern (80 bp):
TTCCATATAGCTATTTCCATATAACCAAATCATATAAACATTTCATATATATATTTCCATACAAT
AAATTCACATAACCA
Found at i:8587385 original size:18 final size:18
Alignment explanation
Indices: 8587325--8587392 Score: 55
Period size: 20 Copynumber: 3.5 Consensus size: 18
8587315 GATTTCAAAT
8587325 AAATTTATTATATCATTCTTA
1 AAATTT-TTATA-CATT-TTA
* * *
8587346 TAATTTTTACAAATATTATA
1 AAATTTTTATACAT-TT-TA
8587366 AAATTTTTATACATTTTA
1 AAATTTTTATACATTTTA
*
8587384 AATTTTTTA
1 AAATTTTTA
8587393 CCATTTTTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
18 10 0.26
19 5 0.13
20 18 0.47
21 5 0.13
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (18 bp):
AAATTTTTATACATTTTA
Found at i:8587418 original size:18 final size:18
Alignment explanation
Indices: 8587364--8587418 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
8587354 ACAAATATTA
*
8587364 TAAAATTTTTATAC-ATTT
1 TAAATTTTTTA-ACAATTT
* *
8587382 TAAATTTTTTACCATTTT
1 TAAATTTTTTAACAATTT
*
8587400 TATATTTTTTAACAATTT
1 TAAATTTTTTAACAATTT
8587418 T
1 T
8587419 TTTTTAATTC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
17 1 0.03
18 29 0.97
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (18 bp):
TAAATTTTTTAACAATTT
Found at i:8589091 original size:18 final size:19
Alignment explanation
Indices: 8589068--8589109 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
8589058 TTTTTGAGAG
8589068 AAAAAA-ATCGAATACAAA
1 AAAAAAGATCGAATACAAA
*
8589086 AAAAAAGATTGAATACAAA
1 AAAAAAGATCGAATACAAA
8589105 AAAAA
1 AAAAA
8589110 TCAAAGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.74, C:0.07, G:0.07, T:0.12
Consensus pattern (19 bp):
AAAAAAGATCGAATACAAA
Found at i:8590262 original size:13 final size:12
Alignment explanation
Indices: 8590239--8590271 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
8590229 TTTGATGTTA
8590239 TTTATTATTTAT
1 TTTATTATTTAT
8590251 TTTATCTATTTA-
1 TTTAT-TATTTAT
8590263 TTTATTATT
1 TTTATTATT
8590272 CTTTCACTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.20
12 10 0.50
13 6 0.30
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTATTATTTAT
Found at i:8606187 original size:2 final size:2
Alignment explanation
Indices: 8606180--8606221 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
8606170 AATTGACATG
*
8606180 AT AT AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8606222 TAAGGAATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8606739 original size:29 final size:30
Alignment explanation
Indices: 8606695--8606752 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
8606685 AATTGAATCA
*
8606695 AAATCAAAATTTCATATATATAATTATACC
1 AAATCAAAATTTCATATATAGAATTATACC
* *
8606725 AAATTAAAA-TTCATATATCGAATTATAC
1 AAATCAAAATTTCATATATAGAATTATAC
8606753 ATTAAACCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.36
Consensus pattern (30 bp):
AAATCAAAATTTCATATATAGAATTATACC
Found at i:8608015 original size:3 final size:3
Alignment explanation
Indices: 8608007--8608094 Score: 160
Period size: 3 Copynumber: 29.7 Consensus size: 3
8607997 ATATTGCCAC
*
8608007 ATT ATT ATT -GT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
8608054 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
8608095 AACCATGTAT
Statistics
Matches: 82, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
2 1 0.01
3 81 0.99
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:8619231 original size:9 final size:9
Alignment explanation
Indices: 8619217--8619248 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
8619207 TACTTTTCTT
8619217 AAAAAAATA
1 AAAAAAATA
8619226 AAAAAAATA
1 AAAAAAATA
8619235 AAAAAAATA
1 AAAAAAATA
8619244 AAAAA
1 AAAAA
8619249 GAGAGAGGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (9 bp):
AAAAAAATA
Found at i:8620529 original size:45 final size:45
Alignment explanation
Indices: 8620464--8620854 Score: 381
Period size: 45 Copynumber: 8.7 Consensus size: 45
8620454 AACAGATTGG
* * * * * *
8620464 TGAAGATAGCAAATCCTATCTTCCTGAGGTTGCAGTGGAGTGGAT
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTACAGTGGAGTGGAC
* * * ***
8620509 TGAAGATAACAAGTCTTATCTCCCTGAAGTTGCAGCGGAGCAAAC
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTACAGTGGAGTGGAC
* * * * * *
8620554 TGAAGATAGCAAATCCTATCTCCTTGAAATTACAGTAGAGTGGAT
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTACAGTGGAGTGGAC
* * * * **
8620599 TAAAGATAGTAAGTTTTATCTCCCTGAAGTTACAGCGGAGCAGAC
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTACAGTGGAGTGGAC
* * * * *
8620644 TAAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGAT
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTACAGTGGAGTGGAC
* **
8620689 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTACAGCGGAGCAGAC
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTACAGTGGAGTGGAC
* * *
8620734 TGAAGATAGCAAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGG-C
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTACAGTGGAG-TGGAC
* * *
8620779 TGAAGATAGCAAATCCTATCTCCCT-AAGGTTACAGTGGAGTGGAT
1 TGAAGATAGCAAGTCTTATCTCCCTGAA-GTTACAGTGGAGTGGAC
* * *
8620824 TGAAGATAGAAAGTCTTATCTCTCTAAAGTT
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTT
8620855 GCAAAGAGCA
Statistics
Matches: 276, Mismatches: 66, Indels: 8
0.79 0.19 0.02
Matches are distributed among these distances:
44 4 0.01
45 269 0.97
46 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (45 bp):
TGAAGATAGCAAGTCTTATCTCCCTGAAGTTACAGTGGAGTGGAC
Found at i:8620618 original size:90 final size:90
Alignment explanation
Indices: 8620464--8620845 Score: 493
Period size: 90 Copynumber: 4.2 Consensus size: 90
8620454 AACAGATTGG
* *
8620464 TGAAGATAGCAAATCCTATCTTCC-TGAGGTTGCAGTGGAGTGGATTGAAGATAACAAGTCTTAT
1 TGAAGATAGCAAATCCTATC-TCCTTGAAGTTGCAGTGGAGTGGATTGAAGATAGCAAGTCTTAT
* *
8620528 CTCCCTGAAGTTGCAGCGGAGCAAAC
65 CTCCCTGAAGTTACAGCGGAGCAGAC
* * * * * *
8620554 TGAAGATAGCAAATCCTATCTCCTTGAAATTACAGTAGAGTGGATTAAAGATAGTAAGTTTTATC
1 TGAAGATAGCAAATCCTATCTCCTTGAAGTTGCAGTGGAGTGGATTGAAGATAGCAAGTCTTATC
8620619 TCCCTGAAGTTACAGCGGAGCAGAC
66 TCCCTGAAGTTACAGCGGAGCAGAC
* *
8620644 TAAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTGAAGATAGCAAGTCTTATC
1 TGAAGATAGCAAATCCTATCTCCTTGAAGTTGCAGTGGAGTGGATTGAAGATAGCAAGTCTTATC
8620709 TCCCTGAAGTTACAGCGGAGCAGAC
66 TCCCTGAAGTTACAGCGGAGCAGAC
* * * * * *
8620734 TGAAGATAGCAAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGG-CTGAAGATAGCAAATCCTAT
1 TGAAGATAGCAAATCCTATCTCCTTGAAGTTGCAGTGGAG-TGGATTGAAGATAGCAAGTCTTAT
* ** *
8620798 CTCCCT-AAGGTTACAGTGGAGTGGAT
65 CTCCCTGAA-GTTACAGCGGAGCAGAC
*
8620824 TGAAGATAG-AAAGTCTTATCTC
1 TGAAGATAGCAAA-TCCTATCTC
8620846 TCTAAAGTTG
Statistics
Matches: 257, Mismatches: 31, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
89 7 0.03
90 248 0.96
91 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.26
Consensus pattern (90 bp):
TGAAGATAGCAAATCCTATCTCCTTGAAGTTGCAGTGGAGTGGATTGAAGATAGCAAGTCTTATC
TCCCTGAAGTTACAGCGGAGCAGAC
Found at i:8620999 original size:44 final size:44
Alignment explanation
Indices: 8620881--8621034 Score: 166
Period size: 44 Copynumber: 3.5 Consensus size: 44
8620871 ATTTAGTCAT
* *
8620881 ATTTCCCTGAAGTTGCAATGGAACAGACTAAATAAACGAATCTG
1 ATTTCCCTGAAGTTGCAATGGAACAGACTGAATAAACCAATCTG
* * *
8620925 ATTTCTCTGAAGTTGCAGTGGAGCAGACTGAATAAACCAATCTG
1 ATTTCCCTGAAGTTGCAATGGAACAGACTGAATAAACCAATCTG
* * * * * **
8620969 ATTTCCCTGAAGTGGCAATGAAATAAACTGAAGAAAATAATTCT-
1 ATTTCCCTGAAGTTGCAATGGAACAGACTGAATAAACCAA-TCTG
* *
8621013 ATCTCCCTGAAGTTGCAGTGGA
1 ATTTCCCTGAAGTTGCAATGGA
8621035 GCGGATTAAA
Statistics
Matches: 90, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
44 87 0.97
45 3 0.03
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.27
Consensus pattern (44 bp):
ATTTCCCTGAAGTTGCAATGGAACAGACTGAATAAACCAATCTG
Found at i:8625309 original size:18 final size:18
Alignment explanation
Indices: 8625286--8625324 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
8625276 TTATGGTGAG
8625286 TAGAAATATCGTATCCAC
1 TAGAAATATCGTATCCAC
8625304 TAGAAATATCGTATCCAC
1 TAGAAATATCGTATCCAC
8625322 TAG
1 TAG
8625325 GACTAACAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (18 bp):
TAGAAATATCGTATCCAC
Found at i:8627290 original size:26 final size:27
Alignment explanation
Indices: 8627260--8627310 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
8627250 TTGAAGAAAC
8627260 AAACTCAG-AAGC-AAAAACAGAAAATG
1 AAACT-AGCAAGCGAAAAACAGAAAATG
*
8627286 AAACTAGCAAGCGAATAACAGAAAA
1 AAACTAGCAAGCGAAAAACAGAAAA
8627311 GAGAGAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 2 0.09
26 9 0.41
27 11 0.50
ACGTcount: A:0.61, C:0.16, G:0.16, T:0.08
Consensus pattern (27 bp):
AAACTAGCAAGCGAAAAACAGAAAATG
Found at i:8629115 original size:26 final size:28
Alignment explanation
Indices: 8629061--8629121 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
8629051 TATTATCAAG
* *
8629061 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
8629089 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
8629115 AATTATA
1 AATTATA
8629122 AAAATTTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:8629239 original size:59 final size:58
Alignment explanation
Indices: 8629173--8629361 Score: 181
Period size: 59 Copynumber: 3.2 Consensus size: 58
8629163 ATTTTATTAA
8629173 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATCTTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTATCTTTTATAGT
* * *** * *
8629232 ATCATATATTATGATTTGAGTAAATTCATAAAAGAATATTAATTATTAAGAATT-T-TATTA-A-
1 ATCATATATT-TTAATT-A--AAA-T-AT-ATTTAATATTAATTATTTA-AATTATCTTTTATAG
8629293 -
58 T
*
8629293 ATCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAATTATCTTTTATAGT
8629352 ATCATATATT
1 ATCATATATT
8629362 ATGATTTGAG
Statistics
Matches: 101, Mismatches: 15, Indels: 28
0.70 0.10 0.19
Matches are distributed among these distances:
54 16 0.16
55 5 0.05
56 5 0.05
57 4 0.04
59 21 0.21
60 8 0.08
61 11 0.11
63 4 0.04
64 5 0.05
65 4 0.04
66 18 0.18
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (58 bp):
ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTATCTTTTATAGT
Found at i:8629286 original size:120 final size:120
Alignment explanation
Indices: 8629162--8629435 Score: 514
Period size: 120 Copynumber: 2.3 Consensus size: 120
8629152 AATTATTTTA
*
8629162 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATCTTT
8629226 TATAGTATCATATATTATGATTTGAGTAAATTCATAAAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATAAAAGAATATTAATTATTAAG
8629282 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
*
8629347 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATAAAAGAATATTAATTATTAAG
8629402 AATTTTATTAAATCATATATTTTAATTAAAATAT
1 AATTTTATTAAATCATATATTTTAATTAAAATAT
8629436 NNNNNNNNNN
Statistics
Matches: 151, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
120 149 0.99
121 2 0.01
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.48
Consensus pattern (120 bp):
AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATAAAAGAATATTAATTATTAAG
Found at i:8629299 original size:61 final size:61
Alignment explanation
Indices: 8629232--8629422 Score: 194
Period size: 61 Copynumber: 3.2 Consensus size: 61
8629222 CTTTTATAGT
8629232 ATCATATATTATGATTTGAGTAAATTCATAAAAGAATATTAATTATTAAGAATTTTATTAA
1 ATCATATATTATGATTTGAGTAAATTCATAAAAGAATATTAATTATTAAGAATTTTATTAA
* * ** * * * ** * ** *
8629293 ATCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAA--ATT-A-TCTTTTA-TAGT
1 ATCATATATTATGATTTGAGTA-AATTCATAA-AAGAATATTAATTATTAAGAATTTTATTA-A
*
8629352 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
1 ATCATATATTATGATTTGAGTAAATTCATAAAAGAATATTAATTATTAAGAATTTTATTAA
8629413 ATCATATATT
1 ATCATATATT
8629423 TTAATTAAAA
Statistics
Matches: 95, Mismatches: 27, Indels: 16
0.69 0.20 0.12
Matches are distributed among these distances:
57 8 0.08
58 8 0.08
59 25 0.26
60 2 0.02
61 35 0.37
62 9 0.09
63 8 0.08
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (61 bp):
ATCATATATTATGATTTGAGTAAATTCATAAAAGAATATTAATTATTAAGAATTTTATTAA
Found at i:8639161 original size:26 final size:26
Alignment explanation
Indices: 8639131--8639182 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
8639121 AATATTAAGA
* *
8639131 TAAATATTATTTATCTTAATGATAAT
1 TAAATAATATTTATATTAATGATAAT
*
8639157 TAAATAATATTTATATTTATGATAAT
1 TAAATAATATTTATATTAATGATAAT
8639183 ACTATTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (26 bp):
TAAATAATATTTATATTAATGATAAT
Found at i:8640767 original size:18 final size:17
Alignment explanation
Indices: 8640727--8640771 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
8640717 ATAAAAGCTA
* **
8640727 TAAAAATTATTAAACTT
1 TAAAAAATATTAAAAAT
8640744 TAAAAAATATTAAAAAT
1 TAAAAAATATTAAAAAT
8640761 TAGAAAAATAT
1 TA-AAAAATAT
8640772 ATATATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (17 bp):
TAAAAAATATTAAAAAT
Found at i:8640958 original size:15 final size:16
Alignment explanation
Indices: 8640938--8640968 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
8640928 ACATGTGGCA
8640938 AAAAAT-CATAAAAAT
1 AAAAATCCATAAAAAT
8640953 AAAAATCCATAAAAAT
1 AAAAATCCATAAAAAT
8640969 TATAGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAAATCCATAAAAAT
Found at i:8641116 original size:10 final size:10
Alignment explanation
Indices: 8641003--8641145 Score: 52
Period size: 10 Copynumber: 14.6 Consensus size: 10
8640993 TTGGTATGAT
8641003 ATTTTTTATA
1 ATTTTTTATA
*
8641013 ATTCTTTTACA
1 ATT-TTTTATA
*
8641024 A-ATTTTAT-
1 ATTTTTTATA
*
8641032 ATTTCTTTA-C
1 ATTT-TTTATA
*
8641042 A-TTTTTATC
1 ATTTTTTATA
*
8641051 ATTTTCTTACA
1 ATTTT-TTATA
* * *
8641062 ACTTTATAAA
1 ATTTTTTATA
*
8641072 ATTTTATATA
1 ATTTTTTATA
8641082 ATTTTTT-TA
1 ATTTTTTATA
8641091 TATTTTTCTAT-
1 -ATTTTT-TATA
8641102 A--TTTTATA
1 ATTTTTTATA
**
8641110 ATTTTTTACG
1 ATTTTTTATA
8641120 A-TTTTTATA
1 ATTTTTTATA
* *
8641129 ATCCTTTTCTA
1 AT-TTTTTATA
8641140 ATTTTT
1 ATTTTT
8641146 AATGAAAAAA
Statistics
Matches: 99, Mismatches: 19, Indels: 30
0.67 0.13 0.20
Matches are distributed among these distances:
7 3 0.03
8 9 0.09
9 19 0.19
10 44 0.44
11 23 0.23
12 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.01, T:0.62
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:8641116 original size:20 final size:20
Alignment explanation
Indices: 8641093--8641148 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 20
8641083 TTTTTTTATA
8641093 TTTTTCTATATTTTATAAT-
1 TTTTTCTATATTTTATAATC
*
8641112 TTTTTACGAT-TTTTATAATC
1 TTTTT-CTATATTTTATAATC
*
8641132 CTTTTCTA-ATTTT-TAAT
1 TTTTTCTATATTTTATAAT
8641149 GAAAAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 4 0.13
19 20 0.65
20 7 0.23
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTTTCTATATTTTATAATC
Found at i:8645713 original size:37 final size:35
Alignment explanation
Indices: 8645620--8645713 Score: 91
Period size: 37 Copynumber: 2.5 Consensus size: 35
8645610 GTCTCCAAAT
* * *
8645620 TCACATTTCAGTTCAATTTCACTTTTTCACTTTCAA
1 TCACAATTCAATTCAA-TTCACTTTTCCACTTTCAA
*
8645656 TCACAATTCAATTCAAAATTCACTTTTCCATTTTTCAA
1 TCACAATTCAATTC--AATTCACTTTTCCA-CTTTCAA
8645694 GTCA-ATATTCAATTCAATTC
1 -TCACA-ATTCAATTCAATTC
8645714 CACACATATA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
36 12 0.24
37 16 0.33
38 9 0.18
39 12 0.24
ACGTcount: A:0.31, C:0.23, G:0.02, T:0.44
Consensus pattern (35 bp):
TCACAATTCAATTCAATTCACTTTTCCACTTTCAA
Found at i:8646942 original size:3 final size:3
Alignment explanation
Indices: 8646922--8646973 Score: 79
Period size: 3 Copynumber: 17.3 Consensus size: 3
8646912 AACTTATTTC
*
8646922 ATA AT- ATA ATA CTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA
8646970 ATA A
1 ATA A
8646974 ATTTATTATT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.04
3 40 0.89
4 3 0.07
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:8649442 original size:18 final size:18
Alignment explanation
Indices: 8649419--8649455 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
8649409 TATGTCGGAC
8649419 TCTATTATGAGGAACAGT
1 TCTATTATGAGGAACAGT
8649437 TCTATTATGAGGAACAGT
1 TCTATTATGAGGAACAGT
8649455 T
1 T
8649456 GCTCCTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.35
Consensus pattern (18 bp):
TCTATTATGAGGAACAGT
Found at i:8655253 original size:19 final size:19
Alignment explanation
Indices: 8655212--8655254 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
8655202 GTACTTTCAT
**
8655212 CAAATTAATAAAAAAAACC
1 CAAATTAATAAAAAAAAAA
8655231 CAAATTAA-AAAAGAAAAAA
1 CAAATTAATAAAA-AAAAAA
8655250 CAAAT
1 CAAAT
8655255 ACCATATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.72, C:0.12, G:0.02, T:0.14
Consensus pattern (19 bp):
CAAATTAATAAAAAAAAAA
Found at i:8659639 original size:24 final size:25
Alignment explanation
Indices: 8659601--8659648 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
8659591 TTTTTACTTT
* *
8659601 TGAAAAAATTATTAATAATTTTAGA
1 TGAAAAAAATATTAAGAATTTTAGA
8659626 TGAAAAAAAT-TTAAGAATTTTAG
1 TGAAAAAAATATTAAGAATTTTAG
8659649 TATATTGGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (25 bp):
TGAAAAAAATATTAAGAATTTTAGA
Found at i:8659747 original size:28 final size:30
Alignment explanation
Indices: 8659683--8659757 Score: 73
Period size: 28 Copynumber: 2.5 Consensus size: 30
8659673 TTATAATTTA
** *
8659683 AATTATTTTTATAAAACTATTGGTTTATATT
1 AATTATTTTTATAAAAC-ATTGAATTATATG
*
8659714 ATTTATTTTTATAAAA-A-TGAATTATATG
1 AATTATTTTTATAAAACATTGAATTATATG
* *
8659742 AATTATATATATAAAA
1 AATTATTTTTATAAAA
8659758 TTTATTTATT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
28 21 0.57
29 1 0.03
31 15 0.41
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.49
Consensus pattern (30 bp):
AATTATTTTTATAAAACATTGAATTATATG
Found at i:8659787 original size:15 final size:15
Alignment explanation
Indices: 8659754--8659786 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
8659744 TTATATATAT
8659754 AAAATTTATTTATTA
1 AAAATTTATTTATTA
8659769 AAAATTTATTT-TTA
1 AAAATTTATTTATTA
8659783 AAAA
1 AAAA
8659787 AAATTGACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAAATTTATTTATTA
Found at i:8666556 original size:27 final size:27
Alignment explanation
Indices: 8666518--8666573 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
8666508 AAGAAAGGAG
* *
8666518 AAAAAAATTGTAGATGAGGAGAAAACA
1 AAAAAAAATGTAGATGAGAAGAAAACA
8666545 AAAAAAAATGTAGATGAGAAGAAAACA
1 AAAAAAAATGTAGATGAGAAGAAAACA
8666572 AA
1 AA
8666574 GAAGAATTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.64, C:0.04, G:0.20, T:0.12
Consensus pattern (27 bp):
AAAAAAAATGTAGATGAGAAGAAAACA
Found at i:8671222 original size:16 final size:17
Alignment explanation
Indices: 8671201--8671232 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
8671191 TGTTCATACT
8671201 AAAAAGAAAA-GAAAAC
1 AAAAAGAAAAGGAAAAC
8671217 AAAAAGAAAAGGAAAA
1 AAAAAGAAAAGGAAAA
8671233 GCCTTACCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAGGAAAAC
Found at i:8671998 original size:3 final size:3
Alignment explanation
Indices: 8671986--8672054 Score: 66
Period size: 3 Copynumber: 22.7 Consensus size: 3
8671976 TAATGTGTGG
* * * *
8671986 TAT TATT TAT TAT TAT TAT TAA CAC TAT TAT AAT TAT TAT TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
8672032 TAG CAT TAT TAT TAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
8672055 AATACCTTTT
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:8677112 original size:11 final size:11
Alignment explanation
Indices: 8677091--8677148 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
8677081 GAATGTTCAA
*
8677091 AAAAAAAAAAG
1 AAAAGAAAAAG
*
8677102 AAAGGAAAAAG
1 AAAAGAAAAAG
8677113 AAAAG-AAAAG
1 AAAAGAAAAAG
8677123 AAGAA-AAAAATG
1 AA-AAGAAAAA-G
8677135 AAAAAGAAAAAG
1 -AAAAGAAAAAG
8677147 AA
1 AA
8677149 GAGCCCAAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
10 7 0.18
11 21 0.54
12 4 0.10
13 7 0.18
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:8677116 original size:16 final size:16
Alignment explanation
Indices: 8677091--8677148 Score: 64
Period size: 16 Copynumber: 3.5 Consensus size: 16
8677081 GAATGTTCAA
* *
8677091 AAAAAAAAAAGAAAGG
1 AAAAAGAAAAGAAAAG
8677107 AAAAAGAAAAGAAAAG
1 AAAAAGAAAAGAAAAG
8677123 AAGAAA-AAAATGAAAAAG
1 AA-AAAGAAAA-G-AAAAG
8677141 AAAAAGAA
1 AAAAAGAA
8677149 GAGCCCAAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
16 20 0.56
17 7 0.19
18 9 0.25
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (16 bp):
AAAAAGAAAAGAAAAG
Found at i:8677121 original size:24 final size:23
Alignment explanation
Indices: 8677089--8677150 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
8677079 ATGAATGTTC
8677089 AAAAA-AAAAAAAGAAAGGAAAAAG
1 AAAAAGAAAAAAAGAAA--AAAAAG
* *
8677113 -AAAAGAAAAGAAGAAAAAAATG
1 AAAAAGAAAAAAAGAAAAAAAAG
8677135 AAAAAGAAAAAGAAGA
1 AAAAAGAAAAA-AAGA
8677151 GCCCAAGGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
22 5 0.16
23 13 0.41
24 14 0.44
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.02
Consensus pattern (23 bp):
AAAAAGAAAAAAAGAAAAAAAAG
Found at i:8677490 original size:49 final size:47
Alignment explanation
Indices: 8677437--8677596 Score: 123
Period size: 49 Copynumber: 3.3 Consensus size: 47
8677427 CATATATTAG
8677437 TAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCTGTGCTCTCAA
1 TAAAATTT-CTATCTTGATTAATTTATTCATTTCGAGCT-TGCTCTCAA
** * * * * *
8677486 TAAAATTTC-ATCTT-ATCCATTGTGATAATCTTTTTC-ATCTT-ATCTTAG
1 TAAAATTTCTATCTTGATTAATT-T-AT--TC-ATTTCGAGCTTGCTCTCAA
* *
8677534 CAAAATTTTCTATCTTGATTAATTTATTCATTTCGAGCTCTGCTCTGAA
1 TAAAA-TTTCTATCTTGATTAATTTATTCATTTCGAGCT-TGCTCTCAA
8677583 TAAAATTTC-ATCTT
1 TAAAATTTCTATCTT
8677597 ATCCATTGTG
Statistics
Matches: 84, Mismatches: 16, Indels: 24
0.68 0.13 0.19
Matches are distributed among these distances:
46 9 0.11
47 16 0.19
48 16 0.19
49 23 0.27
50 11 0.13
51 9 0.11
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.47
Consensus pattern (47 bp):
TAAAATTTCTATCTTGATTAATTTATTCATTTCGAGCTTGCTCTCAA
Found at i:8677604 original size:97 final size:97
Alignment explanation
Indices: 8677433--8677716 Score: 399
Period size: 97 Copynumber: 2.9 Consensus size: 97
8677423 ATTTCATATA
* * *
8677433 TTAGTAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCTGTGCTCTCAATAAAATTTCATC
1 TTAGAAAAATTTACTATCTTGATTAATTTATTCATTTCGAGCTCTGCTCTCAATAAAATTTCATC
8677498 TTATCCATTGTGATAATCTTTTTCATCTTATC
66 TTATCCATTGTGATAATCTTTTTCATCTTATC
* * *
8677530 TTAGCAAAATTTTCTATCTTGATTAATTTATTCATTTCGAGCTCTGCTCTGAATAAAATTTCATC
1 TTAGAAAAATTTACTATCTTGATTAATTTATTCATTTCGAGCTCTGCTCTCAATAAAATTTCATC
8677595 TTATCCATTGTGATAATCTTTTTCATCTTATC
66 TTATCCATTGTGATAATCTTTTTCATCTTATC
** ** ** * * *
8677627 TTAGAAAAATTTACTATCTTGATTGGTTTATTTGTTTAAAGCTTTGCTCTCAACAAAATTTCATT
1 TTAGAAAAATTTACTATCTTGATTAATTTATTCATTTCGAGCTCTGCTCTCAATAAAATTTCATC
* *
8677692 TTGTCCACTT-TAATAATCTTTTTCA
66 TTATCCA-TTGTGATAATCTTTTTCA
8677717 AGTAGTTTTC
Statistics
Matches: 168, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
97 166 0.99
98 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.48
Consensus pattern (97 bp):
TTAGAAAAATTTACTATCTTGATTAATTTATTCATTTCGAGCTCTGCTCTCAATAAAATTTCATC
TTATCCATTGTGATAATCTTTTTCATCTTATC
Found at i:8678889 original size:128 final size:128
Alignment explanation
Indices: 8678670--8679642 Score: 1556
Period size: 128 Copynumber: 7.6 Consensus size: 128
8678660 CCATCTGTCC
* * *
8678670 TATCTCCCTAAGCAGTAGTGGAGCGGACAGGAAA-AAACCAATCCTATCTCCCTGAAGTTGCAGT
1 TATCTCCCTAAGCAGTAGTGGAGCAGAC--GAAAGAAATCAATCCTATCTCCCTGAAGTTACAGT
* * *
8678734 GGAGCGGATTAAAACCCCAGATCTTATCTCTCTGAAATTGCAGTAGAGCAGATCGCATCTAGTCT
64 GGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCT
*
8678799 TATCTCCCTAAGCAGTAGTGGAGAAGACGAAAGAAATCAATCCTATCTCCCTGAAGTTACAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAATCAATCCTATCTCCCTGAAGTTACAGTGG
*
8678864 AGCGGATTAAAACCACGGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCT
66 AGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCT
* *
8678927 TATCTCCCTAAGCAGTAGTGGAGTAGACGAAAGAAATCAATCCTATCTCCCTGAAGTTACAGTAG
1 TATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAATCAATCCTATCTCCCTGAAGTTACAGTGG
* *
8678992 AGCGGATTAAAACCACAGATCTTATCTCTCTGAATTTGCAGTAGAGCAGATCGCATTAAGTCT
66 AGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCT
* * * *
8679055 TATCTCCCTAAACAGTAGTGGAGTAGACAAAAGAAATCAATCCTATCTCCTTGAAGTTACAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAATCAATCCTATCTCCCTGAAGTTACAGTGG
* *
8679120 AGCGGATTAAAACCCCAGATTTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCT
66 AGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCT
* *
8679183 TATCTCCTTAAGCAGTAGTGGAGCAGACGAAAGAAATCAATCCTATCTCCCCGAAGTTACAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAATCAATCCTATCTCCCTGAAGTTACAGTGG
8679248 AGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCT
66 AGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCT
* * *
8679311 TATCTCCCTAAGCAGTAGTGGAGTAGACGAAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAATCAATCCTATCTCCCTGAAGTTACAGTGG
8679376 AGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCT
66 AGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCT
** * * *
8679439 TATCTCCCTGAAGTTGTAGTGGAGCAGACG-AAGAAACCAATCCTGTCTCCCTGAAGTTGCAGTG
1 TATCTCCCT-AAGCAGTAGTGGAGCAGACGAAAGAAATCAATCCTATCTCCCTGAAGTTACAGTG
* * * *
8679503 GAGCAGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCGAGTCT
65 GAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCT
* * * *
8679567 TATCTCCTTAAGCAG-AGTGGAGCAGACGAAAGAAATAAATCCTATCTCCCCGAAGTTGCAGTGG
1 TATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAATCAATCCTATCTCCCTGAAGTTACAGTGG
* *
8679631 AGTGGATAAAAA
66 AGCGGATTAAAA
8679643 TCAATCCTAT
Statistics
Matches: 789, Mismatches: 52, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
126 13 0.02
127 48 0.06
128 685 0.87
129 43 0.05
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (128 bp):
TATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAATCAATCCTATCTCCCTGAAGTTACAGTGG
AGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCT
Found at i:8679230 original size:84 final size:84
Alignment explanation
Indices: 8678886--8679531 Score: 225
Period size: 84 Copynumber: 7.6 Consensus size: 84
8678876 CCACGGATCT
* * * * * *
8678886 TATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGT
1 TATCTCCCTGAAGTTGCAGTAGAGCAGATAGAATCAAGTCTTATCTCCTTAAGCAGCAGTGGAGC
8678951 AGACGAAAGAAATCAATCC
66 AGACGAAAGAAATCAATCC
* * * * * *** *
8678970 TATCTCCCTGAAGTTACAGTAGAGCGGATTAAAACCACAGATCTTATCTCTCTGAATTTGCAGTA
1 TATCTCCCTGAAGTTGCAGTAGAGCAGA-TAGAATCA-AG-TCTTATCTC-CTTAAGCAGCAGTG
* ** *
8679035 GAGCAGATCGCATTAAGTC--T--
62 GAGCAGA-CGAAAGAAATCAATCC
* * * * *
8679055 TATCTCCCTAAACAGTAGTGGAGTAGA-CA-AAAGAAATCAA-TCCTATCTCCTTGAAGTTA-CA
1 TATCTCCCT-GA-AGT--TGCAGTAGAGCAGATAG-AATCAAGTCTTATCTCCTT-AAG-CAGCA
* ** *** **
8679116 GTGGAGCGGATTAAA-ACCCCAGATTT
59 GTGGAGCAGACGAAAGAAATCA-ATCC
* * * *
8679142 TATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCTTATCTCCTTAAGCAGTAGTGGAGC
1 TATCTCCCTGAAGTTGCAGTAGAGCAGATAGAATCAAGTCTTATCTCCTTAAGCAGCAGTGGAGC
8679207 AGACGAAAGAAATCAATCC
66 AGACGAAAGAAATCAATCC
* * * * * * * ** *
8679226 TATCTCCCCGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTA
1 TATCTCCCTGAAGTTGCAGTAGAGCAGA-TAGAATCA-AG-TCTTATCTC-CTTAAGCAGCAGTG
* *
8679291 GAGCAGATC----G-CATCAAGTCT
62 GAGCAGA-CGAAAGAAATCAA-TCC
* * * * * * **
8679311 TATCTCCCTAAGCAGTAGTGGAGTAGA-C-GAAAGAAACCAA-TCCTATCTCCCTGAAGTTGCAG
1 TATCTCCCT--GAAGT--TGCAGTAGAGCAGATAG-AATCAAGTCTTATCT-CCTTAAGCAGCAG
* ** * *
8679373 TGGAGCGGATTAAA-ACCA-CAGATCT
60 TGGAGCAGACGAAAGA-AATCA-ATCC
* * * * ** *
8679398 TATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTGAAGTTGTAGTGGAG
1 TATCTCCCTGAAGTTGCAGTAGAGCAGATAGAATCAAGTCTTATCT-CCTTAAGCAGCAGTGGAG
*
8679463 CAGACG-AAGAAACCAATCC
65 CAGACGAAAGAAATCAATCC
* * *
8679482 TGTCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCTC
1 TATCTCCCTGAAGTTGCAGTAGAGCAGA-TAGAATCA-AG-TCTTATCTC
8679532 TCTGAAGTTG
Statistics
Matches: 410, Mismatches: 103, Indels: 96
0.67 0.17 0.16
Matches are distributed among these distances:
82 2 0.00
83 20 0.05
84 160 0.39
85 93 0.23
86 13 0.03
87 67 0.16
88 34 0.08
89 21 0.05
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (84 bp):
TATCTCCCTGAAGTTGCAGTAGAGCAGATAGAATCAAGTCTTATCTCCTTAAGCAGCAGTGGAGC
AGACGAAAGAAATCAATCC
Found at i:8679632 original size:44 final size:44
Alignment explanation
Indices: 8678709--8679632 Score: 255
Period size: 44 Copynumber: 21.7 Consensus size: 44
8678699 GGAAAAAACC
* * ** *
8678709 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAA-ACCCCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGA-CACA
* * * * *
8678753 GATCTTATCTCTCTGAAATTGCAGTAGAGCAGATC----G-CATCT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CGAAAGACA-CA
* ** * * *
8678794 AGTCTTATCTCCCT-AAGCAGTAGTGGAGAAGACGAAAGAAATC-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGACA-CA
* * * ** *
8678837 AATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAA-ACCACG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGA-CACA
* * *
8678881 GATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATC----G-CATCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CGAAAGACA-CA
* ** * * *
8678922 AGTCTTATCTCCCT-AAGCAGTAGTGGAGTAGACGAAAGAAATC-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGACA-CA
* * * * **
8678965 AATCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAA-ACCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGA-CACA
* * * * *
8679009 GATCTTATCTCTCTGAATTTGCAGTAGAGCAGATC----G-CATTA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CGAAAGACA-CA
* *** * * * *
8679050 AGTCTTATCTCCCT-AAACAGTAGTGGAGTAGACAAAAGAAATC-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGACA-CA
* * * * ** *
8679093 AATCCTATCTCCTTGAAGTTACAGTGGAGCGGATTAAA-ACCCCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGA-CACA
* * * *
8679137 GATTTTATCTCTCTGAAGTTGCAGTAGAGCAGATC----G-CATCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CGAAAGACA-CA
* * ** * *
8679178 AGTCTTATCT-CCTTAAGCAGTAGTGGAGCAGACGAAAGAAATC-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGACA-CA
* * * * **
8679221 AATCCTATCTCCCCGAAGTTACAGTGGAGCGGATTAAA-ACCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGA-CACA
* * *
8679265 GATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATC----G-CATCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CGAAAGACA-CA
* ** * * * *
8679306 AGTCTTATCTCCCT-AAGCAGTAGTGGAGTAGACGAAAGAAACC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGACACA
* * **
8679349 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAA-ACCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGA-CACA
* * *
8679393 GATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATC----G-CATCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CGAAAGACA-CA
* * * *
8679434 AGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACG-AAGAAACC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGACACA
* * **
8679477 AATCCTGTCTCCCTGAAGTTGCAGTGGAGCAGATTAAA-ATCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGA-CACA
* * * *
8679521 GATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATC-----ACATCG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CGAAAGACA-CA
* * ** * *
8679562 AGTCTTATCT-CCTTAAGCAG-AGTGGAGCAGACGAAAGAAATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGACACA
* *
8679604 AATCCTATCTCCCCGAAGTTGCAGTGGAG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAG
8679633 TGGATAAAAA
Statistics
Matches: 611, Mismatches: 197, Indels: 144
0.64 0.21 0.15
Matches are distributed among these distances:
38 1 0.00
39 15 0.02
40 85 0.14
41 98 0.16
42 8 0.01
43 110 0.18
44 294 0.48
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.25
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGACACA
Found at i:8680424 original size:16 final size:17
Alignment explanation
Indices: 8680403--8680434 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
8680393 TGTTCATACT
8680403 AAAAAGAAAA-GAAAAC
1 AAAAAGAAAAGGAAAAC
8680419 AAAAAGAAAAGGAAAA
1 AAAAAGAAAAGGAAAA
8680435 GCCTTACCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAGGAAAAC
Found at i:8681197 original size:3 final size:3
Alignment explanation
Indices: 8681185--8681263 Score: 68
Period size: 3 Copynumber: 25.7 Consensus size: 3
8681175 TAATGTGTGG
* * * * *
8681185 TAT TATT TAT TAT TAT TAT ATAT TAT TAT TAA CAC TAT TAT AAT AAT
1 TAT TA-T TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
8681232 TAT TAT TAG CAT TAT TAT TAT TAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
8681264 AATACCTTTT
Statistics
Matches: 61, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
3 55 0.90
4 6 0.10
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:8683600 original size:28 final size:28
Alignment explanation
Indices: 8683559--8683612 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
8683549 TGCCGCATAG
* *
8683559 ATGCCGCCTTACACTCCTCTTCCAACCA
1 ATGCCGCCTAACACTCCTCCTCCAACCA
*
8683587 ATGCCGCCTAACACTTCTCCTCCAAC
1 ATGCCGCCTAACACTCCTCCTCCAAC
8683613 AAACTAGTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.22, C:0.46, G:0.07, T:0.24
Consensus pattern (28 bp):
ATGCCGCCTAACACTCCTCCTCCAACCA
Found at i:8684091 original size:25 final size:26
Alignment explanation
Indices: 8684042--8684096 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
8684032 ATAAATAATA
8684042 AAAAGAGTAAAAAAAAATAGAAAAGC
1 AAAAGAGTAAAAAAAAATAGAAAAGC
* * * *
8684068 AAAAGAG-AACAAGAAATAGGAAAGT
1 AAAAGAGTAAAAAAAAATAGAAAAGC
8684093 AAAA
1 AAAA
8684097 ATGAACGAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (26 bp):
AAAAGAGTAAAAAAAAATAGAAAAGC
Found at i:8684250 original size:19 final size:19
Alignment explanation
Indices: 8684226--8684266 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
8684216 CAAAATGATA
*
8684226 TATATAA-TATATATTTTAT
1 TATATAATTACATA-TTTAT
8684245 TATATAATTACATATTTAT
1 TATATAATTACATATTTAT
8684264 TAT
1 TAT
8684267 TTTATTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATAATTACATATTTAT
Found at i:8686396 original size:18 final size:17
Alignment explanation
Indices: 8686352--8686398 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
8686342 GGCGCAGGTG
8686352 ATTAAACAA-TTCAAAAA
1 ATTAAA-AATTTCAAAAA
8686369 ATATAGAAAATTTCAAAAA
1 AT-TA-AAAATTTCAAAAA
8686388 CATTAAAAATT
1 -ATTAAAAATT
8686399 ATAATCTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
17 2 0.08
18 10 0.38
19 12 0.46
20 2 0.08
ACGTcount: A:0.62, C:0.09, G:0.02, T:0.28
Consensus pattern (17 bp):
ATTAAAAATTTCAAAAA
Found at i:8704487 original size:2 final size:2
Alignment explanation
Indices: 8704480--8704505 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8704470 CATAGTTTAG
8704480 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
8704506 GTTTTTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8710605 original size:12 final size:12
Alignment explanation
Indices: 8710585--8710616 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
8710575 CTGAAAGGAC
8710585 ATATATATCTAT
1 ATATATATCTAT
*
8710597 ATCTATATCTAT
1 ATATATATCTAT
8710609 ATATATAT
1 ATATATAT
8710617 AAATTCTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (12 bp):
ATATATATCTAT
Found at i:8724492 original size:17 final size:17
Alignment explanation
Indices: 8724466--8724500 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
8724456 AATTGTCATC
*
8724466 ATTTATTTATTTATTTT
1 ATTTAATTATTTATTTT
*
8724483 ATTTAATTATTTGTTTT
1 ATTTAATTATTTATTTT
8724500 A
1 A
8724501 GATATATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
ATTTAATTATTTATTTT
Found at i:8724984 original size:2 final size:2
Alignment explanation
Indices: 8724977--8725010 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
8724967 TATAGTTACC
8724977 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8725011 TGTTGACACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8728123 original size:43 final size:43
Alignment explanation
Indices: 8728039--8728150 Score: 127
Period size: 43 Copynumber: 2.6 Consensus size: 43
8728029 TCTACTCTGT
* * *
8728039 TACAACTCCATGGG-GATGAGATTTGTGGTTTTAGTCTGCTCCAC
1 TACAACT-CA-GGGAGATAAGATCTGTGGTTTTAATCTGCTCCAC
** *
8728083 TACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCTGCTCCAC
1 TACAACTCAGGGAGATAAGATCTGTGGTTTTAATCTGCTCCAC
* *
8728126 TGCAACTCAGGGAGATAGGATCTGT
1 TACAACTCAGGGAGATAAGATCTGT
8728151 TTTTTGATCC
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
42 3 0.05
43 48 0.86
44 5 0.09
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (43 bp):
TACAACTCAGGGAGATAAGATCTGTGGTTTTAATCTGCTCCAC
Found at i:8728228 original size:44 final size:44
Alignment explanation
Indices: 8728178--8728761 Score: 546
Period size: 44 Copynumber: 13.3 Consensus size: 44
8728168 ACAAATATAG
* * *
8728178 GAAGACAGGACCTGCTATCTTCGATCTACTTCGCGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * * * * ***
8728222 GAAGACAAGATCTGCTTTCTTCGATTTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCCAATACAT
* * * *
8728267 GAAGACAAGATCTGC-A-CATTCGATCCACTTC-CTACCAATATAA
1 GAAGACAAGATCTGCTATC-TTCGATCTACTTCAC-GCCAATACAT
* *
8728310 GAAGACAGGATCTGCTTTCTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * * * *
8728354 GAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACTAATATAA
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCAC-GCCAATACAT
*
8728397 GAAGACAGGA-CATGCTATCTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATC-TGCTATCTTCGATCTACTTCACGCCAATACAT
* * *
8728441 GAAGACAAGATCTACTTTCTTCGATCTACTTCACGCTAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
*
8728485 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * *
8728529 GAAGACAATATCTGC-ATCTTCGATCTACTTTCTA--CCAATATAA
1 GAAGACAAGATCTGCTATCTTCGATCTAC-TTC-ACGCCAATACAT
* * * *
8728572 GAAGACAGGACCTGCTATCTTCGATCTACTTCACTGCCAACACAA
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCAC-GCCAATACAT
* * * *
8728617 GAATACAAGATCTGCTTTCTTCGATCTACTT--CGCCACTAGTAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATA-CAT
* * * * *
8728660 GGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACTAATATAG
1 --GAAGACAAGATCTGCTATCTTCGATCTACTTCAC-GCCAATACAT
* * * *
8728705 GAAGACATGACCTGCTTTCTTCGACCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
8728749 GAAGACAAGATCT
1 GAAGACAAGATCT
8728762 ACATCTTTTA
Statistics
Matches: 440, Mismatches: 76, Indels: 48
0.78 0.13 0.09
Matches are distributed among these distances:
42 9 0.02
43 103 0.23
44 246 0.56
45 78 0.18
46 4 0.01
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.28
Consensus pattern (44 bp):
GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
Found at i:8728421 original size:175 final size:174
Alignment explanation
Indices: 8728178--8728692 Score: 520
Period size: 175 Copynumber: 2.9 Consensus size: 174
8728168 ACAAATATAG
* * * * * * * *
8728178 GAAGACAGGACCTGCTATCTTCGATCTACTTCGC-GCCAATACATGAAGACAAGATC-TGCTTTC
1 GAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACCAATATAAGAAGACAGGA-CATGCTATC
* * * ** *
8728241 TTCGATTTACTTCGCCACCAGTATGGGAAGACAAGATCTGC-ACATTCGATCCACTTCCTAC-C-
63 TTCGATCTACTTC-ACACCAATACAGGAAGACAAGATCTACTAC-TTCGATCCACTT-C-ACGCT
* *
8728303 AATATAAGAAGACAGGATCTGCTTTCTTCGATCTACTTCACGCCAATACAT
124 AATACAAGAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAATACAT
*
8728354 GAAGACAAGATCTGCATCTTCGATCCACTTCCTACTAATATAAGAAGACAGGACATGCTATCTTC
1 GAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAAGAAGACAGGACATGCTATCTTC
* * * *
8728419 GATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCACGCTAATACA
66 GATCTACTTCACACCAATACAGGAAGACAAGATCTAC-TACTTCGATCCACTTCACGCTAATACA
*
8728484 TGAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAATACAT
130 AGAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAATACAT
* * * *
8728529 GAAGACAATATCTGCATCTTCGATCTACTTTCTACCAATATAAGAAGACAGGACCTGCTATCTTC
1 GAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAAGAAGACAGGACATGCTATCTTC
* * * * * * * * * *
8728594 GATCTACTTCACTGCCAACACAAGAATACAAGATCTGCTTTCTTCGATCTACTTCGCCACTAGTA
66 GATCTACTTCAC-ACCAATACAGGAAGACAAGATCTAC-TACTTCGATCCACTTC-ACGCTAATA
*** * *
8728659 TGGGAAGACAAGATCTGC-ATCTTCGATCCACTTC
128 CAAGAAGACAAGATCTGCTTTCTTCGATCTACTTC
8728693 CTACTAATAT
Statistics
Matches: 292, Mismatches: 39, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
173 2 0.01
174 24 0.08
175 179 0.61
176 66 0.23
177 21 0.07
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (174 bp):
GAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAAGAAGACAGGACATGCTATCTTC
GATCTACTTCACACCAATACAGGAAGACAAGATCTACTACTTCGATCCACTTCACGCTAATACAA
GAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAATACAT
Found at i:8728722 original size:220 final size:216
Alignment explanation
Indices: 8728156--8728768 Score: 569
Period size: 219 Copynumber: 2.8 Consensus size: 216
8728146 TCTGTTTTTT
* * * * * * *
8728156 GATCCACTTCCTACAAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCGCGCCAATACA
1 GATCCACTTCCTACCAACACAAGAAGACAAGACATGCTATCTTCGATCTACTT-ACGCCAATACA
* * ** * * * ** * *
8728221 TGAAGACAAGATCTGCTTTCTTCGATTTACTTCGCCACCAGTATGGGAAGACAAGATCTGC--AC
65 TGAAGACAAGATCTACTATCTTCGATCCACTTC-ACACTAATACAGGAAGACAAGACCTGCTTTC
* * * * * *
8728284 ATTCGATCC-ACTTC-CTACCAATATAAGAAGACAGGATCTGCTTTCTTCGATCTACTTCACGCC
129 -TTCGA-CCTACTTCAC-GCCAATACATGAAGACAAGATCTAC-ATCTTCGATCTACTTCAC-CC
* *
8728347 AATACATGAAGACAAGATCTGCATCTTC
189 AATACAAGAAGACAAGACCTGCATCTTC
* * * *
8728375 GATCCACTTCCTACTAATATAAGAAGACAGGACATGCTATCTTCGATCTACTTCACGCCAATACA
1 GATCCACTTCCTACCAACACAAGAAGACAAGACATGCTATCTTCGATCTACTT-ACGCCAATACA
* * * * *
8728440 TGAAGACAAGATCTACTTTCTTCGATCTACTTCACGCTAATACATGAAGACAAGATCTGCTTTCT
65 TGAAGACAAGATCTACTATCTTCGATCCACTTCACACTAATACAGGAAGACAAGACCTGCTTTCT
* * *
8728505 TCGATCTACTTCACGCCAATACATGAAGACAATATCTGCATCTTCGATCTACTTTCTA-CCAATA
130 TCGACCTACTTCACGCCAATACATGAAGACAAGATCTACATCTTCGATCTAC-TTC-ACCCAATA
* *
8728569 TAAGAAGACAGGACCTGCTATCTTC
193 CAAGAAGACAAGACCTGC-ATCTTC
* * * * *
8728594 GATCTACTTCACTGCCAACACAAGAATACAAGATC-TGCTTTCTTCGATCTACTT-CGCCACTAG
1 GATCCACTTC-CTACCAACACAAGAAGACAAGA-CATGCTATCTTCGATCTACTTACGCCAATA-
* * * *
8728657 TATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACTAATATAGGAAGACATGACCTGC
63 CAT--GAAGACAAGATCTACTATCTTCGATCCACTTCAC-ACTAATACAGGAAGACAAGACCTGC
8728720 TTTCTTCGACCTACTTCACGCCAATACATGAAGACAAGATCTACATCTT
125 TTTCTTCGACCTACTTCACGCCAATACATGAAGACAAGATCTACATCTT
8728769 TTATAACTTC
Statistics
Matches: 335, Mismatches: 46, Indels: 25
0.83 0.11 0.06
Matches are distributed among these distances:
218 60 0.18
219 143 0.43
220 117 0.35
221 15 0.04
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (216 bp):
GATCCACTTCCTACCAACACAAGAAGACAAGACATGCTATCTTCGATCTACTTACGCCAATACAT
GAAGACAAGATCTACTATCTTCGATCCACTTCACACTAATACAGGAAGACAAGACCTGCTTTCTT
CGACCTACTTCACGCCAATACATGAAGACAAGATCTACATCTTCGATCTACTTCACCCAATACAA
GAAGACAAGACCTGCATCTTC
Found at i:8742516 original size:17 final size:17
Alignment explanation
Indices: 8742490--8742524 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
8742480 AATTGTCATC
*
8742490 ATTTATTTATTTATTTT
1 ATTTAATTATTTATTTT
*
8742507 ATTTAATTATTTGTTTT
1 ATTTAATTATTTATTTT
8742524 A
1 A
8742525 GATATATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
ATTTAATTATTTATTTT
Found at i:8746135 original size:43 final size:43
Alignment explanation
Indices: 8746036--8746140 Score: 122
Period size: 43 Copynumber: 2.4 Consensus size: 43
8746026 TCTACTCTGT
* * *
8746036 TACAACTCCATGGG-GATGAGATTTGTGGTTTTAGTCTGCTCCAC
1 TACAACT-CA-GGGAGATAAGATCTGTGGTTTTAATCTGCTCCAC
** *
8746080 TACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCTGCTCCAC
1 TACAACTCAGGGAGATAAGATCTGTGGTTTTAATCTGCTCCAC
*
8746123 TGCAACTCAGGGAGATAA
1 TACAACTCAGGGAGATAA
8746141 CGACAACGAG
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
42 3 0.06
43 42 0.84
44 5 0.10
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (43 bp):
TACAACTCAGGGAGATAAGATCTGTGGTTTTAATCTGCTCCAC
Found at i:8747635 original size:11 final size:13
Alignment explanation
Indices: 8747609--8747636 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
8747599 ACTTTTTAAA
8747609 ATATGTATTTTAT
1 ATATGTATTTTAT
8747622 ATATGTATTTTAT
1 ATATGTATTTTAT
8747635 AT
1 AT
8747637 TTTATGATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (13 bp):
ATATGTATTTTAT
Found at i:8749462 original size:25 final size:26
Alignment explanation
Indices: 8749434--8749487 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
8749424 TATATTTTTA
*
8749434 CAATAAATAAT-TTTCTAAA-TGAAGT
1 CAATAAAAAATATTT-TAAATTGAAGT
*
8749459 CAATAAAAAATATTTTAAATTTAAGT
1 CAATAAAAAATATTTTAAATTGAAGT
8749485 CAA
1 CAA
8749488 ATTATTAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.52, C:0.07, G:0.06, T:0.35
Consensus pattern (26 bp):
CAATAAAAAATATTTTAAATTGAAGT
Found at i:8753877 original size:29 final size:29
Alignment explanation
Indices: 8753811--8753877 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
8753801 ACTTCGTAAT
*
8753811 ATTTAAAAATATAAGGACTAAATTCTTAA
1 ATTTAAAAATATAAGAACTAAATTCTTAA
**
8753840 AAATAAAAATATACA-AACTAAATTC-TAA
1 ATTTAAAAATATA-AGAACTAAATTCTTAA
8753868 ATTTACAAAA
1 ATTTA-AAAA
8753878 AAATATATGG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
28 6 0.19
29 24 0.77
30 1 0.03
ACGTcount: A:0.58, C:0.09, G:0.03, T:0.30
Consensus pattern (29 bp):
ATTTAAAAATATAAGAACTAAATTCTTAA
Found at i:8754112 original size:106 final size:106
Alignment explanation
Indices: 8753985--8754592 Score: 704
Period size: 106 Copynumber: 5.8 Consensus size: 106
8753975 AATATATGAC
*
8753985 TTCGTATATTTGTATCTGATTCTGACAC-AAAAAAAAGAATTTTTTTTAAAAATTTGTACTGGGT
1 TTCGTATATTTATATCTGATTCTGACACGAAAAAAAAGAATTTTTTTT-AAAATTTGTACTGGGT
**
8754049 GCCAACCATTGACAGGCCAGCACCCAAATTTTTTTTATTTTT
65 GCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTATTTTT
* * *
8754091 TTCGTATATTTATATCTGATTCTG--AC-----AATA-AA-TTTTTTTAAAATTCGTACTTGGTG
1 TTCGTATATTTATATCTGATTCTGACACGAAAAAAAAGAATTTTTTTTAAAATTTGTACTGGGTG
* * *
8754147 CTGGCCATTGACAGGGCAACACCCAAATTTTTTTTA--TTT
66 CCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTATTTTT
8754186 TTCGTATATTTATATCTGATTCTGACACGAAAAAAAAGAATTTTTTTTTTAAAATTTGTACTGGG
1 TTCGTATATTTATATCTGATTCTGACACGAAAAAAAAGAA--TTTTTTTTAAAATTTGTACTGGG
*
8754251 TGCTGGCCATTGACAGGCCAGCACCCCAAATTTTTTTATTTTTATTTTT
64 TGCCGGCCATTGACAGGCCAGCA-CCCAAA----TTT-TTTTTATTTTT
* *
8754300 TT-GTATATTTATATCTGACTCTGACACGAAAAAAAAGTAAAATTTTTTT-AAA-TTGTACTGGG
1 TTCGTATATTTATATCTGATTCTGACACGAAAAAAAAG--AATTTTTTTTAAAATTTGTACTGGG
* *
8754362 TGTCGGCCATTGACAGGCCAGCACCTAAATTTTTTTTATTTTT
64 TGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTATTTTT
* * * *
8754405 TTCGTATATTTATATCTGACTCTGACACGTACAAAAAGAATTTTTTTT-AAA-TTGTACTAGGTG
1 TTCGTATATTTATATCTGATTCTGACACGAAAAAAAAGAATTTTTTTTAAAATTTGTACTGGGTG
*
8754468 CCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTATTTGT
66 CCGGCCATTGACAGGCCAGCACCC-AAATTTTTTTTATTTTT
* ** * * *
8754510 TTCGTATATTTATATCTTATTCTGACAAAAAAAAAGGAAAAATTTTTTTT---A-CTGT--TGAG
1 TTCGTATATTTATATCTGATTCTGACACGAAAAAA--AAGAATTTTTTTTAAAATTTGTACTGGG
8754569 TGCCGGCCATTGACAGGCCAGCAC
64 TGCCGGCCATTGACAGGCCAGCAC
8754593 TTAAAAAATA
Statistics
Matches: 441, Mismatches: 36, Indels: 53
0.83 0.07 0.10
Matches are distributed among these distances:
95 27 0.06
97 48 0.11
98 7 0.02
99 2 0.00
100 3 0.01
102 3 0.01
103 28 0.06
104 47 0.11
105 62 0.14
106 100 0.23
107 18 0.04
110 5 0.01
111 34 0.08
112 9 0.02
113 41 0.09
114 5 0.01
115 2 0.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.40
Consensus pattern (106 bp):
TTCGTATATTTATATCTGATTCTGACACGAAAAAAAAGAATTTTTTTTAAAATTTGTACTGGGTG
CCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTATTTTT
Found at i:8754601 original size:105 final size:106
Alignment explanation
Indices: 8754171--8754610 Score: 422
Period size: 105 Copynumber: 4.1 Consensus size: 106
8754161 GGCAACACCC
* **
8754171 AAATTTTTTTTA-TTTTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAG-AATTTTTTTT
1 AAATTTTTTTTATTTTTTCGTATATTTATATCTGACTCTGACAC-AAAAAAAAGAAAAATTTTTT
* * *
8754234 TTAAAATTTGTACTGGGTGCTGGCCATTGACAGGCCAGCACCCCAAA
65 TT--AA-TTGTA-TGAGTGCCGGCCATTGACAGGCCAGCA-CCTAAA
*** * *
8754281 TTTTTTTATTTTTATTTTTTTGTATATTTATATCTGACTCTGACACGAAAAAAAAGTAAAATTTT
1 -AAATTT-TTTTTATTTTTTCGTATATTTATATCTGACTCTGACAC-AAAAAAAAGAAAAATTTT
* * *
8754346 TTTAAATTGTACTGGGTGTCGGCCATTGACAGGCCAGCACCT---
63 TTTTAATTGTA-TGAGTGCCGGCCATTGACAGGCCAGCACCTAAA
* *
8754388 AAATTTTTTTTATTTTTTTCGTATATTTATATCTGACTCTGACACGTACAAAAAG---AATTTTT
1 AAATTTTTTTTA-TTTTTTCGTATATTTATATCTGACTCTGACAC-AAAAAAAAGAAAAATTTTT
*
8754450 TTTAAATTGTACT-AGGTGCCGGCCATTGACAGGCCAGCACC--CA
64 TTT-AATTGTA-TGA-GTGCCGGCCATTGACAGGCCAGCACCTAAA
* *
8754493 AAATTTTTTTTATTTGTTTCGTATATTTATATCTTATTCTGACA-AAAAAAAAGGAAAAATTTTT
1 AAATTTTTTTTATTT-TTTCGTATATTTATATCTGACTCTGACACAAAAAAAA-GAAAAATTTTT
* *
8754557 TTT-ACTGT-TGAGTGCCGGCCATTGACAGGCCAGCACTTAAA
64 TTTAATTGTATGAGTGCCGGCCATTGACAGGCCAGCACCTAAA
8754598 AAATAATTTTTTT
1 AAAT--TTTTTTT
8754611 TTCTTTTTTT
Statistics
Matches: 284, Mismatches: 27, Indels: 40
0.81 0.08 0.11
Matches are distributed among these distances:
103 41 0.14
104 39 0.14
105 53 0.19
106 42 0.15
107 17 0.06
110 2 0.01
111 34 0.12
112 8 0.03
113 39 0.14
114 9 0.03
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (106 bp):
AAATTTTTTTTATTTTTTCGTATATTTATATCTGACTCTGACACAAAAAAAAGAAAAATTTTTTT
TAATTGTATGAGTGCCGGCCATTGACAGGCCAGCACCTAAA
Found at i:8754892 original size:5 final size:5
Alignment explanation
Indices: 8754882--8754907 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
8754872 CGATGAACAT
8754882 AGGAG AGGAG AGGAG AGGAG AGGAG A
1 AGGAG AGGAG AGGAG AGGAG AGGAG A
8754908 AGACTTGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (5 bp):
AGGAG
Found at i:8761637 original size:28 final size:29
Alignment explanation
Indices: 8761570--8761642 Score: 107
Period size: 28 Copynumber: 2.6 Consensus size: 29
8761560 AATAAAAAAA
8761570 TTTACCAACTTTTAAGGGGCCCAAATTTTT
1 TTTACCAACTTTTAA-GGGCCCAAATTTTT
*
8761600 TTTA--AGCTTTTAAGGGCCCAAA-TTTT
1 TTTACCAACTTTTAAGGGCCCAAATTTTT
8761626 TTTACCAACTTTTAAGG
1 TTTACCAACTTTTAAGG
8761643 AACCTAAAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
26 8 0.21
27 9 0.23
28 18 0.46
30 4 0.10
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (29 bp):
TTTACCAACTTTTAAGGGCCCAAATTTTT
Found at i:8761921 original size:31 final size:31
Alignment explanation
Indices: 8761885--8761954 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
8761875 ATTTAACAAG
* **
8761885 TCAGTGACTTACATAAAAACTTTTGTATAGT
1 TCAGTGACTTAAATAAAAACTTTTAAATAGT
* *
8761916 TCAGTGACTTAAATGAAAGCTTTTAAATAGT
1 TCAGTGACTTAAATAAAAACTTTTAAATAGT
*
8761947 TAAGTGAC
1 TCAGTGAC
8761955 CATTTTCTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (31 bp):
TCAGTGACTTAAATAAAAACTTTTAAATAGT
Found at i:8776786 original size:19 final size:19
Alignment explanation
Indices: 8776762--8776799 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
8776752 GTTATTATAC
8776762 CAAACTAATGAAATTCTTA
1 CAAACTAATGAAATTCTTA
8776781 CAAACTAATGAAATTCTTA
1 CAAACTAATGAAATTCTTA
8776800 AATAGCTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (19 bp):
CAAACTAATGAAATTCTTA
Found at i:8782628 original size:18 final size:17
Alignment explanation
Indices: 8782595--8782633 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
8782585 TTTTATAAAT
8782595 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
8782613 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
8782630 TGTG
1 TGTG
8782634 GANNNNNNNN
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:8782978 original size:23 final size:23
Alignment explanation
Indices: 8782952--8783026 Score: 132
Period size: 23 Copynumber: 3.3 Consensus size: 23
8782942 GTGTTATTGA
*
8782952 TCAGTGGTAGCTTCGGCTACGTT
1 TCAGTGGTAGCTTCGGCTACATT
8782975 TCAGTGGTAGCTTCGGCTACATT
1 TCAGTGGTAGCTTCGGCTACATT
*
8782998 TCAGTGGTAGCTTCGGCTACATA
1 TCAGTGGTAGCTTCGGCTACATT
8783021 TCAGTG
1 TCAGTG
8783027 TTGCACTTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.17, C:0.21, G:0.28, T:0.33
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACATT
Found at i:8800002 original size:4 final size:4
Alignment explanation
Indices: 8799993--8800017 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
8799983 CCTTCAATAG
8799993 GCAT GCAT GCAT GCAT GCAT GCAT G
1 GCAT GCAT GCAT GCAT GCAT GCAT G
8800018 ACTGCATCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (4 bp):
GCAT
Found at i:8805997 original size:23 final size:23
Alignment explanation
Indices: 8805971--8806017 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
8805961 AATATTTGAG
8805971 ATAGATTTAAAAGTAACTTTTAA
1 ATAGATTTAAAAGTAACTTTTAA
8805994 ATAGATTTAAAAGTAACTTTTAA
1 ATAGATTTAAAAGTAACTTTTAA
8806017 A
1 A
8806018 AAGCTAAGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (23 bp):
ATAGATTTAAAAGTAACTTTTAA
Found at i:8807280 original size:1 final size:1
Alignment explanation
Indices: 8807274--8807299 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
8807264 AATTTGGGTT
8807274 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
8807300 AAAAAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:8809906 original size:9 final size:9
Alignment explanation
Indices: 8809894--8809954 Score: 61
Period size: 9 Copynumber: 6.8 Consensus size: 9
8809884 ATATGATATT
*
8809894 TTTTATATA
1 TTTTATTTA
* *
8809903 TTTTATATG
1 TTTTATTTA
*
8809912 TTTAATTTA
1 TTTTATTTA
8809921 TTTTAGTTTA
1 TTTTA-TTTA
*
8809931 ATTTATTTA
1 TTTTATTTA
8809940 -TTTATTTA
1 TTTTATTTA
8809948 TTTTATT
1 TTTTATT
8809955 AATTGAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
8 8 0.18
9 28 0.64
10 8 0.18
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.70
Consensus pattern (9 bp):
TTTTATTTA
Found at i:8814254 original size:158 final size:153
Alignment explanation
Indices: 8813921--8814222 Score: 480
Period size: 158 Copynumber: 1.9 Consensus size: 153
8813911 ATAAGTGGGG
*
8813921 AACTGAATTTAGATTTTTACTCTGCACTTTCTATCATCACCATGAGTATGTTCGATAATTGGTTT
1 AACTGAATGTAGATTTTTACTCTGCACTTTCTATCATCACCATGAGTATGTTCGATAATTGGTTT
*
8813986 CTCTCTCTCACTCTCTCTCTCTCTCTTGCCGTATGGCTTTGCCTAGCTTCTAGCACAAAATAATG
66 CTCTCTCTCA----C-CTCTCTCTCTTGCCGTATGGCTTTGCCTAGCTTCTAACACAAAATAATG
* * *
8814051 ACCCATATTCCTTTTACTGAAAGTGGGG
126 ACCCATATTCCCTTTACTGAAAGTGCGA
* *
8814079 AACTGAATTTAGATTTTTACTCTGCACTTTCTATCATCACCATGAGTATGTTCGTTAATTGGTTT
1 AACTGAATGTAGATTTTTACTCTGCACTTTCTATCATCACCATGAGTATGTTCGATAATTGGTTT
*
8814144 CTCTCTCTCA-CTCTCTCTCTTGCCGTATGGCTTTGCCTAGCTTCTAACACAAAATAATGACCTA
66 CTCTCTCTCACCTCTCTCTCTTGCCGTATGGCTTTGCCTAGCTTCTAACACAAAATAATGACCCA
8814208 TATTCCCTTTACTGA
131 TATTCCCTTTACTGA
8814223 CCACGTTTGC
Statistics
Matches: 140, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
152 66 0.47
158 74 0.53
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.39
Consensus pattern (153 bp):
AACTGAATGTAGATTTTTACTCTGCACTTTCTATCATCACCATGAGTATGTTCGATAATTGGTTT
CTCTCTCTCACCTCTCTCTCTTGCCGTATGGCTTTGCCTAGCTTCTAACACAAAATAATGACCCA
TATTCCCTTTACTGAAAGTGCGA
Found at i:8815593 original size:21 final size:21
Alignment explanation
Indices: 8815556--8815596 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
8815546 TGGTTCAATT
*
8815556 TTATTTAATTTAGTTTGATTA
1 TTATTTAATATAGTTTGATTA
8815577 TTATTTAAATATA-TTTGATT
1 TTATTT-AATATAGTTTGATT
8815597 TGATAATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (21 bp):
TTATTTAATATAGTTTGATTA
Found at i:8826982 original size:15 final size:16
Alignment explanation
Indices: 8826962--8826992 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
8826952 ATCTAGGATT
8826962 TTTTTGGTAT-TTTTA
1 TTTTTGGTATATTTTA
8826977 TTTTTGGTATATTTTA
1 TTTTTGGTATATTTTA
8826993 GATCAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.16, C:0.00, G:0.13, T:0.71
Consensus pattern (16 bp):
TTTTTGGTATATTTTA
Found at i:8829509 original size:2 final size:2
Alignment explanation
Indices: 8829504--8829544 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
8829494 CATATATGTA
8829504 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
8829545 ATAAGTTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:8840442 original size:30 final size:31
Alignment explanation
Indices: 8840408--8840476 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
8840398 TATTAATTAT
* *
8840408 TTTTTAAATTTT-AAAA-TATATTTTTAATAC
1 TTTTTAAATTTTCAAAATTAT-TTTTTAAAAA
*
8840438 TTTTTAATTTTTCAAAATTATTTTTTAAAAA
1 TTTTTAAATTTTCAAAATTATTTTTTAAAAA
8840469 TTTTTAAA
1 TTTTTAAA
8840477 AATCAATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 11 0.33
31 19 0.58
32 3 0.09
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (31 bp):
TTTTTAAATTTTCAAAATTATTTTTTAAAAA
Found at i:8842009 original size:2 final size:2
Alignment explanation
Indices: 8842002--8842028 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8841992 AATAAACCAG
8842002 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
8842029 GGATCCTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8843222 original size:19 final size:19
Alignment explanation
Indices: 8843198--8843251 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
8843188 AATCTTCAAG
*
8843198 GATATGCAATCTTAGATAT
1 GATATGTAATCTTAGATAT
8843217 GATATGTAATCTTAGATAT
1 GATATGTAATCTTAGATAT
8843236 GATATGTAATCTTAGA
1 GATATGTAATCTTAGA
8843252 AGATATGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (19 bp):
GATATGTAATCTTAGATAT
Found at i:8843258 original size:22 final size:21
Alignment explanation
Indices: 8843198--8843277 Score: 96
Period size: 19 Copynumber: 3.9 Consensus size: 21
8843188 AATCTTCAAG
*
8843198 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAAAGATAT
8843217 GATATGTAATCTT--AGATAT
1 GATATGTAATCTTAAAGATAT
8843236 GATATGTAATCTTAGAAGATAT
1 GATATGTAATCTTA-AAGATAT
*
8843258 GATTTTGTAATCTTAAAGAT
1 GA-TATGTAATCTTAAAGAT
8843278 TTAATTTGTA
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
19 31 0.56
22 13 0.24
23 11 0.20
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.40
Consensus pattern (21 bp):
GATATGTAATCTTAAAGATAT
Found at i:8843284 original size:22 final size:23
Alignment explanation
Indices: 8843240--8843284 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
8843230 AGATATGATA
*
8843240 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
8843263 TGTAATCTTA-AAGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
8843285 GTAGATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:8843287 original size:21 final size:23
Alignment explanation
Indices: 8843211--8843287 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 23
8843201 ATGCAATCTT
*
8843211 AGATATG-ATATGTAATCTT---
1 AGATATGAATTTGTAATCTTAGA
*
8843230 AGATATG-ATATGTAATCTTAGA
1 AGATATGAATTTGTAATCTTAGA
*
8843252 AGATATGATTTTGTAATCTTA-A
1 AGATATGAATTTGTAATCTTAGA
*
8843274 AGAT-TTAATTTGTA
1 AGATATGAATTTGTA
8843288 GATACCTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
19 19 0.38
21 8 0.16
22 12 0.24
23 11 0.22
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.43
Consensus pattern (23 bp):
AGATATGAATTTGTAATCTTAGA
Found at i:8843502 original size:23 final size:23
Alignment explanation
Indices: 8843458--8843502 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
8843448 TCTTATTTTG
* *
8843458 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
8843481 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
8843503 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:8843996 original size:18 final size:17
Alignment explanation
Indices: 8843969--8844007 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
8843959 TTTCCTATGG
*
8843969 ATATTTTAATATATATAT
1 ATATTATAATATATA-AT
8843987 ATATTATAATATATAAT
1 ATATTATAATATATAAT
8844004 ATAT
1 ATAT
8844008 ACGCCGCGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATTATAATATATAAT
Found at i:8843998 original size:12 final size:13
Alignment explanation
Indices: 8843975--8844008 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
8843965 ATGGATATTT
8843975 TAATATATATATA
1 TAATATATATATA
*
8843988 TATTATA-ATATA
1 TAATATATATATA
8844000 TAATATATA
1 TAATATATA
8844009 CGCCGCGCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TAATATATATATA
Found at i:8848609 original size:2 final size:2
Alignment explanation
Indices: 8848604--8848628 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8848594 AAAGTAAAAA
8848604 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
8848629 AAAGAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:8850118 original size:88 final size:88
Alignment explanation
Indices: 8849851--8850306 Score: 639
Period size: 88 Copynumber: 5.2 Consensus size: 88
8849841 GTGAAGATAA
* **
8849851 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCATTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
8849916 GTAACGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * * * * * *
8849939 CAAATCTTGCTTTCTTACACCGACAGCAAAGCAGATCGAAGACACTAG-CTTACCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
8850003 GCAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * *
8850026 CAGATCTTACCTTCCTGCACCGACAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTAGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
8850091 ACAGCGGAGTAGGTTAAAAATTA-
66 GCAGCGGAGCAGGTTAAAAA-TAG
* * * *
8850114 CAGATCTTGCCTTCATGCACCGACAACGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGGATT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
8850179 GCAGTGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * *
8850202 CAGATCTTGCCTTCCTGCACCAACAGCGAAACAGATCGAAGACACCAACCTTGCCT-CCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
8850266 GTAGCGAAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
8850289 CAGATCTTGCCTTCCTGC
1 CAGATCTTGCCTTCCTGC
8850307 NNNNNNNNNN
Statistics
Matches: 322, Mismatches: 43, Indels: 7
0.87 0.12 0.02
Matches are distributed among these distances:
87 121 0.38
88 199 0.62
89 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.21
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
GCAGCGGAGCAGGTTAAAAATAG
Found at i:8850148 original size:175 final size:176
Alignment explanation
Indices: 8849851--8850302 Score: 658
Period size: 175 Copynumber: 2.6 Consensus size: 176
8849841 GTGAAGATAA
**
8849851 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCATTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTGGGTT
* * * * *
8849916 GTAACGGAGCAGGTTAAAAATAGCAAATCTTGCTTTCTTACACCGACAGCAAAGCAGATCGAAGA
66 GTAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCATACACCGACAACAAAGCAGATCGAAGA
* *
8849981 CACTAG-CTTACCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAG
131 CACCAGCCTTACCTCCCTGGATTGCAGCGGAGCAGGTTAAAAATAG
* * * *
8850026 CAGATCTTACCTTCCTGCACCGACAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTAGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTGGGTT
** * * *
8850091 ACAGCGGAGTAGGTTAAAAATTA-CAGATCTTGCCTTCATGCACCGACAACGAAGCAGATCGAAG
66 GTAGCGGAGCAGGTTAAAAA-TAGCAGATCTTGCCTTCATACACCGACAACAAAGCAGATCGAAG
* * *
8850155 ACACCAGCCTTGCCTTCCTGGATTGCAGTGGAGCAGGTTAAAAATAG
130 ACACCAGCCTTACCTCCCTGGATTGCAGCGGAGCAGGTTAAAAATAG
* *
8850202 CAGATCTTGCCTTCCTGCACCAACAGCGAAACAGATCGAAGACACCAACCTTGCCT-CCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTGGGTT
*
8850266 GTAGCGAAGCAGGTTAAAAATAGCAGATCTTGCCTTC
66 GTAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTC
8850303 CTGCNNNNNN
Statistics
Matches: 243, Mismatches: 31, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
174 2 0.01
175 153 0.63
176 88 0.36
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.21
Consensus pattern (176 bp):
CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTGGGTT
GTAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCATACACCGACAACAAAGCAGATCGAAGA
CACCAGCCTTACCTCCCTGGATTGCAGCGGAGCAGGTTAAAAATAG
Found at i:8850866 original size:44 final size:44
Alignment explanation
Indices: 8850817--8850937 Score: 167
Period size: 43 Copynumber: 2.8 Consensus size: 44
8850807 TGACCCTAGC
*
8850817 CCTATCTCTCTGGACAGCAGTGGAATAGGTTGAAGATTGT-AAGT
1 CCTATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGTGAA-T
*
8850861 CCTATCTCCCTGGTCAG-AGTGGAATAGGTTGAAGATTGTGAAT
1 CCTATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGTGAAT
* *
8850904 CCTATCTCCCT-GAGCAACAGTGGAGTAGGTTGAA
1 CCTATCTCCCTGGA-CAGCAGTGGAATAGGTTGAA
8850938 AATAGCAGAT
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
42 1 0.01
43 36 0.52
44 32 0.46
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.28
Consensus pattern (44 bp):
CCTATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGTGAAT
Found at i:8851569 original size:44 final size:43
Alignment explanation
Indices: 8851301--8851806 Score: 200
Period size: 44 Copynumber: 11.7 Consensus size: 43
8851291 GAAGATGACG
8851301 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CAAT
* * * * *
8851345 AATCCTATCTCCTTGAAGTCGCAGTGGAGCGGATTAAA--ATCT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCA-AT
* * ** * *
8851387 CAGATCATATCTCTCTGAAGTTGCA-AAGAGCAGATCT-CATC--T
1 -A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT-TAAAGCAAT
** * * *
8851429 TGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTAAGC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAA-T
* * * * * * *
8851472 AAGCCT-TCTTCCTGAAGTTGTAGT-GAGGTAGACTGAAGATGGC--G
1 AATCTTATCTCCCTGAAGTTGCAGTGGA-GCAGA-TTAA-A--GCAAT
8851516 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CAAT
* ** *
8851560 AATCTTATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAATCACA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCA-AT
* ** * * *
8851604 GATCTTATCTATCTGAAGTTGCAG-AGAGCAGA-T--CGCATT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAAT
** * *** * *
8851643 GGGTCTTATCTCCCTGAAGCTGCAGTGGAGCAGACCCAAGAAAGCG
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAA--T
* * * * *
8851689 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCACACTCAAGAAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAAT
* * * * ** *
8851732 CAAGTCTTATCCCCCTGAAATTGCAATGG-GACAGACTAAATAAACA
1 -AA-TCTTATCTCCCTGAAGTTGCAGTGGAG-CAGATTAAAGCAA-T
* * *
8851778 AATCTCATCTCCCTAAAGTTGTAGTGGAG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAG
8851807 TGGATTTGAA
Statistics
Matches: 342, Mismatches: 84, Indels: 71
0.69 0.17 0.14
Matches are distributed among these distances:
39 2 0.01
40 41 0.12
41 18 0.05
42 24 0.07
43 17 0.05
44 139 0.41
45 98 0.29
46 2 0.01
47 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAAT
Found at i:8851657 original size:215 final size:215
Alignment explanation
Indices: 8851286--8851677 Score: 653
Period size: 215 Copynumber: 1.8 Consensus size: 215
8851276 GTAATTTAAA
8851286 AGACTGAAGATGACGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCT
1 AGACTGAAGATGACGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCT
* *
8851351 ATCTCCTTGAAGTCGCAGTGGAGCGGATTAAAATCTCAGATCATATCTCTCTGAAGTTGCAAAGA
66 ATCTCCTTGAAGTCGCAGTGGAGCGGATTAAAATCACAGATCATATCTATCTGAAGTTGCAAAGA
* * *
8851416 GCAGATCTCATCTTGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGCCTTCT
131 GCAGATCGCATCTGGTCTTATCTCCCTGAAGCTGCAGTGGAGCAGACTAAGTAAGCAAGCCTTCT
8851481 TCCTGAAGTTGTAGTGAGGT
196 TCCTGAAGTTGTAGTGAGGT
* *
8851501 AGACTGAAGATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCTT
1 AGACTGAAGATGACGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCT
* * * *
8851566 ATCTTCC-TGAAGTTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTATCTGAAGTTGCAGAG
66 ATC-TCCTTGAAGTCGCAGTGGAGCGGATTAAAATCACAGATCATATCTATCTGAAGTTGCAAAG
8851630 AGCAGATCGCAT-TGGGTCTTATCTCCCTGAAGCTGCAGTGGAGCAGAC
130 AGCAGATCGCATCT-GGTCTTATCTCCCTGAAGCTGCAGTGGAGCAGAC
8851678 CCAAGAAAGC
Statistics
Matches: 164, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
214 1 0.01
215 160 0.98
216 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (215 bp):
AGACTGAAGATGACGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCT
ATCTCCTTGAAGTCGCAGTGGAGCGGATTAAAATCACAGATCATATCTATCTGAAGTTGCAAAGA
GCAGATCGCATCTGGTCTTATCTCCCTGAAGCTGCAGTGGAGCAGACTAAGTAAGCAAGCCTTCT
TCCTGAAGTTGTAGTGAGGT
Found at i:8851756 original size:45 final size:45
Alignment explanation
Indices: 8851645--8851756 Score: 161
Period size: 45 Copynumber: 2.5 Consensus size: 45
8851635 ATCGCATTGG
* * *
8851645 GTCTTATCTCCCTGAAGCTGCAGTGGAGCAGACCCAAGAAAGCGA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCACACCCAAGAAAGCAA
* *
8851690 GTCTTATCTCCCTGAAGTTGCAGTGGAGCACACTCAAGAAATCAA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCACACCCAAGAAAGCAA
* *
8851735 GTCTTATCCCCCTGAAATTGCA
1 GTCTTATCTCCCTGAAGTTGCA
8851757 ATGGGACAGA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 60 1.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (45 bp):
GTCTTATCTCCCTGAAGTTGCAGTGGAGCACACCCAAGAAAGCAA
Found at i:8852347 original size:19 final size:19
Alignment explanation
Indices: 8852319--8852371 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
8852309 ATCTTCAAGA
8852319 ATATGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
*
8852338 ATATGTAATCTTAGATATG
1 ATATGCAATCTTAGATATG
8852357 ATATGCAATCTTAGA
1 ATATGCAATCTTAGA
8852372 AGATATGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (19 bp):
ATATGCAATCTTAGATATG
Found at i:8852347 original size:36 final size:35
Alignment explanation
Indices: 8852307--8852378 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 35
8852297 TATGGAAACA
8852307 TAATCTTCA-AGA-ATATGCAATCTTAGATATGATATG
1 TAATCTT-AGAGAGATATGCAATCTTAGA-A-GATATG
*
8852343 TAATCTTAGATATGATATGCAATCTTAGAAGATATG
1 TAATCTTAGAGA-GATATGCAATCTTAGAAGATATG
8852379 ATTTTGTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
35 1 0.03
36 15 0.47
37 1 0.03
38 15 0.47
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (35 bp):
TAATCTTAGAGAGATATGCAATCTTAGAAGATATG
Found at i:8852622 original size:23 final size:23
Alignment explanation
Indices: 8852578--8852622 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
8852568 TCTTATTTTG
* *
8852578 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
8852601 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
8852623 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:8852858 original size:3 final size:3
Alignment explanation
Indices: 8852850--8852886 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
8852840 TCTTGTATCG
8852850 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
8852887 ATTCATGCGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:8852965 original size:23 final size:22
Alignment explanation
Indices: 8852925--8852975 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
8852915 ATTTATATAT
*
8852925 TGTTTTATATATAGTATACGTA
1 TGTTTTATATATAGTATACATA
**
8852947 TGTTTATATATATTTTATACATA
1 TGTTT-TATATATAGTATACATA
8852970 TGTTTT
1 TGTTTT
8852976 TGTTTTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.29, C:0.04, G:0.10, T:0.57
Consensus pattern (22 bp):
TGTTTTATATATAGTATACATA
Found at i:8854446 original size:13 final size:13
Alignment explanation
Indices: 8854430--8854459 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
8854420 AATTATAAGG
8854430 AAATAAAATAAAT
1 AAATAAAATAAAT
*
8854443 AAATAAAATGAAT
1 AAATAAAATAAAT
8854456 AAAT
1 AAAT
8854460 CACAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:8854549 original size:20 final size:22
Alignment explanation
Indices: 8854510--8854553 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
8854500 TGAAATGAAA
*
8854510 TATTTAATATAAATAATATATG
1 TATTTAATATAAACAATATATG
8854532 TATTT-ATAT-AACAATATATG
1 TATTTAATATAAACAATATATG
8854552 TA
1 TA
8854554 AAAGAGGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.57
21 4 0.19
22 5 0.24
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (22 bp):
TATTTAATATAAACAATATATG
Found at i:8860233 original size:26 final size:26
Alignment explanation
Indices: 8860179--8860235 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
8860169 AAATAACTCT
* *
8860179 TTTTTTATTTTTATTAATGAAAGCAA
1 TTTTTTATATTTATTAATCAAAGCAA
*
8860205 TTTTTTATATTTATTTATCAAA-CATA
1 TTTTTTATATTTATTAATCAAAGCA-A
8860231 TTTTT
1 TTTTT
8860236 AATTTTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 2 0.07
26 25 0.93
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60
Consensus pattern (26 bp):
TTTTTTATATTTATTAATCAAAGCAA
Found at i:8860242 original size:25 final size:25
Alignment explanation
Indices: 8860180--8860242 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 25
8860170 AATAACTCTT
* *
8860180 TTTTTATTTTTATTAATGAAAGCAA
1 TTTTTAATTTTATTAATCAAAGCAA
* *
8860205 TTTTTTATATTTATTTATCAAA-CATA
1 TTTTTAAT-TTTATTAATCAAAGCA-A
8860231 TTTTTAATTTTA
1 TTTTTAATTTTA
8860243 AAAAATGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
25 12 0.39
26 19 0.61
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (25 bp):
TTTTTAATTTTATTAATCAAAGCAA
Found at i:8860365 original size:59 final size:58
Alignment explanation
Indices: 8860287--8860403 Score: 162
Period size: 59 Copynumber: 2.0 Consensus size: 58
8860277 TAAATTCCGT
* *
8860287 CAAATGTCACTAGACTATTAATAAGTTTACATTTTGGTCAATAAACTTTAAAAAGTTA
1 CAAATGTCACTAAACTATTAATAAGTTTACATTTTGGTCAATAAACTTCAAAAAGTTA
* * * * *
8860345 CAAATGGTCACTAAATTATTAGTAAGTTTATATTTTGGTCACTTAACTTCAAAAAGTTA
1 CAAAT-GTCACTAAACTATTAATAAGTTTACATTTTGGTCAATAAACTTCAAAAAGTTA
8860404 AAAGTTACAA
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
58 5 0.10
59 46 0.90
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (58 bp):
CAAATGTCACTAAACTATTAATAAGTTTACATTTTGGTCAATAAACTTCAAAAAGTTA
Found at i:8873955 original size:11 final size:11
Alignment explanation
Indices: 8873935--8873972 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
8873925 GGCCTGGCCC
8873935 ATATTAAATAT
1 ATATTAAATAT
*
8873946 ATATTTAATAT
1 ATATTAAATAT
*
8873957 ATATAAAATAT
1 ATATTAAATAT
8873968 ATATT
1 ATATT
8873973 TGATTAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATATTAAATAT
Found at i:8876536 original size:25 final size:25
Alignment explanation
Indices: 8876502--8876550 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
8876492 ATTTTTTTTC
8876502 TTTTACATTTGAATTACCAAAACCA
1 TTTTACATTTGAATTACCAAAACCA
8876527 TTTTACATTTGAATTACCAAAACC
1 TTTTACATTTGAATTACCAAAACC
8876551 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.37
Consensus pattern (25 bp):
TTTTACATTTGAATTACCAAAACCA
Done.