Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 81 of 444
Found at i:19147682 original size:2 final size:2
Alignment explanation
Indices: 19147668--19147709 Score: 52
Period size: 2 Copynumber: 21.5 Consensus size: 2
19147658 TATTGCGTGA
*
19147668 AT AT AT ACT -T AT AT AT AT AT AT AT AT AT AT -T AT AG AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19147709 A
1 A
19147710 ATAAGACATA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 2 0.06
2 32 0.91
3 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19148162 original size:25 final size:23
Alignment explanation
Indices: 19148134--19148189 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 23
19148124 ACAAATACAC
19148134 GTATATATATACGCATATAATAAGA
1 GTATATA-ATA-GCATATAATAAGA
* *
19148159 GTATACACTAGCATATAATAAGA
1 GTATATAATAGCATATAATAAGA
19148182 GTATATAA
1 GTATATAA
19148190 AAAAAAGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 19 0.70
24 2 0.07
25 6 0.22
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.30
Consensus pattern (23 bp):
GTATATAATAGCATATAATAAGA
Found at i:19150005 original size:33 final size:34
Alignment explanation
Indices: 19149948--19150020 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 34
19149938 ATGATATCAT
* *
19149948 TTCTTTTTTTCCCCGTTTTCCCCCTTCTCTTTTA
1 TTCTTTTTTTCCCCATTTTCCCCCTTCCCTTTTA
19149982 TTCTTTTTTTCCCCATTTT-CCCCTTCCCTTTTA
1 TTCTTTTTTTCCCCATTTTCCCCCTTCCCTTTTA
19150015 TTCTTT
1 TTCTTT
19150021 CCCATTTTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
33 19 0.51
34 18 0.49
ACGTcount: A:0.04, C:0.34, G:0.01, T:0.60
Consensus pattern (34 bp):
TTCTTTTTTTCCCCATTTTCCCCCTTCCCTTTTA
Found at i:19150884 original size:2 final size:2
Alignment explanation
Indices: 19150879--19150911 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
19150869 AAATAATCAA
19150879 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19150912 GGGAGAGAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19153934 original size:15 final size:15
Alignment explanation
Indices: 19153914--19153965 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
19153904 AGTACAAAGC
19153914 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
19153929 ATTTATAATTATAATAAAT
1 ATTTATTA-T-TAAT--AT
*
19153948 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
19153963 ATT
1 ATT
19153966 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:19153951 original size:19 final size:19
Alignment explanation
Indices: 19153927--19153963 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19153917 TATTATTAAT
*
19153927 ATATTTATAATTATAATAA
1 ATATTTATAATTAAAATAA
*
19153946 ATATTTATTATTAAAATA
1 ATATTTATAATTAAAATA
19153964 TTAATATTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTTATAATTAAAATAA
Found at i:19154023 original size:15 final size:15
Alignment explanation
Indices: 19154003--19154032 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
19153993 AAGAATACTA
19154003 TTTAAAATTATTATT
1 TTTAAAATTATTATT
19154018 TTTAAAATTATTATT
1 TTTAAAATTATTATT
19154033 AAAATAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTAAAATTATTATT
Found at i:19154094 original size:25 final size:26
Alignment explanation
Indices: 19154049--19154110 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
19154039 AAATTAAAAT
19154049 ATTA-ATTAATT-TATTAAAATAATAA
1 ATTATATTAATTATATT-AAATAATAA
**
19154074 ATTATATTAATTATATT-AATAATTT
1 ATTATATTAATTATATTAAATAATAA
19154099 ATTATA-TAATTA
1 ATTATATTAATTA
19154111 AAAACAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
24 6 0.18
25 16 0.48
26 7 0.21
27 4 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
ATTATATTAATTATATTAAATAATAA
Found at i:19155630 original size:13 final size:13
Alignment explanation
Indices: 19155612--19155639 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
19155602 GCCGAAGGTA
19155612 AATAGACGTATAG
1 AATAGACGTATAG
19155625 AATAGACGTATAG
1 AATAGACGTATAG
19155638 AA
1 AA
19155640 GTATGCTTCC
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:0.50, C:0.07, G:0.21, T:0.21
Consensus pattern (13 bp):
AATAGACGTATAG
Found at i:19160900 original size:15 final size:16
Alignment explanation
Indices: 19160868--19160900 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
19160858 TGAGAGAGAA
*
19160868 TTTGAATAGTTTGAGT
1 TTTGAATAGTTAGAGT
19160884 TTTGAATA-TTAGAGT
1 TTTGAATAGTTAGAGT
19160899 TT
1 TT
19160901 AAATTTAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.27, C:0.00, G:0.21, T:0.52
Consensus pattern (16 bp):
TTTGAATAGTTAGAGT
Found at i:19161471 original size:14 final size:15
Alignment explanation
Indices: 19161452--19161507 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 15
19161442 TATTAGATGT
19161452 GATATG-CAATCTTA
1 GATATGACAATCTTA
19161466 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
19161483 GATATGATTGCAATCTTA
1 GATATGA---CAATCTTA
19161501 GATATGA
1 GATATGA
19161508 TATGCAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.17
15 1 0.03
17 14 0.39
18 15 0.42
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:19161500 original size:35 final size:37
Alignment explanation
Indices: 19161431--19161528 Score: 132
Period size: 35 Copynumber: 2.7 Consensus size: 37
19161421 GTAATCTTCA
* *
19161431 ATGATATGCAATATTAGATGTGATATGCAATCTTAGAT
1 ATGATA-GCAATCTTAGATATGATATGCAATCTTAGAT
19161469 ATGATA-CAATCTTAGATATGAT-TGCAATCTTAGAT
1 ATGATAGCAATCTTAGATATGATATGCAATCTTAGAT
19161504 ATGATATGCAATCTTAGA-A-GATATG
1 ATGATA-GCAATCTTAGATATGATATG
19161529 ATTTTGTAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
35 22 0.40
36 17 0.31
37 10 0.18
38 6 0.11
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (37 bp):
ATGATAGCAATCTTAGATATGATATGCAATCTTAGAT
Found at i:19161528 original size:17 final size:19
Alignment explanation
Indices: 19161431--19161521 Score: 143
Period size: 19 Copynumber: 4.9 Consensus size: 19
19161421 GTAATCTTCA
*
19161431 ATGATATGCAATATTAGAT
1 ATGATATGCAATCTTAGAT
*
19161450 GTGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
19161469 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
19161486 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
19161504 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
19161522 AGATATGATT
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.24
18 16 0.24
19 34 0.52
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:19161547 original size:22 final size:22
Alignment explanation
Indices: 19161431--19161544 Score: 78
Period size: 19 Copynumber: 5.8 Consensus size: 22
19161421 GTAATCTTCA
*
19161431 ATGATATGCAATATT---AGAT
1 ATGATATGCAATCTTAGAAGAT
*
19161450 GTGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
19161469 ATGATA--CAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
19161486 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
19161504 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
19161526 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
19161545 GATTTAATTT
Statistics
Matches: 83, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
17 16 0.19
18 16 0.19
19 31 0.37
22 8 0.10
23 12 0.14
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:19161836 original size:18 final size:18
Alignment explanation
Indices: 19161811--19161847 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
19161801 TGTTTCCCAG
*
19161811 ATTTTTTTTATATATTTTA
1 ATTTTTTTAATA-ATTTTA
19161830 ATTTTTTTAATAATTTTA
1 ATTTTTTTAATAATTTTA
19161848 GTATCATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
ATTTTTTTAATAATTTTA
Found at i:19165736 original size:24 final size:22
Alignment explanation
Indices: 19165709--19165754 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
19165699 TTAATTTAAT
19165709 TATTAAATTTTCTAATATTAAAAA
1 TATTAAA-TTTCTAA-ATTAAAAA
**
19165733 TATTTTATTTCTAAATTAAAAA
1 TATTAAATTTCTAAATTAAAAA
19165755 ACATTTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (22 bp):
TATTAAATTTCTAAATTAAAAA
Found at i:19165754 original size:23 final size:23
Alignment explanation
Indices: 19165717--19165760 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
19165707 ATTATTAAAT
*
19165717 TTTCTAATATTAAAAATATTTTA
1 TTTCTAATATTAAAAACATTTTA
19165740 TTTCTAA-ATTAAAAAACATTT
1 TTTCTAATATT-AAAAACATTT
19165761 AATACTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (23 bp):
TTTCTAATATTAAAAACATTTTA
Found at i:19175707 original size:46 final size:45
Alignment explanation
Indices: 19175617--19175789 Score: 192
Period size: 46 Copynumber: 3.7 Consensus size: 45
19175607 TAATCGATAC
*
19175617 CATGTCCCAGACATGGTCTTACACTAACTATCATCTC-GTAGCCGATG
1 CATGTCCCAGACATGGTCTTACACTAGCTA-CATCTCAG--GCCGATG
* *
19175664 CATGTCCCAGACAT-GTCTTATACTGGCTTACATCTCAAGGCCGATG
1 CATGTCCCAGACATGGTCTTACACTAGC-TACATCTC-AGGCCGATG
19175710 CATGTCCCAGACAT-GTCTTACACTAGC-ACTCATCTCAGTGCCGATG
1 CATGTCCCAGACATGGTCTTACACTAGCTA--CATCTCAG-GCCGATG
*
19175756 CCATGTCCCATACATGGTCTTACACTAGCATACA
1 -CATGTCCCAGACATGGTCTTACACTAGC-TACA
19175790 CAAGTGACCC
Statistics
Matches: 110, Mismatches: 6, Indels: 19
0.81 0.04 0.14
Matches are distributed among these distances:
44 1 0.01
45 2 0.02
46 61 0.55
47 29 0.26
48 16 0.15
50 1 0.01
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (45 bp):
CATGTCCCAGACATGGTCTTACACTAGCTACATCTCAGGCCGATG
Found at i:19176492 original size:12 final size:12
Alignment explanation
Indices: 19176475--19176499 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19176465 CAAAAATGTA
19176475 AAAATCATCAAG
1 AAAATCATCAAG
19176487 AAAATCATCAAG
1 AAAATCATCAAG
19176499 A
1 A
19176500 TCGCTTACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAATCATCAAG
Found at i:19178258 original size:13 final size:14
Alignment explanation
Indices: 19178231--19178259 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19178221 TTTTTTTTAA
19178231 TTTAATTTTTACAT
1 TTTAATTTTTACAT
19178245 TTTAATTTTT-CAT
1 TTTAATTTTTACAT
19178258 TT
1 TT
19178260 GTTTGATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTAATTTTTACAT
Found at i:19184454 original size:3 final size:3
Alignment explanation
Indices: 19184446--19184517 Score: 114
Period size: 3 Copynumber: 24.7 Consensus size: 3
19184436 TAATTTTCTT
19184446 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19184494 TTA TTA TT- TTA TGT- TTA TT- TTA TT
1 TTA TTA TTA TTA T-TA TTA TTA TTA TT
19184518 TTTTTCATTT
Statistics
Matches: 65, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
2 5 0.08
3 59 0.91
4 1 0.02
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:19185062 original size:3 final size:3
Alignment explanation
Indices: 19185054--19185088 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
19185044 GTTAGTATAT
* *
19185054 TTA TTA TTA TTA CTA TTA TTA TTG TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19185089 CTGTTTGCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:19185169 original size:3 final size:3
Alignment explanation
Indices: 19185139--19185226 Score: 113
Period size: 3 Copynumber: 28.0 Consensus size: 3
19185129 TATTAGTTTT
* *
19185139 TTA TATA TTT TTA TTA TTTA TTGT TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA -TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
*
19185187 TTA TTA TTA TTA TTA TTTA TTA TTA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
19185227 CCCTGTTTAG
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
3 64 0.85
4 11 0.15
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:19187118 original size:41 final size:40
Alignment explanation
Indices: 19186987--19187136 Score: 160
Period size: 41 Copynumber: 3.7 Consensus size: 40
19186977 GTATCACATA
*
19186987 GCCGTGTGGCAGACCATGTGGGTCACACGGTCATGTG-GTAG
1 GCCGTGTGGCAGACCATGTGGGTCACAC-GAC-TGTGTGTAG
*** *
19187028 GCCGTGTAATAGACCATGTGGGTCACAC-AATCGTGTGGTAG
1 GCCGTGTGGCAGACCATGTGGGTCACACGACT-GTGT-GTAG
* * *
19187069 GCCATGTGGCAGACCGTGTGGGTCACACGACTGTGTAGTTG
1 GCCGTGTGGCAGACCATGTGGGTCACACGACTGTGT-GTAG
*
19187110 GTCGTGTGGCAGACCATGTGGGTCACA
1 GCCGTGTGGCAGACCATGTGGGTCACA
19187137 TGGCTTTCTA
Statistics
Matches: 89, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
38 1 0.01
39 3 0.03
41 83 0.93
42 2 0.02
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.23
Consensus pattern (40 bp):
GCCGTGTGGCAGACCATGTGGGTCACACGACTGTGTGTAG
Found at i:19187159 original size:41 final size:41
Alignment explanation
Indices: 19187038--19187159 Score: 120
Period size: 41 Copynumber: 3.0 Consensus size: 41
19187028 GCCGTGTAAT
* * * *
19187038 AGACCATGTGGGTCACAC-AATCGTGTGGTAGGCCATGTGGC
1 AGACCATGTGGGTCACACGACT-GTCTAGTAGGTCATGTGGC
* * * *
19187079 AGACCGTGTGGGTCACACGACTGTGTAGTTGGTCGTGTGGC
1 AGACCATGTGGGTCACACGACTGTCTAGTAGGTCATGTGGC
* * * *
19187120 AGACCATGTGGGTCACATGGCTTTCTAGTAGGTTATGTGG
1 AGACCATGTGGGTCACACGACTGTCTAGTAGGTCATGTGG
19187160 TAGCCTTGTA
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
41 64 0.97
42 2 0.03
ACGTcount: A:0.19, C:0.19, G:0.35, T:0.27
Consensus pattern (41 bp):
AGACCATGTGGGTCACACGACTGTCTAGTAGGTCATGTGGC
Found at i:19191656 original size:112 final size:115
Alignment explanation
Indices: 19191519--19191730 Score: 259
Period size: 115 Copynumber: 1.9 Consensus size: 115
19191509 AAACTATATG
* * * * ** * *
19191519 ATACATACTTTAACATTTTGTGC-AAATATAATATAGAAAATGAT-AAATAACGACATAAATTAT
1 ATACATACATTAACATTTTATGCAAAATACAACATAGAAAACAATGAAATAACAACATAAATTAC
*
19191582 ATAATATACAT-TAACATTTCATGCATATATAATCATAAATAACATAAAC
66 ATAATATACATATAACATTTCATGCAAATATAATCATAAATAACATAAAC
* * *
19191631 ATACATGCATTAACATTTTATGCAAAATACAACATAGAAAACAATGGATATAACAATATAAATTA
1 ATACATACATTAACATTTTATGCAAAATACAACATAGAAAACAAT-GAAATAACAACATAAATTA
* *
19191696 CATAATATATATAATAATATTTCATGCAAATATAA
65 CATAATATACAT-ATAACATTTCATGCAAATATAA
19191731 CAACATAAAT
Statistics
Matches: 81, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
112 20 0.25
113 17 0.21
115 25 0.31
117 19 0.23
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.32
Consensus pattern (115 bp):
ATACATACATTAACATTTTATGCAAAATACAACATAGAAAACAATGAAATAACAACATAAATTAC
ATAATATACATATAACATTTCATGCAAATATAATCATAAATAACATAAAC
Found at i:19192132 original size:7 final size:7
Alignment explanation
Indices: 19192120--19192205 Score: 90
Period size: 7 Copynumber: 12.3 Consensus size: 7
19192110 AATTATACAT
19192120 AATAATA
1 AATAATA
19192127 AATAATA
1 AATAATA
19192134 AATAATA
1 AATAATA
19192141 AATAATA
1 AATAATA
19192148 AATAAT-
1 AATAATA
19192154 AA-AATA
1 AATAATA
*
19192160 TATAATA
1 AATAATA
19192167 CAA-AATA
1 -AATAATA
19192174 AA-AATA
1 AATAATA
*
19192180 ATATAATG
1 A-ATAATA
19192188 AATAATA
1 AATAATA
19192195 TATATAATA
1 -A-ATAATA
19192204 AA
1 AA
19192206 ATGATATAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
5 3 0.04
6 10 0.15
7 42 0.62
8 7 0.10
9 6 0.09
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (7 bp):
AATAATA
Found at i:19192201 original size:21 final size:20
Alignment explanation
Indices: 19192121--19192224 Score: 76
Period size: 21 Copynumber: 5.2 Consensus size: 20
19192111 ATTATACATA
*
19192121 ATAATA-AATAATAAATAATAA
1 ATAATATAATAAT-AAT-ATAT
*
19192142 ATAATA-AATAATAAAATAT
1 ATAATATAATAATAATATAT
*
19192161 ATAATACAA-AATAA-A-A-
1 ATAATATAATAATAATATAT
19192177 ATAATATAATGAATAATATAT
1 ATAATATAAT-AATAATATAT
*
19192198 ATAATAAAATGATATAATATATT
1 ATAATATAAT-A-ATAATATA-T
19192221 ATAA
1 ATAA
19192225 AGCATATAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 14
0.80 0.04 0.16
Matches are distributed among these distances:
16 8 0.11
17 1 0.01
18 6 0.08
19 15 0.21
20 5 0.07
21 23 0.32
22 8 0.11
23 5 0.07
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (20 bp):
ATAATATAATAATAATATAT
Found at i:19192356 original size:29 final size:27
Alignment explanation
Indices: 19192314--19192368 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 27
19192304 TTTATAGCAA
19192314 AAATAAATAATATATAAAATATTTAAAAT
1 AAATAAATAATATA-AAAA-ATTTAAAAT
**
19192343 AAATAAATTGTATAAAAAATTTAAAA
1 AAATAAATAATATAAAAAATTTAAAA
19192369 AGGACTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 8 0.33
28 4 0.17
29 12 0.50
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (27 bp):
AAATAAATAATATAAAAAATTTAAAAT
Found at i:19192364 original size:27 final size:25
Alignment explanation
Indices: 19192313--19192368 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 25
19192303 GTTTATAGCA
*
19192313 AAAATAAATAATATATAAAATATTT
1 AAAATAAATAATATATAAAAAATTT
*
19192338 AAAATAAATAAATTGTATAAAAAATTT
1 AAAATAAAT-AA-TATATAAAAAATTT
19192365 AAAA
1 AAAA
19192369 AGGACTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 9 0.33
26 2 0.07
27 16 0.59
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (25 bp):
AAAATAAATAATATATAAAAAATTT
Found at i:19194154 original size:132 final size:130
Alignment explanation
Indices: 19193826--19194706 Score: 1001
Period size: 132 Copynumber: 6.9 Consensus size: 130
19193816 CCCCATGAAG
* * * *
19193826 TACAGAGACGCCAAATCTGCCATCTTTGATCTGCTCTCTGTCAATACAGAGATGCCAAATTTGCT
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTGCT
* * *
19193891 ATCTTTGATCTGCTCTCTGTCAATACAGAGATGCCAAATCTGCTATCTTCGATCTGCT---TCGA
66 ATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTACTATCTTCGATCTGCTCCGTCGA
* * * * * * * * * *
19193953 TACACGA-ATGTCAGATCTGCTATCTTCGATTTGTTCCCCGTCCATACAGAGATGTCAAATCTGC
1 TACA-GAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTGC
* * *
19194017 TATCTTCGATCTGCTCTCTGTCAATACAAAGACACCAAATCTACTATCTTTGATCTGCTCCCCGT
65 TATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTACTATCTTCGATCTGCT--CCGT
19194082 CGA
128 CGA
* * *
19194085 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTATTAATATAGAGACGCCAAATCTGCT
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTGCT
* * *
19194150 ATCTTCGATCTGCTCTCTGTCAATACAGAGACACCAAATCTACTATCTTTGATCTACTCCCCGTC
66 ATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTACTATCTTCGATCTGCT--CCGTC
*
19194215 AA
129 GA
* * *
19194217 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTATCAATACAGAGACGCCAAAACTGTT
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTGCT
* * * *
19194282 ATCTTTGATCTGCTCTTTGTCAATACAAAGACACCAAATCTACTATCTTCGATCTGCTCTCCGTC
66 ATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTACTATCTTCGATCTG--CTCCGTC
19194347 GA
129 GA
* * *
19194349 TACAGAGACTCCAAATCTGC-ATCTTCGATCT-CTCTCTGTCAATACAGATATGCCAAATCTGCT
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTGCT
* * * ** *
19194412 ATCTTCGATCTACCCTCTGTCAATACAGAGACGCCAAATCTGCTATCTTCGATCTGCATTATGTA
66 ATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTACTATCTTCGATCTGC--TCCGTC
*
19194477 AA
129 GA
* * * *
19194479 TACAGAGACGCCAAATTTGCTATCTTCGATCTGCTTTCTGTCAATATAGAGACGCCAAGTCTGCT
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTGCT
*
19194544 ATCTTCGATCTGCCCTCTGTCAATACAGAGACGCCAAATCTACTATCTTCGA--T-CT--G-C--
66 ATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTACTATCTTCGATCTGCTCCGTCGA
* * * * *
19194601 --C----ACGCCAAATCTACTATCTTCGATCTGCTTTCTATCAATATAGAGACGCCAAATCTACT
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTGCT
* * * * * *
19194660 ATCTTCGATCTGCCCTCTGTTAATATAAAGATGCCAAATCCACTATC
66 ATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTACTATC
19194707 GGTGATCTAC
Statistics
Matches: 660, Mismatches: 81, Indels: 37
0.85 0.10 0.05
Matches are distributed among these distances:
116 95 0.14
120 1 0.00
125 1 0.00
127 103 0.16
128 3 0.00
129 1 0.00
130 99 0.15
131 24 0.04
132 331 0.50
134 2 0.00
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (130 bp):
TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTGCT
ATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTACTATCTTCGATCTGCTCCGTCGA
Found at i:19194601 original size:44 final size:44
Alignment explanation
Indices: 19193826--19194600 Score: 974
Period size: 44 Copynumber: 17.8 Consensus size: 44
19193816 CCCCATGAAG
* *
19193826 TACAGAGACGCCAAATCTGCCATCTTTGATCTGCTCTCTGTCAA
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGTCAA
* * *
19193870 TACAGAGATGCCAAATTTGCTATCTTTGATCTGCTCTCTGTCAA
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGTCAA
*
19193914 TACAGAGATGCCAAATCTGCTATCTTCGATCTGCT-TC-G---A
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGTCAA
* * * * * * * *
19193953 TACACGA-ATGTCAGATCTGCTATCTTCGATTTGTTCCCCGTCCA
1 TACA-GAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGTCAA
* *
19193997 TACAGAGATGTCAAATCTGCTATCTTCGATCTGCTCTCTGTCAA
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGTCAA
* * * * * * *
19194041 TACAAAGACACCAAATCTACTATCTTTGATCTGCTCCCCGTCGA
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGTCAA
* *
19194085 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTATTAA
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGTCAA
*
19194129 TATAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGTCAA
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGTCAA
* * * * * *
19194173 TACAGAGACACCAAATCTACTATCTTTGATCTACTCCCCGTCAA
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGTCAA
*
19194217 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTATCAA
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGTCAA
* * * *
19194261 TACAGAGACGCCAAAACTGTTATCTTTGATCTGCTCTTTGTCAA
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGTCAA
* * * * *
19194305 TACAAAGACACCAAATCTACTATCTTCGATCTGCTCTCCGTCGA
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGTCAA
*
19194349 TACAGAGACTCCAAATCTGC-ATCTTCGATCT-CTCTCTGTCAA
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGTCAA
* * * *
19194391 TACAGATATGCCAAATCTGCTATCTTCGATCTACCCTCTGTCAA
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGTCAA
* *
19194435 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCAT-TATGTAAA
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGC-TCTCTGTCAA
* *
19194479 TACAGAGACGCCAAATTTGCTATCTTCGATCTGCTTTCTGTCAA
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGTCAA
* * *
19194523 TATAGAGACGCCAAGTCTGCTATCTTCGATCTGCCCTCTGTCAA
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGTCAA
*
19194567 TACAGAGACGCCAAATCTACTATCTTCGATCTGC
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGC
19194601 CACGCCAAAT
Statistics
Matches: 629, Mismatches: 91, Indels: 22
0.85 0.12 0.03
Matches are distributed among these distances:
39 29 0.05
40 3 0.00
41 1 0.00
42 27 0.04
43 27 0.04
44 542 0.86
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (44 bp):
TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGTCAA
Found at i:19194614 original size:28 final size:28
Alignment explanation
Indices: 19194574--19194628 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
19194564 CAATACAGAG
19194574 ACGCCAAATCTACTATCTTCGATCTGCC
1 ACGCCAAATCTACTATCTTCGATCTGCC
19194602 ACGCCAAATCTACTATCTTCGATCTGC
1 ACGCCAAATCTACTATCTTCGATCTGC
19194629 TTTCTATCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.35, G:0.11, T:0.29
Consensus pattern (28 bp):
ACGCCAAATCTACTATCTTCGATCTGCC
Found at i:19194647 original size:72 final size:72
Alignment explanation
Indices: 19194530--19194673 Score: 234
Period size: 72 Copynumber: 2.0 Consensus size: 72
19194520 CAATATAGAG
* * *
19194530 ACGCCAAGTCTGCTATCTTCGATCTGCCCTCTGTCAATACAGAGACGCCAAATCTACTATCTTCG
1 ACGCCAAATCTACTATCTTCGATCTGCCCTCTATCAATACAGAGACGCCAAATCTACTATCTTCG
19194595 ATCTGCC
66 ATCTGCC
** *
19194602 ACGCCAAATCTACTATCTTCGATCTGCTTTCTATCAATATAGAGACGCCAAATCTACTATCTTCG
1 ACGCCAAATCTACTATCTTCGATCTGCCCTCTATCAATACAGAGACGCCAAATCTACTATCTTCG
19194667 ATCTGCC
66 ATCTGCC
19194674 CTCTGTTAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.26, C:0.31, G:0.13, T:0.30
Consensus pattern (72 bp):
ACGCCAAATCTACTATCTTCGATCTGCCCTCTATCAATACAGAGACGCCAAATCTACTATCTTCG
ATCTGCC
Found at i:19194652 original size:44 final size:44
Alignment explanation
Indices: 19194602--19194706 Score: 147
Period size: 44 Copynumber: 2.4 Consensus size: 44
19194592 TCGATCTGCC
** *
19194602 ACGCCAAATCTACTATCTTCGATCTGCTTTCTATCAATATAGAG
1 ACGCCAAATCTACTATCTTCGATCTGCCCTCTATCAATATAAAG
* *
19194646 ACGCCAAATCTACTATCTTCGATCTGCCCTCTGTTAATATAAAG
1 ACGCCAAATCTACTATCTTCGATCTGCCCTCTATCAATATAAAG
* *
19194690 ATGCCAAATCCACTATC
1 ACGCCAAATCTACTATC
19194707 GGTGATCTAC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.31
Consensus pattern (44 bp):
ACGCCAAATCTACTATCTTCGATCTGCCCTCTATCAATATAAAG
Found at i:19194696 original size:116 final size:116
Alignment explanation
Indices: 19194486--19194706 Score: 352
Period size: 116 Copynumber: 1.9 Consensus size: 116
19194476 AAATACAGAG
* * * * *
19194486 ACGCCAAATTTGCTATCTTCGATCTGCTTTCTGTCAATATAGAGACGCCAAGTCTGCTATCTTCG
1 ACGCCAAATCTACTATCTTCGATCTGCTTTCTATCAATATAGAGACGCCAAATCTACTATCTTCG
* *
19194551 ATCTGCCCTCTGTCAATACAGAGACGCCAAATCTACTATCTTCGATCTGCC
66 ATCTGCCCTCTGTCAATACAAAGACGCCAAATCCACTATCTTCGATCTGCC
19194602 ACGCCAAATCTACTATCTTCGATCTGCTTTCTATCAATATAGAGACGCCAAATCTACTATCTTCG
1 ACGCCAAATCTACTATCTTCGATCTGCTTTCTATCAATATAGAGACGCCAAATCTACTATCTTCG
* * *
19194667 ATCTGCCCTCTGTTAATATAAAGATGCCAAATCCACTATC
66 ATCTGCCCTCTGTCAATACAAAGACGCCAAATCCACTATC
19194707 GGTGATCTAC
Statistics
Matches: 95, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
116 95 1.00
ACGTcount: A:0.27, C:0.29, G:0.13, T:0.31
Consensus pattern (116 bp):
ACGCCAAATCTACTATCTTCGATCTGCTTTCTATCAATATAGAGACGCCAAATCTACTATCTTCG
ATCTGCCCTCTGTCAATACAAAGACGCCAAATCCACTATCTTCGATCTGCC
Found at i:19196469 original size:16 final size:16
Alignment explanation
Indices: 19196448--19196478 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
19196438 AATGACATCC
19196448 ATGACATCCATGCCCA
1 ATGACATCCATGCCCA
19196464 ATGACATCCATGCCC
1 ATGACATCCATGCCC
19196479 CACATGGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.39, G:0.13, T:0.19
Consensus pattern (16 bp):
ATGACATCCATGCCCA
Found at i:19206260 original size:112 final size:115
Alignment explanation
Indices: 19206135--19206346 Score: 250
Period size: 115 Copynumber: 1.9 Consensus size: 115
19206125 AAACTATATG
* * * * ** * *
19206135 ATACATACTTTAACATTTCGTGC-AAATATAATATAGAAAATGAT-AAATAACGACATAAATTAT
1 ATACATACATTAACATTTCATGCAAAATACAACATAGAAAACAATGAAATAACAACATAAATTAC
*
19206198 ATAATATACAT-TAACATTTCATGCAGATATAATCATAAATAACATAAAC
66 ATAATATACATATAACATTTCATGCAAATATAATCATAAATAACATAAAC
* * * *
19206247 ATACATGCATTAACATTTTATGCAAAATACAACATAGAAAACAATGGATATAACAATATAAATTA
1 ATACATACATTAACATTTCATGCAAAATACAACATAGAAAACAAT-GAAATAACAACATAAATTA
* *
19206312 CATAATATATATAATAATATTTCATGCAAATATAA
65 CATAATATACAT-ATAACATTTCATGCAAATATAA
19206347 CAACATAAAT
Statistics
Matches: 80, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
112 19 0.24
113 17 0.21
115 25 0.31
117 19 0.24
ACGTcount: A:0.51, C:0.12, G:0.06, T:0.31
Consensus pattern (115 bp):
ATACATACATTAACATTTCATGCAAAATACAACATAGAAAACAATGAAATAACAACATAAATTAC
ATAATATACATATAACATTTCATGCAAATATAATCATAAATAACATAAAC
Found at i:19206768 original size:7 final size:7
Alignment explanation
Indices: 19206745--19206806 Score: 51
Period size: 7 Copynumber: 9.0 Consensus size: 7
19206735 AATAATAAAA
*
19206745 AATAAAT
1 AATATAT
19206752 AATA-AT
1 AATATAT
19206758 -ATATAT
1 AATATAT
19206764 AATATAT
1 AATATAT
19206771 AATGA-AT
1 AAT-ATAT
19206778 AATATAT
1 AATATAT
*
19206785 -ATAATAA
1 AAT-ATAT
19206792 AATGATAT
1 AAT-ATAT
19206800 AATATAT
1 AATATAT
19206807 TATAAAGCAT
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
5 3 0.07
6 7 0.15
7 27 0.59
8 9 0.20
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (7 bp):
AATATAT
Found at i:19206772 original size:23 final size:23
Alignment explanation
Indices: 19206746--19206872 Score: 95
Period size: 23 Copynumber: 5.4 Consensus size: 23
19206736 ATAATAAAAA
19206746 ATAAATAATAATATATATAATAT
1 ATAAATAATAATATATATAATAT
19206769 AT-AATGAATAATATATAT-A-AT
1 ATAAAT-AATAATATATATAATAT
*
19206790 A-AAATGATATAATATATTATAAAGCAT
1 ATAAAT-A-ATAATATA-TAT-AA-TAT
* *
19206817 ATAAATAA-AATGTAAAATAATAT
1 ATAAATAATAATAT-ATATAATAT
*
19206840 ATGAAAAAATAATATATAT-ATAT
1 AT-AAATAATAATATATATAATAT
19206863 ATATAATAAT
1 ATA-AATAAT
19206873 TTTTTATATG
Statistics
Matches: 84, Mismatches: 7, Indels: 26
0.72 0.06 0.22
Matches are distributed among these distances:
21 8 0.10
22 13 0.15
23 32 0.38
24 10 0.12
25 11 0.13
26 2 0.02
27 4 0.05
28 4 0.05
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (23 bp):
ATAAATAATAATATATATAATAT
Found at i:19206944 original size:29 final size:27
Alignment explanation
Indices: 19206902--19206956 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 27
19206892 TTTATAGCAA
19206902 AAATAAATAATATATAAAATATTTAAAAT
1 AAATAAATAATATA-AAAA-ATTTAAAAT
**
19206931 AAATAAATTGTATAAAAAATTTAAAA
1 AAATAAATAATATAAAAAATTTAAAA
19206957 AGGACTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 8 0.33
28 4 0.17
29 12 0.50
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (27 bp):
AAATAAATAATATAAAAAATTTAAAAT
Found at i:19206952 original size:27 final size:25
Alignment explanation
Indices: 19206901--19206956 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 25
19206891 GTTTATAGCA
*
19206901 AAAATAAATAATATATAAAATATTT
1 AAAATAAATAATATATAAAAAATTT
*
19206926 AAAATAAATAAATTGTATAAAAAATTT
1 AAAATAAAT-AA-TATATAAAAAATTT
19206953 AAAA
1 AAAA
19206957 AGGACTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 9 0.33
26 2 0.07
27 16 0.59
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (25 bp):
AAAATAAATAATATATAAAAAATTT
Found at i:19215069 original size:21 final size:22
Alignment explanation
Indices: 19215036--19215079 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
19215026 ATAAAATAAT
*
19215036 AAACATATTTAA-TAATACATGA
1 AAACATATGTAATTAATA-ATGA
19215058 AAACATA-GTAATTAATAATGA
1 AAACATATGTAATTAATAATGA
19215079 A
1 A
19215080 TTTTGAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (22 bp):
AAACATATGTAATTAATAATGA
Found at i:19215407 original size:10 final size:10
Alignment explanation
Indices: 19215394--19215481 Score: 58
Period size: 10 Copynumber: 8.7 Consensus size: 10
19215384 AAATATGAAG
19215394 TAATATAATA
1 TAATATAATA
*
19215404 TAATAAAATA
1 TAATATAATA
19215414 TAAGTA-AATAA
1 TAA-TATAAT-A
*
19215425 TAATATAAAA
1 TAATATAATA
19215435 T-ATATAATA
1 TAATATAATA
*
19215444 -CATATATATA
1 TAATATA-ATA
*
19215454 TATATATTAAAA
1 TA-ATA-TAATA
*
19215466 TAAAATAATA
1 TAATATAATA
19215476 T-ATATA
1 TAATATA
19215482 CAATTTAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 17
0.71 0.09 0.20
Matches are distributed among these distances:
9 16 0.26
10 27 0.44
11 10 0.16
12 7 0.11
13 2 0.03
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (10 bp):
TAATATAATA
Found at i:19215413 original size:15 final size:16
Alignment explanation
Indices: 19215394--19215475 Score: 69
Period size: 15 Copynumber: 4.9 Consensus size: 16
19215384 AAATATGAAG
19215394 TAATATAATATAATAA
1 TAATATAATATAATAA
19215410 -AATATAAGTA-AATAA
1 TAATATAA-TATAATAA
*
19215425 TAATATAAAATATATAA
1 TAATATAATATA-ATAA
*
19215442 TACATATATATATATATAT
1 TA-ATATA-ATATA-ATAA
* *
19215461 TAAAATAAAATAATA
1 TAATATAATATAATA
19215476 TATATACAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
15 13 0.24
16 13 0.24
17 10 0.18
18 9 0.16
19 10 0.18
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (16 bp):
TAATATAATATAATAA
Found at i:19215456 original size:26 final size:25
Alignment explanation
Indices: 19215262--19215481 Score: 95
Period size: 23 Copynumber: 8.5 Consensus size: 25
19215252 AATAATGTGA
* * *
19215262 AATAATATAT-TGT-TAAAATGTAA
1 AATAATATATATATATAAAATATAT
19215285 AATAATATATAAATATATAAATATTATGTGAT
1 AATAATATAT--ATATATAAA-A-TA--T-AT
*
19215317 AAAAATATA-ATATA-ATAAATA-AT
1 AATAATATATATATATA-AAATATAT
*
19215340 AAGTAATGATATATGT-TAAAATATAT
1 AA-TAAT-ATATATATATAAAATATAT
* *
19215366 ATTAATATGATA-ATAGAAAA-ATAT
1 AATAATAT-ATATATATAAAATATAT
19215390 GAAGTAATATA-ATATAATAAAATATA-
1 -AA-TAATATATATAT-ATAAAATATAT
*
19215416 AGTAA-ATA-ATAATATAAAATATAT
1 AATAATATATAT-ATATAAAATATAT
* *
19215440 AATACATATATATATATATATTAAAATAA
1 AATA-ATATATATATATA-A--AATATAT
19215469 AATAATATATATA
1 AATAATATATATA
19215482 CAATTTAAAA
Statistics
Matches: 152, Mismatches: 15, Indels: 55
0.68 0.07 0.25
Matches are distributed among these distances:
23 29 0.19
24 19 0.12
25 25 0.16
26 28 0.18
27 12 0.08
28 12 0.08
29 17 0.11
31 1 0.01
32 9 0.06
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.36
Consensus pattern (25 bp):
AATAATATATATATATAAAATATAT
Found at i:19215511 original size:25 final size:27
Alignment explanation
Indices: 19215460--19215517 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
19215450 TATATATATA
*
19215460 TTAAAATAAAATAATATATATACAA-T
1 TTAAAATAAAATAATATATAAACAATT
*
19215486 TTAAAAT-AAATAAGT-TATAAATAATT
1 TTAAAATAAAATAA-TATATAAACAATT
19215512 TTAAAA
1 TTAAAA
19215518 GGGATAAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 13 0.46
26 15 0.54
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (27 bp):
TTAAAATAAAATAATATATAAACAATT
Found at i:19217472 original size:206 final size:206
Alignment explanation
Indices: 19217109--19217656 Score: 848
Period size: 206 Copynumber: 2.7 Consensus size: 206
19217099 AAATCTGCTT
* *
19217109 CTTCAATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCATAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
* **
19217174 GCGAAAACCAAATCAGCTATGTCTTCGATTTACTCCTTGTAAGCACAAGGATACCAAACCATCTT
66 GTGAAAACCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAACCATCTT
* * ** *
19217239 GGATCTGCTTCAGTTTAATCATCTGAAGGTTAGATCTGCTATGTGTCTGC-CTTCCGTCGAATAT
131 GGATCTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTATCTGCTC-TCCGTCGAATAT
19217303 GGAGACGCCAAA
195 GGAGACGCCAAA
* * *
19217315 CTTCGATTTGTTCTTTGACAATACAGAGATGCCAAATTATCTTAGACTTGCTTCAGCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
* * * * *
19217380 ATGAAAGCTAAATCAGCTATGAT-TTCGATTTGTTCCTTGTAAACACAAGGATACCAAATCATCT
66 GTGAAAACCAAATCAGCTATG-TCTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAACCATCT
* *
19217444 TGGATCTGCTTTAGTATAAACGTCTGAAGGCCAGATCTGCTATGTATCTGCTCTCCGTCGAATAT
130 TGGATCTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTATCTGCTCTCCGTCGAATAT
19217509 GGAGACGCCAAA
195 GGAGACGCCAAA
* *
19217521 CTTTGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
* *
19217586 GTGAAATCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GTGAAAACCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAACCATCTT
19217651 GGATCT
131 GGATCT
19217657 TACTTCAGCC
Statistics
Matches: 308, Mismatches: 31, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
205 1 0.00
206 305 0.99
207 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (206 bp):
CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
GTGAAAACCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAACCATCTT
GGATCTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTATCTGCTCTCCGTCGAATATG
GAGACGCCAAA
Found at i:19218556 original size:1 final size:1
Alignment explanation
Indices: 19218552--19218615 Score: 56
Period size: 1 Copynumber: 64.0 Consensus size: 1
19218542 TCCTCTTCTC
* * * ** * * *
19218552 TTTTTTTTCTTTTTTTTTTTTCTTTTTTTTTTTTCTGATTTTTGTTTGTTTTTTTTTATTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
19218616 GATTTTCGAA
Statistics
Matches: 48, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.03, C:0.05, G:0.05, T:0.88
Consensus pattern (1 bp):
T
Found at i:19218568 original size:13 final size:13
Alignment explanation
Indices: 19218552--19218608 Score: 78
Period size: 13 Copynumber: 4.4 Consensus size: 13
19218542 TCCTCTTCTC
19218552 TTTTTTTTCTTTT
1 TTTTTTTTCTTTT
19218565 TTTTTTTTCTTTT
1 TTTTTTTTCTTTT
**
19218578 TTTTTTTTCTGAT
1 TTTTTTTTCTTTT
* *
19218591 TTTTGTTTGTTTT
1 TTTTTTTTCTTTT
19218604 TTTTT
1 TTTTT
19218609 ATTTTTTGAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.02, C:0.05, G:0.05, T:0.88
Consensus pattern (13 bp):
TTTTTTTTCTTTT
Found at i:19218622 original size:36 final size:35
Alignment explanation
Indices: 19218555--19218622 Score: 91
Period size: 36 Copynumber: 1.9 Consensus size: 35
19218545 TCTTCTCTTT
* **
19218555 TTTTTCTTTTTTTTTTTTCTTTTTTTTTTTTCTGA
1 TTTTTCTTTTTTTTTTTTATTTTTTGATTTTCTGA
*
19218590 TTTTTGTTTGTTTTTTTTTATTTTTTGATTTTC
1 TTTTTCTTT-TTTTTTTTTATTTTTTGATTTTC
19218623 GAAACCTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 8 0.29
36 20 0.71
ACGTcount: A:0.04, C:0.06, G:0.06, T:0.84
Consensus pattern (35 bp):
TTTTTCTTTTTTTTTTTTATTTTTTGATTTTCTGA
Found at i:19229630 original size:21 final size:22
Alignment explanation
Indices: 19229597--19229640 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
19229587 ATAAAATAAT
*
19229597 AAACATATTTAA-TAATACATGA
1 AAACATATGTAATTAATA-ATGA
19229619 AAACATA-GTAATTAATAATGA
1 AAACATATGTAATTAATAATGA
19229640 A
1 A
19229641 TTTTGAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (22 bp):
AAACATATGTAATTAATAATGA
Found at i:19229827 original size:16 final size:15
Alignment explanation
Indices: 19229755--19229829 Score: 59
Period size: 14 Copynumber: 4.9 Consensus size: 15
19229745 AATATCAATT
19229755 TAATATGAA-AATAA
1 TAATATGAATAATAA
*
19229769 TAATGTGAATAATAA
1 TAATATGAATAATAA
*
19229784 T-ATACCTGAAAATATATA
1 TAATA--TGAATA-ATA-A
19229802 TAATA-G-ATAATAA
1 TAATATGAATAATAA
19229815 TAATATGAAATAATA
1 TAATATG-AATAATA
19229830 TATTGTTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 16
0.71 0.06 0.24
Matches are distributed among these distances:
13 6 0.12
14 14 0.29
15 8 0.17
16 12 0.25
17 3 0.06
18 2 0.04
19 3 0.06
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.32
Consensus pattern (15 bp):
TAATATGAATAATAA
Found at i:19229936 original size:44 final size:42
Alignment explanation
Indices: 19229778--19229944 Score: 117
Period size: 44 Copynumber: 3.9 Consensus size: 42
19229768 ATAATGTGAA
** * *
19229778 TAATAATATACCTGAAAATATATATAATAGATAATAATAATATG
1 TAATAATATATGTTAAAATATATATAAT--ATAATAATAATAAG
* * * *
19229822 AAATAATATATTGTTAAAATGTAAAATAATATAATAAT-ATTA-
1 TAATAATATA-TGTTAAAATAT-ATATAATATAATAATAATAAG
* * *
19229864 TATTTATATTATGTGATAAA-A-ATATAATATAATAAATAATAAG
1 TAATAATA-TATGTTA-AAATATATATAATATAAT-AATAATAAG
* *
19229907 TAATGATATATGTTAAAATATATATTAATATGATAATA
1 TAATAATATATGTTAAAATATATA-TAATATAATAATA
19229945 GAAAAATATG
Statistics
Matches: 94, Mismatches: 19, Indels: 21
0.70 0.14 0.16
Matches are distributed among these distances:
40 11 0.12
41 6 0.06
42 19 0.20
43 20 0.21
44 25 0.27
45 7 0.07
46 6 0.06
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.38
Consensus pattern (42 bp):
TAATAATATATGTTAAAATATATATAATATAATAATAATAAG
Found at i:19229971 original size:10 final size:10
Alignment explanation
Indices: 19229958--19230043 Score: 65
Period size: 10 Copynumber: 8.7 Consensus size: 10
19229948 AAATATGAAG
19229958 TAATATAATA
1 TAATATAATA
*
19229968 TAATAAAATA
1 TAATATAATA
19229978 TAAGTA-AATAA
1 TAA-TATAAT-A
*
19229989 TAATATAAAA
1 TAATATAATA
19229999 T-ATATAATA
1 TAATATAATA
*
19230008 -CATATATATA
1 TAATATA-ATA
19230018 TATATATAA-A
1 TA-ATATAATA
*
19230028 TAAAATAATA
1 TAATATAATA
19230038 T-ATATA
1 TAATATA
19230044 CAATTTAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
9 21 0.34
10 27 0.44
11 9 0.15
12 5 0.08
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (10 bp):
TAATATAATA
Found at i:19230020 original size:26 final size:25
Alignment explanation
Indices: 19229843--19230043 Score: 109
Period size: 26 Copynumber: 7.9 Consensus size: 25
19229833 TGTTAAAATG
*
19229843 TAAAATAATATAATAATATTATATTTA
1 TAAAAT-ATATAATAATA-TATATATA
** * *
19229870 TATTATGTGATAAAAATATA-ATATA
1 TAAAATAT-ATAATAATATATATATA
*
19229895 -ATAAATA-ATAAGTAATGATATATGT-
1 TA-AAATATATAA-TAAT-ATATATATA
*
19229920 TAAAATATATATTAATATGATA-ATA
1 TAAAATATATAATAATAT-ATATATA
*
19229945 GAAAA-ATATGAAGTAATATA-ATATAA
1 TAAAATATAT-AA-TAATATATATAT-A
*
19229971 TAAAATATA-AGTAA-ATA-ATAATA
1 TAAAATATATAATAATATATAT-ATA
19229994 TAAAATATATAATACATATATATATA
1 TAAAATATATAATA-ATATATATATA
*
19230020 TATATAA-ATAAAATAATATATATA
1 TA-A-AATATATAATAATATATATA
19230044 CAATTTAAAA
Statistics
Matches: 135, Mismatches: 18, Indels: 43
0.69 0.09 0.22
Matches are distributed among these distances:
23 19 0.14
24 20 0.15
25 31 0.23
26 38 0.28
27 25 0.19
28 2 0.01
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (25 bp):
TAAAATATATAATAATATATATATA
Found at i:19230027 original size:30 final size:27
Alignment explanation
Indices: 19230004--19230056 Score: 56
Period size: 26 Copynumber: 2.0 Consensus size: 27
19229994 TAAAATATAT
*
19230004 AATACATATATATA-TATATATAAATAA-
1 AATA-ATATATATACAATATA-AAATAAT
*
19230031 AATAATATATATACAATTTAAAATAA
1 AATAATATATATACAATATAAAATAA
19230057 ATAAGTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (27 bp):
AATAATATATATACAATATAAAATAAT
Found at i:19230037 original size:75 final size:74
Alignment explanation
Indices: 19229884--19230043 Score: 170
Period size: 75 Copynumber: 2.1 Consensus size: 74
19229874 ATGTGATAAA
* * *
19229884 AATATAATATAATAAATAATAAGTAATGATATATGTTAAAATATATATTAATATGATAATAGAAA
1 AATATAATATAATAAATAATAAGTAATAATATATGATAAAATATATAATAATATGATAATAGAAA
*
19229949 AATATGAAGT
66 AATA-GAAAT
19229959 AATATAATATAATAAA-ATATAAGTAAATAATA-AT-ATAAAATATATAATACATAT-ATATATA
1 AATATAATATAATAAATA-ATAAGT-AATAATATATGATAAAATATATAATA-ATATGATA-ATA
*
19230020 TATATAAATA-AAAT
62 GA-A-AAATAGAAAT
19230034 AATAT-ATATA
1 AATATAATATA
19230044 CAATTTAAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 13
0.80 0.05 0.14
Matches are distributed among these distances:
74 22 0.30
75 40 0.54
76 7 0.09
77 5 0.07
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.35
Consensus pattern (74 bp):
AATATAATATAATAAATAATAAGTAATAATATATGATAAAATATATAATAATATGATAATAGAAA
AATAGAAAT
Found at i:19233812 original size:18 final size:18
Alignment explanation
Indices: 19233789--19233826 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
19233779 AATATATATT
19233789 AACCCAAGTACCCAACCC
1 AACCCAAGTACCCAACCC
*
19233807 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
19233825 AA
1 AA
19233827 TCATAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.47, G:0.03, T:0.08
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:19233819 original size:13 final size:13
Alignment explanation
Indices: 19233803--19233827 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19233793 CAAGTACCCA
19233803 ACCCAACCCAATT
1 ACCCAACCCAATT
19233816 ACCCAACCCAAT
1 ACCCAACCCAAT
19233828 CATAAAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:19233893 original size:7 final size:6
Alignment explanation
Indices: 19233852--19233892 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
19233842 ATAATTTAAT
*
19233852 AAATAA AAATAA AAATCTAA AACTAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAA--TAA AAATAA AAATAA AAATAA AAA
19233893 ACATATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 26 0.84
8 5 0.16
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:19233893 original size:20 final size:20
Alignment explanation
Indices: 19233855--19233894 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
19233845 ATTTAATAAA
**
19233855 TAAAAATAAAAATCTAAAAC
1 TAAAAATAAAAATAAAAAAC
19233875 TAAAAATAAAAATAAAAAAC
1 TAAAAATAAAAATAAAAAAC
19233895 ATATAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.17
Consensus pattern (20 bp):
TAAAAATAAAAATAAAAAAC
Found at i:19233933 original size:9 final size:9
Alignment explanation
Indices: 19233911--19233988 Score: 50
Period size: 9 Copynumber: 8.7 Consensus size: 9
19233901 TTATATACAA
19233911 ATAATTCGG
1 ATAATTCGG
* *
19233920 TTAATTTGG
1 ATAATTCGG
19233929 ATAATTCGG
1 ATAATTCGG
* *
19233938 GTAATTAGG
1 ATAATTCGG
* **
19233947 GTAATTTTG
1 ATAATTCGG
*
19233956 TTAATTC-G
1 ATAATTCGG
19233964 ATTAATTCGG
1 A-TAATTCGG
*
19233974 TTAATTCGG
1 ATAATTCGG
*
19233983 TTAATT
1 ATAATT
19233989 TTATACTTAT
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
8 1 0.02
9 53 0.96
10 1 0.02
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.45
Consensus pattern (9 bp):
ATAATTCGG
Found at i:19233934 original size:18 final size:18
Alignment explanation
Indices: 19233911--19233979 Score: 68
Period size: 18 Copynumber: 3.8 Consensus size: 18
19233901 TTATATACAA
19233911 ATAATTCGGTTAATTTGG
1 ATAATTCGGTTAATTTGG
* *
19233929 ATAATTCGGGTAATTAGG
1 ATAATTCGGTTAATTTGG
* ** *
19233947 GTAATTTTGTTAA-TTCG
1 ATAATTCGGTTAATTTGG
19233964 ATTAATTCGGTTAATT
1 A-TAATTCGGTTAATT
19233980 CGGTTAATTT
Statistics
Matches: 38, Mismatches: 11, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
17 2 0.05
18 35 0.92
19 1 0.03
ACGTcount: A:0.29, C:0.06, G:0.20, T:0.45
Consensus pattern (18 bp):
ATAATTCGGTTAATTTGG
Found at i:19233951 original size:27 final size:27
Alignment explanation
Indices: 19233912--19233963 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
19233902 TATATACAAA
* *
19233912 TAATTCGGTTAATTTGGATAATTCGGG
1 TAATTAGGGTAATTTGGATAATTCGGG
* *
19233939 TAATTAGGGTAATTTTGTTAATTCG
1 TAATTAGGGTAATTTGGATAATTCG
19233964 ATTAATTCGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.27, C:0.06, G:0.23, T:0.44
Consensus pattern (27 bp):
TAATTAGGGTAATTTGGATAATTCGGG
Found at i:19233980 original size:18 final size:18
Alignment explanation
Indices: 19233912--19233988 Score: 66
Period size: 18 Copynumber: 4.3 Consensus size: 18
19233902 TATATACAAA
*
19233912 TAATTCGGTTAATTTGGA-
1 TAATTCGGTTAA-TTCGAT
* * **
19233930 TAATTCGGGTAATTAGGG
1 TAATTCGGTTAATTCGAT
**
19233948 TAATTTTGTTAATTCGAT
1 TAATTCGGTTAATTCGAT
*
19233966 TAATTCGGTTAATTCGGT
1 TAATTCGGTTAATTCGAT
19233984 TAATT
1 TAATT
19233989 TTATACTTAT
Statistics
Matches: 46, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
17 3 0.07
18 43 0.93
ACGTcount: A:0.27, C:0.06, G:0.21, T:0.45
Consensus pattern (18 bp):
TAATTCGGTTAATTCGAT
Found at i:19234447 original size:10 final size:9
Alignment explanation
Indices: 19234434--19234495 Score: 54
Period size: 9 Copynumber: 6.6 Consensus size: 9
19234424 AAAAACATAA
19234434 AAAATTCATT
1 AAAATT-ATT
*
19234444 AAAATTATA
1 AAAATTATT
**
19234453 AAAAAAATT
1 AAAATTATT
19234462 AAAATT-TAT
1 AAAATTAT-T
19234471 AAAATTATT
1 AAAATTATT
19234480 AGAAATTAATT
1 A-AAATT-ATT
19234491 AAAAT
1 AAAAT
19234496 CATAAAAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
8 1 0.02
9 21 0.50
10 16 0.38
11 4 0.10
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (9 bp):
AAAATTATT
Found at i:19234455 original size:18 final size:17
Alignment explanation
Indices: 19234415--19234487 Score: 56
Period size: 18 Copynumber: 4.0 Consensus size: 17
19234405 AGATGCATTC
* *
19234415 TAAAATTATAAAAACATA
1 TAAAATTATTAAAA-TTA
*
19234433 AAAAATTCATTAAAATTA
1 TAAAATT-ATTAAAATTA
**
19234451 TAAAAAAAATTAAAATTTA
1 T-AAAATTATTAAAA-TTA
19234470 TAAAATTATTAGAAATTA
1 TAAAATTATTA-AAATTA
19234488 ATTAAAATCA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
18 26 0.60
19 17 0.40
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (17 bp):
TAAAATTATTAAAATTA
Found at i:19234465 original size:28 final size:27
Alignment explanation
Indices: 19234411--19234510 Score: 86
Period size: 28 Copynumber: 3.7 Consensus size: 27
19234401 GCCCAGATGC
19234411 ATTC-TAAAATTATAAAAACATAA--AAA
1 ATTCATAAAATTATAAAAA-A-AATTAAA
19234437 ATTCATTAAAATTATAAAAAAAATTAAA
1 ATTCA-TAAAATTATAAAAAAAATTAAA
* **
19234465 ATTTATAAAATTATTAGAAATTAATTAAA
1 ATTCATAAAATTA-TA-AAAAAAATTAAA
19234494 A-TCATAAAA--ATAAAAAA
1 ATTCATAAAATTATAAAAAA
19234511 TATTTTTATA
Statistics
Matches: 62, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
24 3 0.05
25 2 0.03
26 7 0.11
27 9 0.15
28 30 0.48
29 11 0.18
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.31
Consensus pattern (27 bp):
ATTCATAAAATTATAAAAAAAATTAAA
Found at i:19240778 original size:12 final size:12
Alignment explanation
Indices: 19240763--19240791 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
19240753 ATATATTTAA
19240763 AAATATTAAAAT
1 AAATATTAAAAT
19240775 AAATATTAAAAT
1 AAATATTAAAAT
19240787 AAATA
1 AAATA
19240792 AAAATAATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAATATTAAAAT
Found at i:19240778 original size:24 final size:25
Alignment explanation
Indices: 19240720--19240780 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 25
19240710 CTTATTTCAT
* *
19240720 TAAATAAAAAAATTTAAAAATATAA
1 TAAATAAATATATTTAAAAATATAA
*
19240745 TAAATCAAATATATTTAAAAATATTA
1 TAAAT-AAATATATTTAAAAATATAA
19240771 -AAATAAATAT
1 TAAATAAATAT
19240781 TAAAATAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 9 0.28
26 17 0.53
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (25 bp):
TAAATAAATATATTTAAAAATATAA
Found at i:19240885 original size:15 final size:16
Alignment explanation
Indices: 19240855--19240887 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
19240845 AAATAGTTAT
19240855 ATTAAAAATTTAAAATA
1 ATTAAAAA-TTAAAATA
19240872 ATTAAAAA-TAAAATA
1 ATTAAAAATTAAAATA
19240887 A
1 A
19240888 AAATTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAATTAAAATA
Found at i:19241147 original size:21 final size:20
Alignment explanation
Indices: 19241108--19241147 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
19241098 TATAAGATTT
*
19241108 GTTAATTATTATTATTTTAA
1 GTTAATTATTATTAATTTAA
*
19241128 GTTAATTTTGTATTAATTTA
1 GTTAATTAT-TATTAATTTA
19241148 TTATTAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (20 bp):
GTTAATTATTATTAATTTAA
Found at i:19242504 original size:23 final size:23
Alignment explanation
Indices: 19242452--19242508 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
19242442 TTATAGCTTG
* **
19242452 CTGCTCTAGCACGTCTCTGTCTG
1 CTGCTCTAGCACGACTCTGTCAA
* *
19242475 CTACTCTAGCACGACTTTGTCAA
1 CTGCTCTAGCACGACTCTGTCAA
19242498 CTGCTCTAGCA
1 CTGCTCTAGCA
19242509 TGCTTAGGGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.18, C:0.33, G:0.18, T:0.32
Consensus pattern (23 bp):
CTGCTCTAGCACGACTCTGTCAA
Found at i:19253002 original size:18 final size:18
Alignment explanation
Indices: 19252970--19253007 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
19252960 GTGTCTAGAA
19252970 TTATTGTGTACTTATATTT
1 TTATTGTGTACTTAT-TTT
*
19252989 TTATT-TGTATTTATTTT
1 TTATTGTGTACTTATTTT
19253006 TT
1 TT
19253008 GCTAACTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 8 0.44
19 5 0.28
ACGTcount: A:0.18, C:0.03, G:0.08, T:0.71
Consensus pattern (18 bp):
TTATTGTGTACTTATTTT
Found at i:19253005 original size:16 final size:19
Alignment explanation
Indices: 19252970--19253006 Score: 53
Period size: 16 Copynumber: 2.1 Consensus size: 19
19252960 GTGTCTAGAA
19252970 TTATTGTGTACTTATATTT
1 TTATTGTGTACTTATATTT
19252989 TTATT-TGTA-TT-TATTT
1 TTATTGTGTACTTATATTT
19253005 TT
1 TT
19253007 TGCTAACTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.39
17 2 0.11
18 4 0.22
19 5 0.28
ACGTcount: A:0.19, C:0.03, G:0.08, T:0.70
Consensus pattern (19 bp):
TTATTGTGTACTTATATTT
Found at i:19258399 original size:28 final size:27
Alignment explanation
Indices: 19258349--19258456 Score: 121
Period size: 27 Copynumber: 3.9 Consensus size: 27
19258339 GGCTGCTAGA
* *
19258349 ACAGATAATGTGACAGAGTCACCAGAT
1 ACAGATAATGTGGCAGAGCCACCAGAT
19258376 ACAGATAATCGTGGCAGAGCCACCAGA-
1 ACAGATAAT-GTGGCAGAGCCACCAGAT
* *
19258403 ATAGATATATGGGGCAGAGCCACCAGAT
1 ACAGATA-ATGTGGCAGAGCCACCAGAT
*
19258431 -CAGATAATTTGTGGCATAGCCACCAG
1 ACAGATAA--TGTGGCAGAGCCACCAG
19258457 GACGCTTCCT
Statistics
Matches: 69, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
26 1 0.01
27 36 0.52
28 32 0.46
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (27 bp):
ACAGATAATGTGGCAGAGCCACCAGAT
Found at i:19259919 original size:24 final size:24
Alignment explanation
Indices: 19259887--19259960 Score: 121
Period size: 24 Copynumber: 3.1 Consensus size: 24
19259877 ACACAGTTCA
19259887 CCCTAATCAGCTCCTAAATCCTCT
1 CCCTAATCAGCTCCTAAATCCTCT
*
19259911 CCCTGATCAGCTCCTAAATCCTCT
1 CCCTAATCAGCTCCTAAATCCTCT
* *
19259935 CCCTTATCAGCTCCTAAATCTTCT
1 CCCTAATCAGCTCCTAAATCCTCT
19259959 CC
1 CC
19259961 AGACAGACTT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.22, C:0.42, G:0.05, T:0.31
Consensus pattern (24 bp):
CCCTAATCAGCTCCTAAATCCTCT
Found at i:19264763 original size:6 final size:6
Alignment explanation
Indices: 19264748--19264818 Score: 135
Period size: 6 Copynumber: 12.0 Consensus size: 6
19264738 ATGGAATTTT
19264748 AAAT-A AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
19264795 AAATAA AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA
19264819 TAGTAAAATA
Statistics
Matches: 65, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 4 0.06
6 61 0.94
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:19270046 original size:14 final size:14
Alignment explanation
Indices: 19270027--19270053 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19270017 CTATTTTTAT
19270027 TATGTGTGAAATTA
1 TATGTGTGAAATTA
19270041 TATGTGTGAAATT
1 TATGTGTGAAATT
19270054 TTCATGATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TATGTGTGAAATTA
Found at i:19271592 original size:2 final size:2
Alignment explanation
Indices: 19271585--19271641 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
19271575 TAAATGAGAG
19271585 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19271627 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
19271642 GAAGATCTAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19273654 original size:5 final size:5
Alignment explanation
Indices: 19273644--19273678 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
19273634 AATTGTGAAA
19273644 AAAAT AAAAT AAAAT AAAAAT AAAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT -AAAAT -AAAAT AAAAT AAA
19273679 GAACACACAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 18 0.62
6 11 0.38
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:19273663 original size:11 final size:11
Alignment explanation
Indices: 19273643--19273678 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
19273633 TAATTGTGAA
19273643 AAAAATAAAAT
1 AAAAATAAAAT
19273654 -AAAATAAAAAT
1 AAAAAT-AAAAT
19273665 AAAAATAAAAT
1 AAAAATAAAAT
19273676 AAA
1 AAA
19273679 GAACACACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 5 0.22
11 13 0.57
12 5 0.22
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:19278109 original size:18 final size:17
Alignment explanation
Indices: 19278081--19278116 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
19278071 CCAAATTGTG
19278081 AAAATAAAATAAAATAA
1 AAAATAAAATAAAATAA
19278098 AAAATAAAAATAAAATAA
1 AAAAT-AAAATAAAATAA
19278116 A
1 A
19278117 GAACACACAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (17 bp):
AAAATAAAATAAAATAA
Found at i:19284204 original size:130 final size:129
Alignment explanation
Indices: 19284013--19284346 Score: 390
Period size: 130 Copynumber: 2.6 Consensus size: 129
19284003 TATTCATTTA
* * * *
19284013 AAAATTCTTTAAAATGAAGGCAATG-CCGATGTTTGGAAATTCGGGAAAACGTGCCCTATCGTGC
1 AAAATTCTTTAAAA-GAAGGCAATGTTCGATGTTTAGAAATTCGGGGAATCGTGCCCTATCGTGC
* * * ** *
19284077 TGTGTTACGATTTCCTGTTTGCTCAAAATAATCGAACATTCCTTTGGAATTTCACTCATGTCTTT
65 TGGGTTACGATTTCCCGTTTGCTCAAAATAATCGAACATCCCTTTAAAATTTCACTCATAT-TTT
19284142 -
129 C
* * *
19284142 AAAATTCTTTAAAACGAAGGAAATGTTCGATGTTTAGCAATTCGGGGAATCGTACCCTATCGTGC
1 AAAATTCTTTAAAA-GAAGGCAATGTTCGATGTTTAGAAATTCGGGGAATCGTGCCCTATCGTGC
* * * *
19284207 TGGGTTGCAATTTCCCGTTTGTTCAAAATAATTGAACATCCCTTTAAAATTTCACTCATATTTTC
65 TGGGTTACGATTTCCCGTTTGCTCAAAATAATCGAACATCCCTTTAAAATTTCACTCATATTTTC
* * * * *
19284272 TAAA--CTTTAAAATAAGGCAATGTTCGATGTCTAGAAATTCGAGGAATCATGCCCTA-CTGTGC
1 AAAATTCTTTAAAAGAAGGCAATGTTCGATGTTTAGAAATTCGGGGAATCGTGCCCTATC-GTGC
*
19284334 TGGGTTTCGATTT
65 TGGGTTACGATTT
19284347 TTCGTTGGAC
Statistics
Matches: 174, Mismatches: 28, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
126 1 0.01
127 52 0.30
128 8 0.05
129 26 0.15
130 87 0.50
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (129 bp):
AAAATTCTTTAAAAGAAGGCAATGTTCGATGTTTAGAAATTCGGGGAATCGTGCCCTATCGTGCT
GGGTTACGATTTCCCGTTTGCTCAAAATAATCGAACATCCCTTTAAAATTTCACTCATATTTTC
Found at i:19285173 original size:5 final size:5
Alignment explanation
Indices: 19285163--19285219 Score: 60
Period size: 5 Copynumber: 10.6 Consensus size: 5
19285153 AAAATTTCAA
* *
19285163 AAATT AAATT AAATAT TATTT AATATT GAACATT AAATT AAATT AAATT
1 AAATT AAATT AAAT-T AAATT AA-ATT -AA-ATT AAATT AAATT AAATT
19285212 AAATT AAA
1 AAATT AAA
19285220 AACAGTAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
5 32 0.73
6 7 0.16
7 5 0.11
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:19287567 original size:14 final size:14
Alignment explanation
Indices: 19287532--19287569 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
19287522 TATAAGATTC
*
19287532 ATTAT-TTGTTTTA
1 ATTATATTGTTTGA
19287545 ATATATATTGTTTGA
1 AT-TATATTGTTTGA
19287560 ATTATATTGT
1 ATTATATTGT
19287570 ATATATTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 2 0.09
14 11 0.50
15 9 0.41
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.61
Consensus pattern (14 bp):
ATTATATTGTTTGA
Found at i:19290990 original size:19 final size:19
Alignment explanation
Indices: 19290966--19291012 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
19290956 CGCCTTTTTT
*
19290966 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTACAT-CA
19290985 TTTGCATTACATTACATCA
1 TTTGCATTACATTACATCA
*
19291004 TATGCATTA
1 TTTGCATTA
19291013 AAGTCAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTACATCA
Found at i:19291176 original size:12 final size:12
Alignment explanation
Indices: 19291145--19291194 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
19291135 GGAAAGGTTG
19291145 GAACAAATGC-A
1 GAACAAATGCAA
*
19291156 GAAAGAAATGCAA
1 G-AACAAATGCAA
19291169 GAACAAATGCAA
1 GAACAAATGCAA
* *
19291181 GCACACATGCAA
1 GAACAAATGCAA
19291193 GA
1 GA
19291195 GCAACTAGCT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
11 1 0.03
12 29 0.91
13 2 0.06
ACGTcount: A:0.54, C:0.18, G:0.20, T:0.08
Consensus pattern (12 bp):
GAACAAATGCAA
Found at i:19298822 original size:11 final size:11
Alignment explanation
Indices: 19298806--19298834 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
19298796 TGCTATGATT
19298806 TGTTGCAAGCA
1 TGTTGCAAGCA
19298817 TGTTGCAAGCA
1 TGTTGCAAGCA
19298828 TGTTGCA
1 TGTTGCA
19298835 TTGAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (11 bp):
TGTTGCAAGCA
Found at i:19299668 original size:44 final size:45
Alignment explanation
Indices: 19299620--19299721 Score: 145
Period size: 44 Copynumber: 2.3 Consensus size: 45
19299610 AGCCACCAGC
* *
19299620 CTTATTTCCCTGAGGTAGCAAGGGAACAAGCTGAAGATTGTAG-T
1 CTTATTTCCCTGAGGTAGCAAGGGAACAAACTGAAGATTGAAGAT
*
19299664 CTTATCTT-CCTGAGGTAGCAAGGGAGCAAACTGAAGATTGAAGAT
1 CTTAT-TTCCCTGAGGTAGCAAGGGAACAAACTGAAGATTGAAGAT
*
19299709 CTTATCTCCCTGA
1 CTTATTTCCCTGA
19299722 AATAACGGTG
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
44 38 0.75
45 13 0.25
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (45 bp):
CTTATTTCCCTGAGGTAGCAAGGGAACAAACTGAAGATTGAAGAT
Found at i:19299689 original size:88 final size:88
Alignment explanation
Indices: 19299577--19299867 Score: 282
Period size: 88 Copynumber: 3.3 Consensus size: 88
19299567 ACGGCGAATT
* * * * *
19299577 TTATCTTCCCAAGGTAGCAGGGGAGCAGATTTTAGCCACCAGCCTTATTTCCCTGAGGTAGCAAG
1 TTATCTTCCCGAGGTAGCAAGGGAGCAAATTTTAGCCACCAGACTTATTTCCCTGAAGTAGCAAG
*
19299642 GGAACAAGCTGAAGATTGTAGTC
66 GGAGCAAGCTGAAGATTGTAGTC
* * ** ***** * * * *
19299665 TTATCTTCCTGAGGTAGCAAGGGAGCAAACTGAAGATTGAAGATCTTATCTCCCTGAAATAAC-G
1 TTATCTTCCCGAGGTAGCAAGGGAGCAAATTTTAGCCACCAGA-CTTATTTCCCTGAAGTAGCAA
* * * *
19299729 GTGGAGC-AGATCGAAGATGGCGAATC
65 G-GGAGCAAGCT-GAAGATTG-TAGTC
*
19299755 TTATCTTCCCGAGGTAGCAAGGGAGCAAATTTTAGCCACCAGACTTATTTCCTTGAAGTAGCAAG
1 TTATCTTCCCGAGGTAGCAAGGGAGCAAATTTTAGCCACCAGACTTATTTCCCTGAAGTAGCAAG
*
19299820 GGAGCAGGCT-AATGATTGTAGTC
66 GGAGCAAGCTGAA-GATTGTAGTC
*
19299843 TTATCTTCCTGAGGTAGCAAGGGAG
1 TTATCTTCCCGAGGTAGCAAGGGAG
19299868 TAGACTGATC
Statistics
Matches: 153, Mismatches: 43, Indels: 14
0.73 0.20 0.07
Matches are distributed among these distances:
88 63 0.41
89 50 0.33
90 40 0.26
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.25
Consensus pattern (88 bp):
TTATCTTCCCGAGGTAGCAAGGGAGCAAATTTTAGCCACCAGACTTATTTCCCTGAAGTAGCAAG
GGAGCAAGCTGAAGATTGTAGTC
Found at i:19299780 original size:45 final size:45
Alignment explanation
Indices: 19299620--19299783 Score: 151
Period size: 45 Copynumber: 3.7 Consensus size: 45
19299610 AGCCACCAGC
* * * *
19299620 CTTAT-TTCCCTGAGGTAGCAAGGGAACAAGCTGAAGATTGTAGT
1 CTTATCTTCCCTGAGGTAGCAAGGGAGCAAACTGAAGATTGAAAT
19299664 CTTATCTT-CCTGAGGTAGCAAGGGAGCAAACTGAAGATTGAAGAT
1 CTTATCTTCCCTGAGGTAGCAAGGGAGCAAACTGAAGATTGAA-AT
** * * * * *
19299709 CTTATC-TCCCTGAAATAAC-GGTGGAGCAGA-TCGAAGATGGCGAAT
1 CTTATCTTCCCTGAGGTAGCAAG-GGAGCAAACT-GAAGATTG-AAAT
19299754 CTTATCTTCCC-GAGGTAGCAAGGGAGCAAA
1 CTTATCTTCCCTGAGGTAGCAAGGGAGCAAA
19299784 TTTTAGCCAC
Statistics
Matches: 96, Mismatches: 16, Indels: 15
0.76 0.13 0.12
Matches are distributed among these distances:
44 39 0.41
45 51 0.53
46 6 0.06
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (45 bp):
CTTATCTTCCCTGAGGTAGCAAGGGAGCAAACTGAAGATTGAAAT
Found at i:19299850 original size:178 final size:178
Alignment explanation
Indices: 19299527--19300290 Score: 780
Period size: 178 Copynumber: 4.4 Consensus size: 178
19299517 GTGAATTCAC
* * * * * * *
19299527 AGATTTTATCTTCCTGAGATGGCAGTGGAGCAGATCGAAGACGGCGAATTTTATCTTCCCAAGGT
1 AGATCTTATCTCCCTGAAATAGCAGTGGAGCAGATCGAAAATGGCGAATCTTATCTTCCCAAGGT
* * * * *
19299592 AGCAGGGGAGCAGATTTTAGCCACCAGCCTTATTTCCCTGAGGTAGCAAGGGAACAAGCTGAAGA
66 AGCAGGGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAAGTAGCAAGAGAGCAAGCTGAAGA
* * *
19299657 TTGTAGTCTTATCTTCCTGAGGTAGCAAGGGAGCAAACTGAAGATTGA
131 TTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAAGATTGT
* * * *
19299705 AGATCTTATCTCCCTGAAATAACGGTGGAGCAGATCGAAGATGGCGAATCTTATCTTCCCGAGGT
1 AGATCTTATCTCCCTGAAATAGCAGTGGAGCAGATCGAAAATGGCGAATCTTATCTTCCCAAGGT
* * * * * *
19299770 AGCAAGGGAGCAAATTTTAGCCACCAGACTTATTTC-CTTGAAGTAGCAAGGGAGCAGGCT-AAT
66 AGCAGGGGAGCAGATTTTAGCCACCAGCCTTATCTCTC-TGAAGTAGCAAGAGAGCAAGCTGAA-
*
19299833 GATTGTAGTCTTATCTTCCTGAGGTAGCAAGG--G-AG--T--AGA--CT
129 GATTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAAGATTGT
* * * * * **
19299874 -GATCTTGTCT-CCTCGAGATAGCAGT-GAGGAAAATCGAAAATGGTGAATCTTATCTTCCCGGG
1 AGATCTTATCTCCCT-GAAATAGCAGTGGA-GCAGATCGAAAATGGCGAATCTTATCTTCCCAAG
* * * * * *
19299936 GTAGTAGGGGAGTAGTTTTTAGCCATCAGCCTTATCTCTCT-AAGGTAGCAAGAGAGCAAGTTAA
64 GTAGCAGGGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAA-GTAGCAAGAGAGCAAGCTGA
* *
19300000 AGTTTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAGTAGACTGAAGATTGT
128 AGATTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAAGATTGT
** * * * *
19300051 AGATCTTATCTCCCT-AAGCAGTAGTGGAGCAGATCGAAAATGGCGAATCTCATGTTCCAAAGGT
1 AGATCTTATCTCCCTGAAATAGCAGTGGAGCAGATCGAAAATGGCGAATCTTATCTTCCCAAGGT
* *
19300115 AGCAGGGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAGGTAGCAAGAGAG-AAGGTTGAAG
66 AGCAGGGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAAGTAGCAAGAGAGCAA-GCTGAAG
* *
19300179 ATTGTAG---AATCTTCCTGAGGTAGCAAGGAAGCAGACTGAGGATTGT
130 ATTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAAGATTGT
** * * * * * *
19300225 AGATCTTATCTCCCT-AAGCAGTAATGGAGCAGATC-AAAGATAGAGAATTTTATCTTCTCAAGG
1 AGATCTTATCTCCCTGAAATAGCAGTGGAGCAGATCGAAA-ATGGCGAATCTTATCTTCCCAAGG
19300288 TAG
65 TAG
19300291 TAAAGGAGTA
Statistics
Matches: 493, Mismatches: 71, Indels: 48
0.81 0.12 0.08
Matches are distributed among these distances:
167 7 0.01
168 123 0.25
169 3 0.01
170 1 0.00
171 5 0.01
173 5 0.01
174 90 0.18
175 4 0.01
176 3 0.01
177 97 0.20
178 152 0.31
179 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (178 bp):
AGATCTTATCTCCCTGAAATAGCAGTGGAGCAGATCGAAAATGGCGAATCTTATCTTCCCAAGGT
AGCAGGGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAAGTAGCAAGAGAGCAAGCTGAAGA
TTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAAGATTGT
Found at i:19300223 original size:41 final size:40
Alignment explanation
Indices: 19300152--19300231 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 40
19300142 CCTTATCTCT
**
19300152 CTGAGGTAGCAAGAGAGAAGGTTGAAGATTGTAGAATCTTC
1 CTGAGGTAGCAAGAGAGAAGACTGAAGATTGTAG-ATCTTC
* *
19300193 CTGAGGTAGCAAG-GAAGCAGACTGAGGATTGTAGATCTT
1 CTGAGGTAGCAAGAG-AGAAGACTGAAGATTGTAGATCTT
19300232 ATCTCCCTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 6 0.18
41 28 0.82
ACGTcount: A:0.33, C:0.11, G:0.33, T:0.24
Consensus pattern (40 bp):
CTGAGGTAGCAAGAGAGAAGACTGAAGATTGTAGATCTTC
Found at i:19300313 original size:174 final size:175
Alignment explanation
Indices: 19299956--19300329 Score: 477
Period size: 174 Copynumber: 2.1 Consensus size: 175
19299946 AGTAGTTTTT
* * *
19299956 AGCCATCAGCCTTATCTCTCTAAGGTAGCAAGAGAGCAAGTTAAAGTTTGTAGTCTTATCTTCCT
1 AGCCACCAGCCTTATCTCTCTAAGGTAGCAAGAGAGCAAGTTAAAGATTGTAG--TAATCTTCCT
* *
19300021 GAGGTAGCAAGGAAGTAGACTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
64 GAGGTAGCAAGGAAGCAGACTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAATGGAGCAGATC
* * * ** * **
19300086 GAAAATGGCGAATCTCATGTTCCAAAGGTAGCAGGGGAGCAGATTTT
129 GAAAATAGAGAATCTCATCTTCCAAAGGTAGCAAAGGAGCAAATTGA
* *
19300133 AGCCACCAGCCTTATCTCTCTGAGGTAGCAAGAGAG-AAGGTTGAAGATTGTAG-AATCTTCCTG
1 AGCCACCAGCCTTATCTCTCTAAGGTAGCAAGAGAGCAA-GTTAAAGATTGTAGTAATCTTCCTG
*
19300196 AGGTAGCAAGGAAGCAGACTGAGGATTGTAGATCTTATCTCCCTAAGCAGTAATGGAGCAGATC-
65 AGGTAGCAAGGAAGCAGACTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAATGGAGCAGATCG
* * * *
19300260 AAAGATAGAGAATTTTATCTTCTC-AAGGTAGTAAAGGAGTAAATTGA
130 AAA-ATAGAGAATCTCATCTTC-CAAAGGTAGCAAAGGAGCAAATTGA
* *
19300307 AGCCACCTGCCTTATCTCCCTAA
1 AGCCACCAGCCTTATCTCTCTAA
19300330 AGTTGTAGTG
Statistics
Matches: 171, Mismatches: 23, Indels: 9
0.84 0.11 0.04
Matches are distributed among these distances:
173 3 0.02
174 119 0.70
175 1 0.01
176 2 0.01
177 46 0.27
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (175 bp):
AGCCACCAGCCTTATCTCTCTAAGGTAGCAAGAGAGCAAGTTAAAGATTGTAGTAATCTTCCTGA
GGTAGCAAGGAAGCAGACTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAATGGAGCAGATCGA
AAATAGAGAATCTCATCTTCCAAAGGTAGCAAAGGAGCAAATTGA
Found at i:19301882 original size:14 final size:14
Alignment explanation
Indices: 19301847--19301884 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
19301837 TATAAGATTC
*
19301847 ATTAT-TTGTTTTA
1 ATTATATTGTTTGA
19301860 ATATATATTGTTTGA
1 AT-TATATTGTTTGA
19301875 ATTATATTGT
1 ATTATATTGT
19301885 ATATATTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 2 0.09
14 11 0.50
15 9 0.41
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.61
Consensus pattern (14 bp):
ATTATATTGTTTGA
Found at i:19301931 original size:2 final size:2
Alignment explanation
Indices: 19301924--19301959 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
19301914 TATTTTTGAA
*
19301924 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19301960 TTTCTTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:19302443 original size:6 final size:6
Alignment explanation
Indices: 19302432--19302456 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19302422 TTATGAATTA
19302432 TTTATT TTTATT TTTATT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT T
19302457 ATTTTATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:19302444 original size:22 final size:20
Alignment explanation
Indices: 19302418--19302472 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 20
19302408 TTAAACTTTA
19302418 TATTTTATGAATTATTTATTTT
1 TATTTTATGAATTATTTA--TT
19302440 TATTTT-T--ATT-TTTATT
1 TATTTTATGAATTATTTATT
*
19302456 TATTTTATGATTTATTT
1 TATTTTATGAATTATTT
19302473 CAATTTTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 10
0.72 0.03 0.26
Matches are distributed among these distances:
16 8 0.29
17 1 0.04
18 4 0.14
19 5 0.18
20 3 0.11
21 1 0.04
22 6 0.21
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.73
Consensus pattern (20 bp):
TATTTTATGAATTATTTATT
Found at i:19302468 original size:12 final size:11
Alignment explanation
Indices: 19302430--19302472 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
19302420 TTTTATGAAT
19302430 TATTTATTTTTA
1 TATTTA-TTTTA
*
19302442 TTTTTATTTT-
1 TATTTATTTTA
19302452 TATTTATTTTA
1 TATTTATTTTA
19302463 TGATTTATTT
1 T-ATTTATTT
19302473 CAATTTTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.33
11 5 0.19
12 13 0.48
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (11 bp):
TATTTATTTTA
Found at i:19302478 original size:22 final size:22
Alignment explanation
Indices: 19302431--19302478 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
19302421 TTTATGAATT
* **
19302431 ATTTATTTTTATTTTTATTTTT
1 ATTTATTTTTATATTTATTTCA
19302453 ATTTA-TTTTATGATTTATTTCA
1 ATTTATTTTTAT-ATTTATTTCA
19302475 ATTT
1 ATTT
19302479 TTTGCATGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (22 bp):
ATTTATTTTTATATTTATTTCA
Found at i:19307954 original size:13 final size:13
Alignment explanation
Indices: 19307936--19307960 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19307926 ATTAAAACTA
19307936 TAATTAACTAAAT
1 TAATTAACTAAAT
19307949 TAATTAACTAAA
1 TAATTAACTAAA
19307961 GAACATGACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (13 bp):
TAATTAACTAAAT
Found at i:19310859 original size:60 final size:60
Alignment explanation
Indices: 19310724--19310862 Score: 156
Period size: 60 Copynumber: 2.3 Consensus size: 60
19310714 TTTAGTGTTA
* *
19310724 ACTGGGCCTTAGCCCATATCAATATTAATCTGGACCATAGCCCCTTACAGTAAAAGAGTAT
1 ACTGGGCCTT-GCCCATATCAATATCAATCTGGACCATAGCCCATTACAGTAAAAGAGTAT
* * * * **
19310785 ACTGGGCCTAGCCCATATCAGTATCAATCTGGGCCGTAGCCCTATTACAAGT-CGAGA-TAT
1 ACTGGGCCTTGCCCATATCAATATCAATCTGGACCATAGCCC-ATTAC-AGTAAAAGAGTAT
*
19310845 ATTGGGCCTTGCCCATAT
1 ACTGGGCCTTGCCCATAT
19310863 TAACACAGTT
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
60 47 0.71
61 16 0.24
62 3 0.05
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (60 bp):
ACTGGGCCTTGCCCATATCAATATCAATCTGGACCATAGCCCATTACAGTAAAAGAGTAT
Found at i:19310898 original size:19 final size:20
Alignment explanation
Indices: 19310855--19310910 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
19310845 ATTGGGCCTT
19310855 GCCCATATTAACACAGTTGG
1 GCCCATATTAACACAGTTGG
* *
19310875 GCCCATTTTAATACAGTT-G
1 GCCCATATTAACACAGTTGG
* *
19310894 GCCCATAATAAAACAGT
1 GCCCATATTAACACAGT
19310911 CTCATATGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (20 bp):
GCCCATATTAACACAGTTGG
Found at i:19313020 original size:12 final size:12
Alignment explanation
Indices: 19313005--19313029 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19312995 ACAGTAAATA
19313005 ATAAAAATTTTC
1 ATAAAAATTTTC
19313017 ATAAAAATTTTC
1 ATAAAAATTTTC
19313029 A
1 A
19313030 AACATACATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAAAAATTTTC
Found at i:19313080 original size:19 final size:18
Alignment explanation
Indices: 19313043--19313086 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
19313033 ATACATACAG
19313043 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
19313060 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
19313079 TACTAATT
1 TAATAATT
19313087 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:19316131 original size:63 final size:63
Alignment explanation
Indices: 19316006--19316232 Score: 260
Period size: 63 Copynumber: 3.6 Consensus size: 63
19315996 ACATCCTGCC
* * * *
19316006 ACACGGCCTAGGCACACGCCCATGTGCCTTGGCCGTGTGGTTTTTA-A-GTACAAACAGTAAGTT
1 ACACGGCCTGGGCACACGCCCGTGT-CCTTGGCCGTGTGGTTTTTATACCT-CAAATAGTAAGTT
* * * *
19316069 ACACGGCCTGGACACATGTCCGTGTCCCTGGCCGTGTGGTTTTTATACCTCAAATAGTAAGTT
1 ACACGGCCTGGGCACACGCCCGTGTCCTTGGCCGTGTGGTTTTTATACCTCAAATAGTAAGTT
* * ** * *
19316132 ACACGGCCTGGGCACACACCCATGTCCTTGGATGTGTGGTTTTTATACCCCAAATAGTGAGTT
1 ACACGGCCTGGGCACACGCCCGTGTCCTTGGCCGTGTGGTTTTTATACCTCAAATAGTAAGTT
* * * *
19316195 GCACAGCCTGGGTACACGCCCGTGTCTTTGGCCGTGTG
1 ACACGGCCTGGGCACACGCCCGTGTCCTTGGCCGTGTG
19316233 AACCCTGCAC
Statistics
Matches: 136, Mismatches: 26, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
62 19 0.14
63 116 0.85
64 1 0.01
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.27
Consensus pattern (63 bp):
ACACGGCCTGGGCACACGCCCGTGTCCTTGGCCGTGTGGTTTTTATACCTCAAATAGTAAGTT
Found at i:19320703 original size:21 final size:21
Alignment explanation
Indices: 19320656--19320710 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 21
19320646 AAAATTTATA
19320656 ATATGATTTATGAAAATCATAT
1 ATATGATTTAT-AAAATCATAT
19320678 -T-TGATTTA-ATAAATCATAT
1 ATATGATTTATA-AAATCATAT
*
19320697 ATATGATTTTTAAA
1 ATATGATTTATAAA
19320711 TTTATGCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
18 1 0.04
19 9 0.32
20 8 0.29
21 9 0.32
22 1 0.04
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (21 bp):
ATATGATTTATAAAATCATAT
Found at i:19323289 original size:24 final size:22
Alignment explanation
Indices: 19323261--19323315 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 22
19323251 AAATATAAAT
19323261 TTTAAATATTTGTAAGCAA-TTAA
1 TTTAAATATTTGTAA--AATTTAA
*
19323284 TATTAATTATTTGTAAAATTTAA
1 T-TTAAATATTTGTAAAATTTAA
19323307 TTTAAATAT
1 TTTAAATAT
19323316 ATAATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 9 0.32
23 6 0.21
24 13 0.46
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (22 bp):
TTTAAATATTTGTAAAATTTAA
Found at i:19333979 original size:2 final size:2
Alignment explanation
Indices: 19333974--19334029 Score: 71
Period size: 2 Copynumber: 28.5 Consensus size: 2
19333964 TGGTGTGTAT
* *
19333974 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TGA TA -A TC TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
19334015 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
19334030 GTTTTAATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
1 2 0.04
2 44 0.94
3 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:19335984 original size:54 final size:54
Alignment explanation
Indices: 19335886--19336013 Score: 136
Period size: 54 Copynumber: 2.4 Consensus size: 54
19335876 CAAAGCTTGC
19335886 GACATGGCCGTGTGACCCAAGTTAGTGAGTTACAAGGGCTGAGACACGGGTTGA
1 GACATGGCCGTGTGACCCAAGTTAGTGAGTTACAAGGGCTGAGACACGGGTTGA
* * * * *
19335940 GACATGGTCGTGTG-CCTCAAGTCT-GTGAGTTACATGGG-TAGAGACTCGGGCTGG
1 GACATGGCCGTGTGACC-CAAGT-TAGTGAGTTACAAGGGCT-GAGACACGGGTTGA
* * *
19335994 GACACGGCCATGTGCCCCAA
1 GACATGGCCGTGTGACCCAA
19336014 CTTTGAAAGT
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
53 3 0.05
54 56 0.90
55 3 0.05
ACGTcount: A:0.23, C:0.22, G:0.34, T:0.21
Consensus pattern (54 bp):
GACATGGCCGTGTGACCCAAGTTAGTGAGTTACAAGGGCTGAGACACGGGTTGA
Found at i:19340963 original size:38 final size:38
Alignment explanation
Indices: 19340921--19341080 Score: 207
Period size: 38 Copynumber: 4.2 Consensus size: 38
19340911 GCAAGCTATA
19340921 TGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
1 TGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
19340959 TGCTGGTAA-TATATCCGGGTTAAATCCCGCAGGCTTCG
1 TGCTGG-AATTATATCCGGGTTAAATCCCGCAGGCTTCG
* * *
19340997 TACTGGTATTATATCCGGGTTAAATCCCGCAGG-TCTAG
1 TGCTGGAATTATATCCGGGTTAAATCCCGCAGGCT-TCG
* * * *
19341035 TGCTGGTATTATATCTGAGTTTAAAGTCCCGTAGGCTTCG
1 TGCTGGAATTATATCCG-GGTTAAA-TCCCGCAGGCTTCG
19341075 TGCTGG
1 TGCTGG
19341081 TGTTATGTTT
Statistics
Matches: 108, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
37 2 0.02
38 81 0.75
39 8 0.07
40 16 0.15
41 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (38 bp):
TGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
Found at i:19342748 original size:64 final size:64
Alignment explanation
Indices: 19342644--19342774 Score: 253
Period size: 64 Copynumber: 2.0 Consensus size: 64
19342634 TTATCAGAAG
*
19342644 CAATGCCCTGAATCACAAGATATCTAAGAAAGATTTTATTCCCTTTATTGTGTGAACACAACAT
1 CAATGCCCTGAATCACAAGATATCTAAGAAAGATTATATTCCCTTTATTGTGTGAACACAACAT
19342708 CAATGCCCTGAATCACAAGATATCTAAGAAAGATTATATTCCCTTTATTGTGTGAACACAACAT
1 CAATGCCCTGAATCACAAGATATCTAAGAAAGATTATATTCCCTTTATTGTGTGAACACAACAT
19342772 CAA
1 CAA
19342775 CTAATGAATT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (64 bp):
CAATGCCCTGAATCACAAGATATCTAAGAAAGATTATATTCCCTTTATTGTGTGAACACAACAT
Found at i:19345301 original size:23 final size:23
Alignment explanation
Indices: 19345275--19345322 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
19345265 GTCATAATTT
*
19345275 AAAATTTTAACTATGTAAAAAAC
1 AAAATTTTAACTATATAAAAAAC
*
19345298 AAAATTTTAACTTTATAAAAAAC
1 AAAATTTTAACTATATAAAAAAC
19345321 AA
1 AA
19345323 CTGTGATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.31
Consensus pattern (23 bp):
AAAATTTTAACTATATAAAAAAC
Found at i:19350150 original size:20 final size:22
Alignment explanation
Indices: 19350121--19350160 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
19350111 ATTGATTTAT
*
19350121 GGAAATTATA-AT-TATTATTA
1 GGAAAATATATATATATTATTA
19350141 GGAAAATATATATATATTAT
1 GGAAAATATATATATATTAT
19350161 CGTATTTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 2 0.12
22 6 0.35
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.42
Consensus pattern (22 bp):
GGAAAATATATATATATTATTA
Found at i:19352656 original size:22 final size:22
Alignment explanation
Indices: 19352631--19352672 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
19352621 ATTCCCCACA
*
19352631 GGAAGTGTAGGGATGGATGGAG
1 GGAAGTGCAGGGATGGATGGAG
*
19352653 GGAAGTGCAGGGTTGGATGG
1 GGAAGTGCAGGGATGGATGG
19352673 GGTTATCATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.02, G:0.55, T:0.19
Consensus pattern (22 bp):
GGAAGTGCAGGGATGGATGGAG
Found at i:19352909 original size:62 final size:61
Alignment explanation
Indices: 19352744--19352918 Score: 180
Period size: 61 Copynumber: 2.9 Consensus size: 61
19352734 CTAACTGTGT
* * * * * * *
19352744 TGATATGGGCAAGACCCAATATA-TCTCGA-CTTGTAATAGGGCTACGGCCCAGACTGATAT
1 TGATATGGGCTAGGCCCAGTATACTCT-GATATTGTAATAGGGCTATGGCCCAGACTAATAC
* *
19352804 TGATATGGGCTAGGCCCAGTATGCTCTGATATTGTAATAGGGCTATGGCCCAGATTAATAC
1 TGATATGGGCTAGGCCCAGTATACTCTGATATTGTAATAGGGCTATGGCCCAGACTAATAC
*
19352865 TGATATGGGCTAAGGCCCAGT-TAACTCTGAT-TTCTGAATAGGGCT-TAGGCCCAG
1 TGATATGGGCT-AGGCCCAGTAT-ACTCTGATATTGT-AATAGGGCTAT-GGCCCAG
19352919 TAAAGCTTGA
Statistics
Matches: 98, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
60 21 0.21
61 45 0.46
62 32 0.33
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (61 bp):
TGATATGGGCTAGGCCCAGTATACTCTGATATTGTAATAGGGCTATGGCCCAGACTAATAC
Found at i:19359142 original size:19 final size:19
Alignment explanation
Indices: 19359120--19359159 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
19359110 GAAGAAAATG
* * *
19359120 AAAAATAAAGATAGAAAGA
1 AAAAAGAAAGAGAAAAAGA
19359139 AAAAAGAAAGAGAAAAAGA
1 AAAAAGAAAGAGAAAAAGA
19359158 AA
1 AA
19359160 GAAAAAGGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (19 bp):
AAAAAGAAAGAGAAAAAGA
Found at i:19359156 original size:12 final size:11
Alignment explanation
Indices: 19359132--19359165 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
19359122 AAATAAAGAT
19359132 AGAAAGAAAAA
1 AGAAAGAAAAA
19359143 AGAAAGAGAAAA
1 AGAAAGA-AAAA
19359155 AGAAAGAAAAA
1 AGAAAGAAAAA
19359166 GGTTGAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AGAAAGAAAAA
Done.