Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 47 of 171
Found at i:19915641 original size:4 final size:4
Alignment explanation
Indices: 19915634--19915659 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
19915624 AATAAATAAT
19915634 AAAC AAAC AAAC AAAC AAAC AAAC AA
1 AAAC AAAC AAAC AAAC AAAC AAAC AA
19915660 TAAAAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:19915734 original size:12 final size:12
Alignment explanation
Indices: 19915717--19915764 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
19915707 TCATTAATAA
19915717 ATAAACGAGCTT
1 ATAAACGAGCTT
**
19915729 ATAAACGAGCCA
1 ATAAACGAGCTT
*
19915741 ATAAACGCGCTT
1 ATAAACGAGCTT
*
19915753 TTAAACGAGCTT
1 ATAAACGAGCTT
19915765 GTTCATGAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.23
Consensus pattern (12 bp):
ATAAACGAGCTT
Found at i:19915752 original size:24 final size:24
Alignment explanation
Indices: 19915716--19915762 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
19915706 ATCATTAATA
19915716 AATAAACGAGCTTATAAACGAGCC
1 AATAAACGAGCTTATAAACGAGCC
* *
19915740 AATAAACGCGCTTTTAAACGAGC
1 AATAAACGAGCTTATAAACGAGC
19915763 TTGTTCATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (24 bp):
AATAAACGAGCTTATAAACGAGCC
Found at i:19931355 original size:18 final size:20
Alignment explanation
Indices: 19931325--19931361 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
19931315 TTTTTTTAAA
19931325 TTTTTAATTTTTAA-AAAAC
1 TTTTTAATTTTTAATAAAAC
19931344 TTTTTAA-TTTTAATAAAA
1 TTTTTAATTTTTAATAAAA
19931362 TTATAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTTAATTTTTAATAAAAC
Found at i:19937926 original size:2 final size:2
Alignment explanation
Indices: 19937919--19937954 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
19937909 TTATATTCAA
19937919 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19937955 TGAGTTTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19938040 original size:20 final size:20
Alignment explanation
Indices: 19938015--19938059 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
19938005 TATTTTTTTG
* *
19938015 AAATGGAAACTACATTGTTA
1 AAATGGAAACAAAATTGTTA
* *
19938035 AAATGGGAACAAAATTGTTG
1 AAATGGAAACAAAATTGTTA
19938055 AAATG
1 AAATG
19938060 AACGTGTATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.27
Consensus pattern (20 bp):
AAATGGAAACAAAATTGTTA
Found at i:19940570 original size:2 final size:2
Alignment explanation
Indices: 19940504--19940551 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
19940494 ACTAAACATA
* *
19940504 TC TC TC TC CC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19940546 TC TC TC
1 TC TC TC
19940552 ATGGATTCTC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
TC
Found at i:19945619 original size:16 final size:17
Alignment explanation
Indices: 19945569--19945617 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
19945559 CATATACAGC
*
19945569 TTTTTATTGCATGAAAT
1 TTTTTATTGCACGAAAT
19945586 TTTTTATTGCACGAAAT
1 TTTTTATTGCACGAAAT
19945603 TTTTTATTGCACGAA
1 TTTTTATTGCACGAA
19945618 TTAATTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.49
Consensus pattern (17 bp):
TTTTTATTGCACGAAAT
Found at i:19945625 original size:16 final size:17
Alignment explanation
Indices: 19945572--19945626 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
19945562 ATACAGCTTT
* **
19945572 TTATTGCATGAAATTTT
1 TTATTGCACGAAATTAA
**
19945589 TTATTGCACGAAATTTT
1 TTATTGCACGAAATTAA
19945606 TTATTGCACG-AATTAA
1 TTATTGCACGAAATTAA
19945622 TTATT
1 TTATT
19945627 TTTTTTAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
16 9 0.26
17 26 0.74
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.49
Consensus pattern (17 bp):
TTATTGCACGAAATTAA
Found at i:19962060 original size:11 final size:11
Alignment explanation
Indices: 19962044--19962068 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19962034 GTTTTTAATT
19962044 AAAAAGAAAAG
1 AAAAAGAAAAG
19962055 AAAAAGAAAAG
1 AAAAAGAAAAG
19962066 AAA
1 AAA
19962069 CCTCTCTGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:19967304 original size:5 final size:5
Alignment explanation
Indices: 19967294--19967330 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
19967284 TCGATTGAGC
19967294 AGAGG AGAGG AGAGG AGAGG AGAGG AGAGG AG-GG AGA
1 AGAGG AGAGG AGAGG AGAGG AGAGG AGAGG AGAGG AGA
19967331 AGAATGTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (5 bp):
AGAGG
Found at i:19970712 original size:21 final size:22
Alignment explanation
Indices: 19970673--19970713 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
19970663 AGTTTTCGTA
*
19970673 TTTTTATTTTTAAGGATTTATT
1 TTTTTATTTTTAAGAATTTATT
*
19970695 TTTTTATTTTT-CGAATTTA
1 TTTTTATTTTTAAGAATTTA
19970714 AAATTTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.68
Consensus pattern (22 bp):
TTTTTATTTTTAAGAATTTATT
Found at i:19977252 original size:20 final size:20
Alignment explanation
Indices: 19977229--19977266 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19977219 AAATAATAAA
19977229 AATCAAACAAAAAC-ATAATT
1 AATCAAA-AAAAACTATAATT
*
19977249 AATCCAAAAAAACTATAA
1 AATCAAAAAAAACTATAA
19977267 AATACACGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.66, C:0.16, G:0.00, T:0.18
Consensus pattern (20 bp):
AATCAAAAAAAACTATAATT
Found at i:19978081 original size:29 final size:29
Alignment explanation
Indices: 19978048--19978107 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
19978038 TTTAGTCTAA
* *
19978048 TGTGC-ATTTCTATACATGAACTTTGAATT
1 TGTGCAATTT-TATACATAAAATTTGAATT
*
19978077 TGTGCAATTTTATACATAAAATTTTAATT
1 TGTGCAATTTTATACATAAAATTTGAATT
19978106 TG
1 TG
19978108 ATGTAATTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 23 0.85
30 4 0.15
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.47
Consensus pattern (29 bp):
TGTGCAATTTTATACATAAAATTTGAATT
Found at i:19978265 original size:31 final size:31
Alignment explanation
Indices: 19978230--19978321 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
19978220 ATTAAAAGTG
*
19978230 TATAATTGAATCAAAATTAAAGTTTCATGTA
1 TATAATTGAATCAAAATCAAAGTTTCATGTA
* * * *
19978261 TATAATTGAACCACAATCAAAATTTCATGTG
1 TATAATTGAATCAAAATCAAAGTTTCATGTA
* * *
19978292 TGTAATTG-TTCTAAATCAAAGTTT-ATGTA
1 TATAATTGAATCAAAATCAAAGTTTCATGTA
19978321 T
1 T
19978322 CAAATTACAT
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 5 0.10
30 11 0.22
31 33 0.67
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (31 bp):
TATAATTGAATCAAAATCAAAGTTTCATGTA
Found at i:19982904 original size:20 final size:22
Alignment explanation
Indices: 19982861--19982904 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
19982851 CTCAATTTGG
19982861 AAATGACTAATATACATTTCTATT
1 AAATGACTAATAT--ATTTCTATT
19982885 AAATGACTAATAT-TTT-TATT
1 AAATGACTAATATATTTCTATT
19982905 TTGATGATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.20
21 3 0.15
24 13 0.65
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (22 bp):
AAATGACTAATATATTTCTATT
Found at i:19987116 original size:124 final size:121
Alignment explanation
Indices: 19986896--19987266 Score: 438
Period size: 124 Copynumber: 3.0 Consensus size: 121
19986886 AAAAAGGTGC
* * * ** *
19986896 ATGACCAACACGAAAAAATTTAATTTTTTTATTAGATAAATAAGTAGTGTCAACCAATGCATGGC
1 ATGACCAACACGAAAAAATTTAATTTTTTTATCAGATAAATAGGTGGTGTCGGCC-ATGCATGGT
* *
19986961 CAACACAAAAAAAAAATTAAATTTTTTTATTAGATAAAAAGGTGGTGTTGGTCATGAAA
65 CAACAC-CAAAAAAATTTAAATTTTTTTATTAGATAAAAAGGTGGTGTTGGTCATG-AA
*
19987020 ATGACCAACACGAAAAAATTTAATTTTTTTATCAGATAAATAGGTGGTGTCGGTCATTGCATGGT
1 ATGACCAACACGAAAAAATTTAATTTTTTTATCAGATAAATAGGTGGTGTCGGCCA-TGCATGGT
* * *
19987085 CAACACCAAAAAAATTTAAAATTTTTTTATTAGATAAAAA-ATGGTGTCGGTCATGCA
65 CAACACCAAAAAAATTT-AAATTTTTTTATTAGATAAAAAGGTGGTGTTGGTCATGAA
** * * * *
19987142 ATGGTCAATACCAAAAAATTTAAATTTTTTATCAGATAAAAAGGTGGTGTGGTGTCGGCCATGCA
1 ATGACCAACACGAAAAAATTTAATTTTTTTATCAGAT--AAA--TAG-GTGGTGTCGGCCATGC-
* * *
19987207 ATGATCAACACCAAAAAAATTTGAATTTTTTTTATCAGATAAAAAGGTGGTGTTGGTCAT
60 ATGGTCAACACCAAAAAAATTT-AAATTTTTTTATTAGATAAAAAGGTGGTGTTGGTCAT
19987267 TGCAATTTGA
Statistics
Matches: 213, Mismatches: 25, Indels: 14
0.85 0.10 0.06
Matches are distributed among these distances:
122 33 0.15
123 23 0.11
124 87 0.41
126 5 0.02
127 53 0.25
128 12 0.06
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (121 bp):
ATGACCAACACGAAAAAATTTAATTTTTTTATCAGATAAATAGGTGGTGTCGGCCATGCATGGTC
AACACCAAAAAAATTTAAATTTTTTTATTAGATAAAAAGGTGGTGTTGGTCATGAA
Found at i:19987134 original size:62 final size:61
Alignment explanation
Indices: 19986908--19987266 Score: 336
Period size: 63 Copynumber: 5.8 Consensus size: 61
19986898 GACCAACACG
* * *** * *
19986908 AAAAAATTT-AATTTTTTTATTAGATAAATAA-GTAGTGTCAACCAATGCATGGCCAACACAAA
1 AAAAAATTTAAATTTTTTTATCAGATAAA-AAGGTGGTGTCGGTC-ATGCATGGTCAACAC-CA
* * * * ** *
19986970 AAAAAAATTAAATTTTTTTATTAGATAAAAAGGTGGTGTTGGTCATGAAAATGACCAACA-CG
1 AAAAAATTTAAATTTTTTTATCAGATAAAAAGGTGGTGTCGGTCATG--CATGGTCAACACCA
*
19987032 AAAAAATTT-AATTTTTTTATCAGATAAATAGGTGGTGTCGGTCATTGCATGGTCAACACCA
1 AAAAAATTTAAATTTTTTTATCAGATAAAAAGGTGGTGTCGGTCA-TGCATGGTCAACACCA
* * *
19987093 AAAAAATTTAAAATTTTTTTATTAGATAAAAA-ATGGTGTCGGTCATGCAATGGTCAATACC-
1 AAAAAATTT-AAATTTTTTTATCAGATAAAAAGGTGGTGTCGGTCATGC-ATGGTCAACACCA
* *
19987154 AAAAAATTTAAA-TTTTTTATCAGATAAAAAGGTGGTGTGGTGTCGGCCATGCAATGATCAACAC
1 AAAAAATTTAAATTTTTTTATCAGATAAAAA----G-GTGGTGTCGGTCATGC-ATGGTCAACAC
19987218 CA
60 CA
* *
19987220 AAAAAATTTGAATTTTTTTTATCAGATAAAAAGGTGGTGTTGGTCAT
1 AAAAAATTT-AAATTTTTTTATCAGATAAAAAGGTGGTGTCGGTCAT
19987267 TGCAATTTGA
Statistics
Matches: 249, Mismatches: 30, Indels: 35
0.79 0.10 0.11
Matches are distributed among these distances:
59 17 0.07
60 11 0.04
61 54 0.22
62 46 0.18
63 57 0.23
64 10 0.04
65 25 0.10
66 9 0.04
67 2 0.01
68 18 0.07
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.33
Consensus pattern (61 bp):
AAAAAATTTAAATTTTTTTATCAGATAAAAAGGTGGTGTCGGTCATGCATGGTCAACACCA
Found at i:19987240 original size:127 final size:122
Alignment explanation
Indices: 19986896--19987503 Score: 420
Period size: 124 Copynumber: 5.1 Consensus size: 122
19986886 AAAAAGGTGC
* * * * * ** * **
19986896 ATGACCAACACGAAAAAATTTAATTTTTTTATTAGATAAATAAGTAGTGTCAACCAATGCATGGC
1 ATGACCAACACCAAAAAATTTAAATTTTTTATCAGATAAATAGGTGGTGTCGGCCATTGCATGAT
* * *
19986961 CAACACAAAAAAAAAATTAAATTTTTTTATTAGATAAAAAGGTGGTGTTGGTCATGAAA
66 CAACAC-CAAAAAAATTTAAATTTTTTTATTAGATAAAAAGGTGGTGTTGGTCATG-CA
* * * *
19987020 ATGACCAACACGAAAAAATTTAATTTTTTTATCAGATAAATAGGTGGTGTCGGTCATTGCATGGT
1 ATGACCAACACCAAAAAATTTAAATTTTTTATCAGATAAATAGGTGGTGTCGGCCATTGCATGAT
* *
19987085 CAACACCAAAAAAATTTAAAATTTTTTTATTAGATAAAAA-ATGGTGTCGGTCATGCA
66 CAACACCAAAAAAATTT-AAATTTTTTTATTAGATAAAAAGGTGGTGTTGGTCATGCA
** * *
19987142 ATGGTCAATACCAAAAAATTTAAATTTTTTATCAGATAAAAAGGTGGTGTGGTGTCGGCCA-TGC
1 ATGACCAACACCAAAAAATTTAAATTTTTTATCAGAT--AAA--TAG-GTGGTGTCGGCCATTGC
* *
19987206 AATGATCAACACCAAAAAAATTTGAATTTTTTTTATCAGATAAAAAGGTGGTGTTGGTCAT---
61 -ATGATCAACACCAAAAAAATTT-AAATTTTTTTATTAGATAAAAAGGTGGTGTTGGTCATGCA
* * * * * *
19987267 -TG--------C---AATTTGAATTTTTTTATCAAATAAAAAGGTGGTGTC-G--A--CCAT--T
1 ATGACCAACACCAAAAAATTTAAATTTTTTATCAGATAAATAGGTGGTGTCGGCCATTGCATGAT
* ** * *
19987313 --------AAAAAATTTAAATTTTTTTATCAGATAAAAAAAATGGTGTCGGCCATGCA
66 CAACACCAAAAAAATTTAAATTTTTTTATTAGAT-AAAAAGGTGGTGTTGGTCATGCA
* * * **
19987363 ATGACCAATACCAAAAAAATTTAAATTTTTTATCAGATAAAAAGGTGGCGTCAACCA-TGCAATG
1 ATGACCAACACC-AAAAAATTTAAATTTTTTATCAGATAAATAGGTGGTGTCGGCCATTGC-ATG
* * * * *
19987427 ACCAACA-CAAAAAAATTTTAAATTTTTTTATCAGATAAAAAAGTGGTGTCGGCCATGCA
64 ATCAACACCAAAAAAA-TTTAAATTTTTTTATTAGATAAAAAGGTGGTGTTGGTCATGCA
* *
19987486 ATGGCTAACACCAAAAAA
1 ATGACCAACACCAAAAAA
19987504 AAATTGTTCA
Statistics
Matches: 394, Mismatches: 50, Indels: 82
0.75 0.10 0.16
Matches are distributed among these distances:
92 16 0.04
93 25 0.06
97 2 0.01
101 1 0.00
103 2 0.01
104 1 0.00
105 2 0.01
107 1 0.00
108 8 0.02
109 32 0.08
111 3 0.01
112 1 0.00
113 19 0.05
114 2 0.01
116 1 0.00
122 39 0.10
123 59 0.15
124 110 0.28
126 5 0.01
127 53 0.13
128 12 0.03
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (122 bp):
ATGACCAACACCAAAAAATTTAAATTTTTTATCAGATAAATAGGTGGTGTCGGCCATTGCATGAT
CAACACCAAAAAAATTTAAATTTTTTTATTAGATAAAAAGGTGGTGTTGGTCATGCA
Found at i:19987327 original size:47 final size:47
Alignment explanation
Indices: 19987220--19987343 Score: 153
Period size: 45 Copynumber: 2.7 Consensus size: 47
19987210 ATCAACACCA
* * **
19987220 AAAAAATTTGAATTTTTTTTATCAGATAAAAAGGTGGTGTTGGTCATT
1 AAAAAATTT-AAATTTTTTTATCAGATAAAAAGGTGGTGTCGACCATT
** * *
19987268 --GCAATTTGAATTTTTTTATCAAATAAAAAGGTGGTGTCGACCATT
1 AAAAAATTTAAATTTTTTTATCAGATAAAAAGGTGGTGTCGACCATT
19987313 AAAAAATTTAAATTTTTTTATCAGATAAAAA
1 AAAAAATTTAAATTTTTTTATCAGATAAAAA
19987344 AAATGGTGTC
Statistics
Matches: 62, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
45 32 0.52
46 5 0.08
47 25 0.40
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.40
Consensus pattern (47 bp):
AAAAAATTTAAATTTTTTTATCAGATAAAAAGGTGGTGTCGACCATT
Found at i:19987421 original size:61 final size:62
Alignment explanation
Indices: 19987313--19987504 Score: 280
Period size: 62 Copynumber: 3.1 Consensus size: 62
19987303 GTCGACCATT
* *
19987313 AAAAAATTTAAATTTTTTTATCAGATAAAAAAAATGGTGTCGGCCATGCAATGACCAATACCA
1 AAAAAATTTAAATTTTTTTATCAGAT-AAAAAAGTGGTGTCGGCCATGCAATGACCAACACCA
* * **
19987376 AAAAAATTTAAA-TTTTTTATCAGATAAAAAGGTGGCGTCAACCATGCAATGACCAACA-CA
1 AAAAAATTTAAATTTTTTTATCAGATAAAAAAGTGGTGTCGGCCATGCAATGACCAACACCA
* *
19987436 AAAAAATTTTAAATTTTTTTATCAGATAAAAAAGTGGTGTCGGCCATGCAATGGCTAACACCA
1 AAAAAA-TTTAAATTTTTTTATCAGATAAAAAAGTGGTGTCGGCCATGCAATGACCAACACCA
19987499 AAAAAA
1 AAAAAA
19987505 AATTGTTCAA
Statistics
Matches: 114, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
60 8 0.07
61 33 0.29
62 53 0.46
63 20 0.18
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.27
Consensus pattern (62 bp):
AAAAAATTTAAATTTTTTTATCAGATAAAAAAGTGGTGTCGGCCATGCAATGACCAACACCA
Found at i:19991201 original size:29 final size:28
Alignment explanation
Indices: 19991169--19991227 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
19991159 ATTAAATAAC
*
19991169 ATATT-TTTAAAATTTTTGGATTTTTTAAA
1 ATATTCTTCAAAATTTTT--ATTTTTTAAA
* *
19991198 ATATTCTTCATAATTTTTATTTTTTTAA
1 ATATTCTTCAAAATTTTTATTTTTTAAA
19991226 AT
1 AT
19991228 GAATTATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 11 0.42
29 5 0.19
30 10 0.38
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.61
Consensus pattern (28 bp):
ATATTCTTCAAAATTTTTATTTTTTAAA
Found at i:19993411 original size:30 final size:30
Alignment explanation
Indices: 19993373--19993578 Score: 183
Period size: 30 Copynumber: 6.9 Consensus size: 30
19993363 AAGAATTCGG
*
19993373 GGTTAAAATGTAATTTTGAAAAAGTTTAGA
1 GGTTAAAATGTAATTTTGGAAAAGTTTAGA
* * * *
19993403 GGTAAAAATATAATTTTGGAGAAGTTT-GG
1 GGTTAAAATGTAATTTTGGAAAAGTTTAGA
* * *
19993432 GGTTAAAATGTAATTTTAGAGAAGTGTAG-
1 GGTTAAAATGTAATTTTGGAAAAGTTTAGA
* *
19993461 GAGTCAAAAAATGTAGAATTTT--AAAA-TTTAGG
1 G-GT--TAAAATGT--AATTTTGGAAAAGTTTAGA
* *
19993493 GGTTAAAATGTGAA-TTTGGAGAAGTTTGGA
1 GGTTAAAATGT-AATTTTGGAAAAGTTTAGA
*
19993523 GGTTAAAATGCAATTTTGGAAAAGTTTA-A
1 GGTTAAAATGTAATTTTGGAAAAGTTTAGA
19993552 GGCTTAAAATGTAATTTTGGAAAAGTT
1 GG-TTAAAATGTAATTTTGGAAAAGTT
19993579 CAAGGACTTA
Statistics
Matches: 144, Mismatches: 20, Indels: 24
0.77 0.11 0.13
Matches are distributed among these distances:
27 3 0.02
28 3 0.02
29 40 0.28
30 75 0.52
31 6 0.04
32 11 0.08
34 6 0.04
ACGTcount: A:0.40, C:0.01, G:0.24, T:0.34
Consensus pattern (30 bp):
GGTTAAAATGTAATTTTGGAAAAGTTTAGA
Found at i:19993435 original size:59 final size:59
Alignment explanation
Indices: 19993371--19993578 Score: 176
Period size: 59 Copynumber: 3.5 Consensus size: 59
19993361 CGAAGAATTC
*
19993371 GGGGTTAAAATGTAATTTTGAAAAAGTTTAGAGGTAAAAATATAATTTTGGAGAAGTTT-
1 GGGGTTAAAATGTAATTTTGAAAAAGTTTAGAGGTAAAAATACAATTTTGGA-AAGTTTA
* * * *
19993430 GGGGTTAAAATGTAATTTT-AGAGAAGTGTAG-GAGTCAAAAAATGTAGAATTTT--AAAATTTA
1 GGGGTTAAAATGTAATTTTGA-AAAAGTTTAGAG-GT--AAAAA--TACAATTTTGGAAAGTTTA
* * * * *
19993491 GGGGTTAAAATGTGAA-TTTGGAGAAGTTTGGAGGTTAAAATGCAATTTTGGAAAAGTTTA
1 GGGGTTAAAATGT-AATTTTGAAAAAGTTTAGAGGTAAAAATACAATTTTGG-AAAGTTTA
* * *
19993551 AGGCTTAAAATGTAATTTTGGAAAAGTT
1 GGGGTTAAAATGTAATTTTGAAAAAGTT
19993579 CAAGGACTTA
Statistics
Matches: 121, Mismatches: 14, Indels: 27
0.75 0.09 0.17
Matches are distributed among these distances:
57 7 0.06
58 2 0.02
59 35 0.29
60 34 0.28
61 32 0.26
62 3 0.02
63 8 0.07
ACGTcount: A:0.39, C:0.01, G:0.25, T:0.34
Consensus pattern (59 bp):
GGGGTTAAAATGTAATTTTGAAAAAGTTTAGAGGTAAAAATACAATTTTGGAAAGTTTA
Found at i:19994532 original size:18 final size:18
Alignment explanation
Indices: 19994509--19994551 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
19994499 GACTTGCTTT
*
19994509 TTTATTATTTATTAAGTA
1 TTTATTATTTAATAAGTA
**
19994527 TTTATTATTTAATATTTA
1 TTTATTATTTAATAAGTA
19994545 TTTATTA
1 TTTATTA
19994552 AAACGTCTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTATTATTTAATAAGTA
Found at i:19994534 original size:14 final size:14
Alignment explanation
Indices: 19994513--19994552 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
19994503 TGCTTTTTTA
19994513 TTATTTATTAAGTAT
1 TTATTTATTAA-TAT
19994528 TTA-TTATTTAATAT
1 TTATTTA-TTAATAT
19994542 TTATTTATTAA
1 TTATTTATTAA
19994553 AACGTCTCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (14 bp):
TTATTTATTAATAT
Found at i:19995495 original size:29 final size:29
Alignment explanation
Indices: 19995463--19995660 Score: 128
Period size: 29 Copynumber: 6.8 Consensus size: 29
19995453 GGTTGAAATT
*
19995463 GGGTCAAAATGG-GATTTTGGAAAGTTCGA
1 GGGT-AAAATGGTAATTTTGGAAAGTTCGA
*
19995492 GGGTAAAATGGTAATTTATGGTAAA-ATCG-
1 GGGTAAAATGGTAATTT-TGG-AAAGTTCGA
* *
19995521 GGGTTAAAAATGG-AATTTTAGAAAGTTTGA
1 GGG-T-AAAATGGTAATTTTGGAAAGTTCGA
19995551 GGGTAAAATGGTAATTTTGGTGAAA--TCGA
1 GGGTAAAATGGTAATTTT-G-GAAAGTTCGA
* ** *
19995580 GGTTAAAAATGG-AATTTTAAAAAGTTTG-
1 GGGT-AAAATGGTAATTTTGGAAAGTTCGA
**
19995608 GGGATAAAATGGTAATTTT-GATAAAATCGA
1 GGG-TAAAATGGTAATTTTGGA-AAGTTCGA
*
19995638 GGGTAAAAAT-GAAATTTTGGAAA
1 GGGT-AAAATGGTAATTTTGGAAA
19995661 ACTTAGGGGT
Statistics
Matches: 133, Mismatches: 17, Indels: 38
0.71 0.09 0.20
Matches are distributed among these distances:
27 3 0.02
28 27 0.20
29 57 0.43
30 32 0.24
31 14 0.11
ACGTcount: A:0.39, C:0.03, G:0.27, T:0.31
Consensus pattern (29 bp):
GGGTAAAATGGTAATTTTGGAAAGTTCGA
Found at i:19995604 original size:58 final size:58
Alignment explanation
Indices: 19995439--19995660 Score: 279
Period size: 58 Copynumber: 3.8 Consensus size: 58
19995429 ACCAGGGGGC
* * * * * *
19995439 AAAATGGTAATTTTGGTTGAAATTG-GG-TCAAAATGGGATTTTGGAAAGTTCGAGGGT
1 AAAATGGTAATTTTGG-TAAAATCGAGGTTAAAAATGGAATTTTAGAAAGTTTGAGGGT
*
19995496 AAAATGGTAATTTATGGTAAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTTGAGGGT
1 AAAATGGTAATTT-TGGTAAAATCGAGGTTAAAAATGGAATTTTAGAAAGTTTGAGGGT
* *
19995555 AAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAAGTTTG-GGGAT
1 AAAATGGTAATTTTGGTAAAATCGAGGTTAAAAATGGAATTTTAGAAAGTTTGAGGG-T
* * * *
19995613 AAAATGGTAATTTTGATAAAATCGAGGGTAAAAATGAAATTTTGGAAA
1 AAAATGGTAATTTTGGTAAAATCGAGGTTAAAAATGGAATTTTAGAAA
19995661 ACTTAGGGGT
Statistics
Matches: 146, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
57 22 0.15
58 85 0.58
59 39 0.27
ACGTcount: A:0.39, C:0.02, G:0.27, T:0.32
Consensus pattern (58 bp):
AAAATGGTAATTTTGGTAAAATCGAGGTTAAAAATGGAATTTTAGAAAGTTTGAGGGT
Found at i:19995671 original size:116 final size:115
Alignment explanation
Indices: 19995434--19995683 Score: 294
Period size: 116 Copynumber: 2.2 Consensus size: 115
19995424 TGGATACCAG
* * * * **
19995434 GGGGCAAAATGGTAATTTTGGTTGAAATTGGGTCAAAATGGGATTTTGGAAAGTTCGAGGGTAAA
1 GGGGTAAAATGGTAATTTTGGTTGAAATCGGGTAAAAATGGAATTTTAAAAAGTTCGAGGGTAAA
* * * *
19995499 ATGGTAATTTATGGTAAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTT
66 ATGGTAATTTATGATAAAATCGGGGTTAAAAATGAAATTTTAGAAACTTA
*
19995549 GAGGGTAAAATGGTAATTTTGG-TGAAATCGAGGTTAAAAATGGAATTTTAAAAAGTTTG-GGGA
1 G-GGGTAAAATGGTAATTTTGGTTGAAATCG-GG-TAAAAATGGAATTTTAAAAAGTTCGAGGG-
*
19995612 TAAAATGGTAATTT-TGATAAAATCGAGGG-TAAAAATGAAATTTTGGAAAACTTA
62 TAAAATGGTAATTTATGATAAAATCG-GGGTTAAAAATGAAATTTTAG-AAACTTA
*
19995666 GGGGTAAAA-AGTAATTTT
1 GGGGTAAAATGGTAATTTT
19995684 TAGAAAATTT
Statistics
Matches: 116, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
115 16 0.14
116 57 0.49
117 43 0.37
ACGTcount: A:0.38, C:0.03, G:0.27, T:0.32
Consensus pattern (115 bp):
GGGGTAAAATGGTAATTTTGGTTGAAATCGGGTAAAAATGGAATTTTAAAAAGTTCGAGGGTAAA
ATGGTAATTTATGATAAAATCGGGGTTAAAAATGAAATTTTAGAAACTTA
Found at i:19995674 original size:58 final size:57
Alignment explanation
Indices: 19995434--19995683 Score: 258
Period size: 58 Copynumber: 4.3 Consensus size: 57
19995424 TGGATACCAG
* * * * * * *
19995434 GGGGCAAAATGGTAATTTTGGTTGAAAT--TGGGTCAAAATGGGATTTTGGAAAGTTC
1 GGGGTAAAATGGTAATTTTGG-TAAAATCGAGGGTAAAAATGGAATTTTGAAAAGTTT
19995490 GAGGGTAAAATGGTAATTTATGGTAAAATCG-GGGTTAAAAATGGAATTTT-AGAAAGTTT
1 G-GGGTAAAATGGTAATTT-TGGTAAAATCGAGGG-TAAAAATGGAATTTTGA-AAAGTTT
* * *
19995549 GAGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAAGTTT
1 G-GGGTAAAATGGTAATTTTGGTAAAATCGAGGGTAAAAATGGAATTTTGAAAAGTTT
* * * *
19995607 GGGGATAAAATGGTAATTTTGATAAAATCGAGGGTAAAAATGAAATTTTGGAAAACTTA
1 GGGG-TAAAATGGTAATTTTGGTAAAATCGAGGGTAAAAATGGAATTTT-GAAAAGTTT
*
19995666 GGGGTAAAA-AGTAATTTT
1 GGGGTAAAATGGTAATTTT
19995684 TAGAAAATTT
Statistics
Matches: 168, Mismatches: 16, Indels: 19
0.83 0.08 0.09
Matches are distributed among these distances:
56 1 0.01
57 32 0.19
58 84 0.50
59 51 0.30
ACGTcount: A:0.38, C:0.03, G:0.27, T:0.32
Consensus pattern (57 bp):
GGGGTAAAATGGTAATTTTGGTAAAATCGAGGGTAAAAATGGAATTTTGAAAAGTTT
Found at i:19995684 original size:29 final size:29
Alignment explanation
Indices: 19995638--19995713 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 29
19995628 ATAAAATCGA
*
19995638 GGGTAAAAATGAAATTTTGGAAAACTTAG
1 GGGTAAAAATGAAATTTTAGAAAACTTAG
* * *
19995667 GGGTAAAAA-GTAATTTTTAGAAAATTTTG
1 GGGTAAAAATG-AAATTTTAGAAAACTTAG
19995696 GGGTCAAAATAT-AAATTT
1 GGGT-AAAA-ATGAAATTT
19995714 CAAAAAGTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 1 0.03
29 27 0.71
30 9 0.24
31 1 0.03
ACGTcount: A:0.43, C:0.03, G:0.21, T:0.33
Consensus pattern (29 bp):
GGGTAAAAATGAAATTTTAGAAAACTTAG
Found at i:19995803 original size:29 final size:29
Alignment explanation
Indices: 19995663--19995815 Score: 139
Period size: 30 Copynumber: 5.2 Consensus size: 29
19995653 TTTGGAAAAC
* *
19995663 TTAGGGGTAAAA-AGTAATTTTTAGAAAATT
1 TTAGGGTTAAAATA-TAATTTTTAG-AAAGT
* * * * *
19995693 TTGGGGTCAAAATATAAATTTCAAAAAGTT
1 TTAGGGTTAAAATATAATTTTTAGAAAG-T
*
19995723 TTAGGGTTAAAATATAA-TTTTGGAGAAGT
1 TTAGGGTTAAAATATAATTTTTAGA-AAGT
* *
19995752 TTGGTGGTTAAAATGTAATTTTTAGAAAGT
1 TTAG-GGTTAAAATATAATTTTTAGAAAGT
* *
19995782 TTAGGGTTAAAATATAATTTTTGGATAGT
1 TTAGGGTTAAAATATAATTTTTAGAAAGT
19995811 TTAGG
1 TTAGG
19995816 AACTTTCAGG
Statistics
Matches: 99, Mismatches: 19, Indels: 11
0.77 0.15 0.09
Matches are distributed among these distances:
29 38 0.38
30 54 0.55
31 7 0.07
ACGTcount: A:0.38, C:0.01, G:0.22, T:0.39
Consensus pattern (29 bp):
TTAGGGTTAAAATATAATTTTTAGAAAGT
Found at i:19996128 original size:32 final size:32
Alignment explanation
Indices: 19996078--19996146 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
19996068 AATAGCTGGG
*
19996078 CTAAATTAAAATTAATTAAAAATATGAAAAGGA
1 CTAAATTAAAATTAATTAAAAATACG-AAAGGA
* *
19996111 CTAAATTGAAA-TAATTAAAAATACGGAAGGA
1 CTAAATTAAAATTAATTAAAAATACGAAAGGA
19996142 CTAAA
1 CTAAA
19996147 CGCGCAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 10 0.30
32 13 0.39
33 10 0.30
ACGTcount: A:0.58, C:0.06, G:0.12, T:0.25
Consensus pattern (32 bp):
CTAAATTAAAATTAATTAAAAATACGAAAGGA
Found at i:19996831 original size:28 final size:30
Alignment explanation
Indices: 19996779--19996850 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
19996769 ATAAATATTA
*
19996779 ATTATTATTATTTAATACAACTATTATTGAT
1 ATTATTATTATTTAATA-AACTATTATTAAT
*
19996810 ATTATTATTATTTACT-AA-TATTATTAAT
1 ATTATTATTATTTAATAAACTATTATTAAT
*
19996838 ATTAATTACTATT
1 ATT-ATTATTATT
19996851 AATGTCGTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 12 0.32
29 10 0.27
31 15 0.41
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (30 bp):
ATTATTATTATTTAATAAACTATTATTAAT
Found at i:19997599 original size:17 final size:17
Alignment explanation
Indices: 19997573--19997641 Score: 75
Period size: 17 Copynumber: 3.8 Consensus size: 17
19997563 AATTTGATTG
*
19997573 AATTTAAAATTTAAAGCA
1 AATTT-AAATTTAAAGTA
19997591 AATTTAAATTTAAAAAGATA
1 AATTTAAATTT--AAAG-TA
*
19997611 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAGTA
*
19997628 AATTTAGATTTAAA
1 AATTTAAATTTAAA
19997642 AATAAATTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
17 21 0.47
18 8 0.18
19 4 0.09
20 12 0.27
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (17 bp):
AATTTAAATTTAAAGTA
Found at i:19997623 original size:37 final size:36
Alignment explanation
Indices: 19997573--19997650 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 36
19997563 AATTTGATTG
*
19997573 AATTTAAAATTTAAAGCAAATTTAAATTTAAAAAGATA
1 AATTTAAAATTTAAAACAAATTTAAATTT-AAAA-ATA
* *
19997611 AATTT-AAATTTAAAATAAATTTAGATTTAAAAATA
1 AATTTAAAATTTAAAACAAATTTAAATTTAAAAATA
19997646 AATTT
1 AATTT
19997651 GAATCAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 8 0.22
36 4 0.11
37 20 0.54
38 5 0.14
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.38
Consensus pattern (36 bp):
AATTTAAAATTTAAAACAAATTTAAATTTAAAAATA
Found at i:19997642 original size:17 final size:18
Alignment explanation
Indices: 19997590--19997650 Score: 88
Period size: 18 Copynumber: 3.3 Consensus size: 18
19997580 AATTTAAAGC
19997590 AAATTTAAATTTAAAAAGAT
1 AAATTTAAATTT-AAAA-AT
19997610 AAATTTAAATTT-AAAAT
1 AAATTTAAATTTAAAAAT
*
19997627 AAATTTAGATTTAAAAAT
1 AAATTTAAATTTAAAAAT
19997645 AAATTT
1 AAATTT
19997651 GAATCAATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
17 13 0.33
18 14 0.36
20 12 0.31
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.39
Consensus pattern (18 bp):
AAATTTAAATTTAAAAAT
Found at i:19998317 original size:101 final size:101
Alignment explanation
Indices: 19998071--19998648 Score: 861
Period size: 101 Copynumber: 5.7 Consensus size: 101
19998061 CCGGGTTCGT
* * * * *
19998071 CGTTGCGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTAGATCTGCCATTGCGGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTTGTGTTTTTGCGGTACTGGATCTGCCATTGCGGTCTTAGA
19998136 TCTTTCCCTT-CATGCTTTTGAGGTACACGGTCCGC
66 TCTTTCCCTTCCATGCTTTTGAGGTACACGGTCCGC
* * * * *
19998171 CGTTGTGACTTAAACCTTTCCCTTTTCTATTTTTGCTGTACTGGATCTGCCATTGCGGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTTGTGTTTTTGCGGTACTGGATCTGCCATTGCGGTCTTAGA
*
19998236 TCTTTCCCTTCCATGCTTCTGAGGTACACGGTCCGC
66 TCTTTCCCTTCCATGCTTTTGAGGTACACGGTCCGC
* * * * * * *
19998272 CGTTACGACTTAGACCTGTCCCTGTTGTGTTTTGGCGGTATTGGATCTGCCATTGCGATTTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTTGTGTTTTTGCGGTACTGGATCTGCCATTGCGGTCTTAGA
* *
19998337 TCTTTCCCTTCCATGCTTCTGAGGTACACGGTCCGT
66 TCTTTCCCTTCCATGCTTTTGAGGTACACGGTCCGC
* **
19998373 CGTTGCGACTTAGACCTTTCCCTGTTGTGTTTTTGCAATACTGGATCTGCCATTGCGGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTTGTGTTTTTGCGGTACTGGATCTGCCATTGCGGTCTTAGA
19998438 TCTTTCCCTTCCATGCTTTTGAGGTACACGGTCCGC
66 TCTTTCCCTTCCATGCTTTTGAGGTACACGGTCCGC
* * * * * *
19998474 CGTTGCGACTTATACCTTCCCCTTTTATGTTTTTGTGGTACTAGATCTGCCATTGCGGTTTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTTGTGTTTTTGCGGTACTGGATCTGCCATTGCGGTCTTAGA
**
19998539 TCTTTCCCTTCCATGCTTTTGAGGTACACGGTCCAT
66 TCTTTCCCTTCCATGCTTTTGAGGTACACGGTCCGC
*
19998575 CGTTGCGACATAGACCTTTCCCTTTTGTGTTTTTGCGGTACTGGATCTGCCATTGCGGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTTGTGTTTTTGCGGTACTGGATCTGCCATTGCGGTCTTAGA
19998640 TCTTTCCCT
66 TCTTTCCCT
19998649 GCCAAACCTG
Statistics
Matches: 429, Mismatches: 48, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
100 69 0.16
101 360 0.84
ACGTcount: A:0.14, C:0.26, G:0.21, T:0.39
Consensus pattern (101 bp):
CGTTGCGACTTAGACCTTTCCCTTTTGTGTTTTTGCGGTACTGGATCTGCCATTGCGGTCTTAGA
TCTTTCCCTTCCATGCTTTTGAGGTACACGGTCCGC
Found at i:19998615 original size:50 final size:50
Alignment explanation
Indices: 19998071--19998615 Score: 294
Period size: 50 Copynumber: 10.8 Consensus size: 50
19998061 CCGGGTTCGT
* * * * * * *
19998071 CGTTGCGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTA-GATCTGC
1 CGTTGCGACTTAGACCTTTCCCTTTTATGTTTTTGAGGTAC-ACGGTCCGC
* * * * *
19998121 CATTGCGGTCTTAGATCTTTCCC-TTCATGCTTTTGAGGTACACGGTCCGC
1 CGTTGC-GACTTAGACCTTTCCCTTTTATGTTTTTGAGGTACACGGTCCGC
* * * * ** * *
19998171 CGTTGTGACTTAAACCTTTCCCTTTTCTATTTTTGCTGTAC-TGGATCTGC
1 CGTTGCGACTTAGACCTTTCCCTTTTATGTTTTTGAGGTACACGG-TCCGC
* * * ** * *
19998221 CATTGCGGTCTTAGATCTTTCCCTTCCATGCTTCTGAGGTACACGGTCCGC
1 CGTTGC-GACTTAGACCTTTCCCTTTTATGTTTTTGAGGTACACGGTCCGC
* * * * * * ** *
19998272 CGTTACGACTTAGACCTGTCCCTGTTGTGTTTTGGCGGTA-TTGGATCTGC
1 CGTTGCGACTTAGACCTTTCCCTTTTATGTTTTTGAGGTACACGG-TCCGC
* * * ** * * *
19998322 CATTGCGATTTTAGATCTTTCCCTTCCATGCTTCTGAGGTACACGGTCCGT
1 CGTTGCGA-CTTAGACCTTTCCCTTTTATGTTTTTGAGGTACACGGTCCGC
* * * * *
19998373 CGTTGCGACTTAGACCTTTCCCTGTTGTGTTTTTGCA-ATAC-TGGATCTGC
1 CGTTGCGACTTAGACCTTTCCCTTTTATGTTTTTG-AGGTACACGG-TCCGC
* * * ** *
19998423 CATTGCGGTCTTAGATCTTTCCCTTCCATGCTTTTGAGGTACACGGTCCGC
1 CGTTGC-GACTTAGACCTTTCCCTTTTATGTTTTTGAGGTACACGGTCCGC
* * * * *
19998474 CGTTGCGACTTATACCTTCCCCTTTTATGTTTTTGTGGTACTA-GATCTGC
1 CGTTGCGACTTAGACCTTTCCCTTTTATGTTTTTGAGGTAC-ACGGTCCGC
* ** * ** * **
19998524 CATTGCGGTTTTAGATCTTTCCCTTCCATGCTTTTGAGGTACACGGTCCAT
1 CGTTGC-GACTTAGACCTTTCCCTTTTATGTTTTTGAGGTACACGGTCCGC
* * *
19998575 CGTTGCGACATAGACCTTTCCCTTTTGTGTTTTTGCGGTAC
1 CGTTGCGACTTAGACCTTTCCCTTTTATGTTTTTGAGGTAC
19998616 TGGATCTGCC
Statistics
Matches: 346, Mismatches: 132, Indels: 34
0.68 0.26 0.07
Matches are distributed among these distances:
49 20 0.06
50 174 0.50
51 146 0.42
52 6 0.02
ACGTcount: A:0.14, C:0.26, G:0.21, T:0.39
Consensus pattern (50 bp):
CGTTGCGACTTAGACCTTTCCCTTTTATGTTTTTGAGGTACACGGTCCGC
Found at i:19999553 original size:7 final size:7
Alignment explanation
Indices: 19999536--19999629 Score: 79
Period size: 7 Copynumber: 13.6 Consensus size: 7
19999526 CCTCTCCTTT
19999536 TTTTTTC
1 TTTTTTC
19999543 -TTTTTC
1 TTTTTTC
19999549 TTTTTTC
1 TTTTTTC
*
19999556 TTTTTTTT
1 -TTTTTTC
*
19999564 TGTTTTTG
1 T-TTTTTC
*
19999572 TTTTTTA
1 TTTTTTC
*
19999579 TTTTTTG
1 TTTTTTC
19999586 TTTTTT-
1 TTTTTTC
19999592 TTTTTTC
1 TTTTTTC
*
19999599 TCTTTTTG
1 T-TTTTTC
19999607 TTTTTTC
1 TTTTTTC
*
19999614 -TTCTTC
1 TTTTTTC
19999620 -TTTTTC
1 TTTTTTC
19999626 TTTT
1 TTTT
19999630 ATTCATTGAA
Statistics
Matches: 73, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
6 22 0.30
7 33 0.45
8 18 0.25
ACGTcount: A:0.01, C:0.10, G:0.04, T:0.85
Consensus pattern (7 bp):
TTTTTTC
Found at i:19999554 original size:13 final size:12
Alignment explanation
Indices: 19999533--19999629 Score: 92
Period size: 11 Copynumber: 8.2 Consensus size: 12
19999523 CGACCTCTCC
19999533 TTTTTTTTTCTT
1 TTTTTTTTTCTT
19999545 TTTCTTTTTTCTT
1 TTT-TTTTTTCTT
*
19999558 TTTTTTTGT-TT
1 TTTTTTTTTCTT
* *
19999569 TTGTTTTTT-AT
1 TTTTTTTTTCTT
*
19999580 TTTTTGTTT-TT
1 TTTTTTTTTCTT
*
19999591 TTTTTTTCTCTT
1 TTTTTTTTTCTT
19999603 TTTGTTTTTTCTT
1 TTT-TTTTTTCTT
* *
19999616 CTTCTTTTTCTT
1 TTTTTTTTTCTT
19999628 TT
1 TT
19999630 ATTCATTGAA
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
11 25 0.36
12 22 0.32
13 22 0.32
ACGTcount: A:0.01, C:0.09, G:0.04, T:0.86
Consensus pattern (12 bp):
TTTTTTTTTCTT
Found at i:19999576 original size:35 final size:36
Alignment explanation
Indices: 19999537--19999629 Score: 74
Period size: 36 Copynumber: 2.6 Consensus size: 36
19999527 CTCTCCTTTT
*
19999537 TTTTTC-TTTT-TCTTTTTTCTTTTTTTT-TGTTTTTG
1 TTTTTCTTTTTCT-TTT-TTCTTTTTTTTCTCTTTTTG
19999572 TTTTT-TATTTT-TTGTTTT-TTTTTTTTCTCTTTTTG
1 TTTTTCT-TTTTCTT-TTTTCTTTTTTTTCTCTTTTTG
*
19999607 TTTTTTCTTCTTC-TTTTTCTTTT
1 -TTTTTCTTTTTCTTTTTTCTTTT
19999630 ATTCATTGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
34 8 0.17
35 19 0.40
36 20 0.42
37 1 0.02
ACGTcount: A:0.01, C:0.10, G:0.04, T:0.85
Consensus pattern (36 bp):
TTTTTCTTTTTCTTTTTTCTTTTTTTTCTCTTTTTG
Found at i:19999624 original size:1 final size:1
Alignment explanation
Indices: 19999533--19999612 Score: 70
Period size: 1 Copynumber: 80.0 Consensus size: 1
19999523 CGACCTCTCC
* * * * * * *
19999533 TTTTTTTTTCTTTTTCTTTTTTCTTTTTTTTTGTTTTTGTTTTTTATTTTTTGTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
19999598 CTCTTTTTGTTTTTT
1 TTTTTTTTTTTTTTT
19999613 CTTCTTCTTT
Statistics
Matches: 59, Mismatches: 20, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.01, C:0.06, G:0.05, T:0.88
Consensus pattern (1 bp):
T
Found at i:20003345 original size:6 final size:6
Alignment explanation
Indices: 20003319--20003360 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
20003309 TGTATTGGAC
*
20003319 ATTTAAA ATTTAA A-GTAA ATTTAA ATTTAA ATTTAAA ATTTA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA ATTTA
20003361 TTTATTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
5 4 0.13
6 17 0.55
7 10 0.32
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:20003349 original size:12 final size:12
Alignment explanation
Indices: 20003319--20003360 Score: 50
Period size: 11 Copynumber: 3.4 Consensus size: 12
20003309 TGTATTGGAC
20003319 ATTTAAAATTTAA
1 ATTT-AAATTTAA
*
20003332 A-GTAAATTTAA
1 ATTTAAATTTAA
20003343 ATTTAAATTTAAA
1 ATTTAAATTT-AA
20003356 ATTTA
1 ATTTA
20003361 TTTATTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 9 0.36
12 8 0.32
13 8 0.32
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (12 bp):
ATTTAAATTTAA
Found at i:20006475 original size:21 final size:21
Alignment explanation
Indices: 20006442--20006509 Score: 84
Period size: 21 Copynumber: 3.1 Consensus size: 21
20006432 CTTAGCTAAA
20006442 ATTTTATTTTTATTTTTTATAT
1 ATTTTA-TTTTATTTTTTATAT
20006464 ATTTTATTTTATTTTATTATAT
1 ATTTTATTTTATTTT-TTATAT
* *
20006486 A-TATATATTATTATTTTATAT
1 ATTTTATTTTATT-TTTTATAT
20006507 ATT
1 ATT
20006510 AAAAATATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
21 25 0.61
22 16 0.39
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
ATTTTATTTTATTTTTTATAT
Found at i:20006488 original size:26 final size:26
Alignment explanation
Indices: 20006442--20006508 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 26
20006432 CTTAGCTAAA
* * *
20006442 ATTTTATTTTTATTTTTTATATATTTT
1 ATTTTA-TTTTATTATATATATATATT
20006469 ATTTTATTTTATTATATATATATATT
1 ATTTTATTTTATTATATATATATATT
20006495 A--TTATTTTA-TATAT
1 ATTTTATTTTATTATAT
20006509 TAAAAATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
23 5 0.14
24 8 0.22
26 18 0.49
27 6 0.16
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (26 bp):
ATTTTATTTTATTATATATATATATT
Found at i:20006509 original size:28 final size:28
Alignment explanation
Indices: 20006459--20006519 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
20006449 TTTTATTTTT
* * *
20006459 TATATATTTTATTTTATTTTATTATATA
1 TATATATTTTATTTTATTATATTAAAAA
20006487 TATATATTATTATTTTA-TATATTAAAAA
1 TATATATT-TTATTTTATTATATTAAAAA
20006515 TATAT
1 TATAT
20006520 TTAATTGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 21 0.72
29 8 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
TATATATTTTATTTTATTATATTAAAAA
Found at i:20006517 original size:24 final size:23
Alignment explanation
Indices: 20006468--20006522 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
20006458 TTATATATTT
* *
20006468 TATTTTATTTTATTATATATATA
1 TATTTTATTTTATTATATAAAAA
20006491 TATTATTATTTTA-TATATTAAAAA
1 TATT-TTATTTTATTATA-TAAAAA
20006515 TATATTTA
1 TAT-TTTA
20006523 ATTGATTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 8 0.30
24 18 0.67
25 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TATTTTATTTTATTATATAAAAA
Found at i:20010524 original size:3 final size:3
Alignment explanation
Indices: 20010516--20010548 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
20010506 TCACATTCCA
20010516 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
20010549 TCTTCTTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:20014468 original size:20 final size:21
Alignment explanation
Indices: 20014439--20014481 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
20014429 AACCATCATT
20014439 AAAATATATAAAAAAACTATA
1 AAAATATATAAAAAAACTATA
*
20014460 AAAAT-TATAAAAAAATTATA
1 AAAATATATAAAAAAACTATA
20014480 AA
1 AA
20014482 CAAAATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAATATATAAAAAAACTATA
Found at i:20014491 original size:13 final size:11
Alignment explanation
Indices: 20014439--20014506 Score: 61
Period size: 11 Copynumber: 6.1 Consensus size: 11
20014429 AACCATCATT
20014439 AAAATATATAAA
1 AAAAT-TATAAA
*
20014451 AAAACTAT--A
1 AAAATTATAAA
20014460 AAAATTATAAA
1 AAAATTATAAA
20014471 AAAATTATAAA
1 AAAATTATAAA
*
20014482 CAAAATT-TATAT
1 -AAAATTATA-AA
20014494 AAAATTATTAAA
1 AAAATTA-TAAA
20014506 A
1 A
20014507 TAATAAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
9 8 0.17
11 23 0.50
12 13 0.28
13 2 0.04
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (11 bp):
AAAATTATAAA
Found at i:20014514 original size:17 final size:17
Alignment explanation
Indices: 20014492--20014541 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
20014482 CAAAATTTAT
20014492 ATAAAATTATTAA-AATA
1 ATAAAA-TATTAATAATA
*
20014509 ATAAAAATATAAATAATA
1 AT-AAAATATTAATAATA
*
20014527 TTAAAATATTAATAA
1 ATAAAATATTAATAA
20014542 GTTATAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 19 0.68
18 9 0.32
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATAAAATATTAATAATA
Found at i:20025658 original size:30 final size:31
Alignment explanation
Indices: 20025624--20025692 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
20025614 TAAAAATATA
*
20025624 ATTTTTAAAA-GATTAAATTAAAATTTTATT
1 ATTTTTAAAAGGATTAAAATAAAATTTTATT
*
20025654 ATTTTTAAAAGGATTAAAATATAATTTTATT
1 ATTTTTAAAAGGATTAAAATAAAATTTTATT
20025685 -TTTATTAA
1 ATTT-TTAA
20025693 TTTAAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
30 13 0.37
31 22 0.63
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (31 bp):
ATTTTTAAAAGGATTAAAATAAAATTTTATT
Found at i:20026212 original size:22 final size:22
Alignment explanation
Indices: 20026165--20026205 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
20026155 TAATCTAATA
20026165 AAAATGGTAGCAAAACAACATC
1 AAAATGGTAGCAAAACAACATC
20026187 AAAATGGTAGC-AAACAACA
1 AAAATGGTAGCAAAACAACA
20026206 ATTAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.56, C:0.17, G:0.15, T:0.12
Consensus pattern (22 bp):
AAAATGGTAGCAAAACAACATC
Found at i:20026631 original size:11 final size:11
Alignment explanation
Indices: 20026615--20026640 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
20026605 TTTTTAAAAT
20026615 TTAAAAAATTA
1 TTAAAAAATTA
20026626 TTAAAAAATTA
1 TTAAAAAATTA
20026637 TTAA
1 TTAA
20026641 TTTCTCCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TTAAAAAATTA
Found at i:20030963 original size:6 final size:6
Alignment explanation
Indices: 20030952--20030983 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
20030942 AAGGTTCAAG
20030952 GTTTGA GTTTGA GTTT-- GTTTGA GTTTGA GTTT
1 GTTTGA GTTTGA GTTTGA GTTTGA GTTTGA GTTT
20030984 TGGTTCAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 4 0.17
6 20 0.83
ACGTcount: A:0.12, C:0.00, G:0.31, T:0.56
Consensus pattern (6 bp):
GTTTGA
Found at i:20030973 original size:16 final size:16
Alignment explanation
Indices: 20030952--20030983 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
20030942 AAGGTTCAAG
20030952 GTTTGAGTTTGAGTTT
1 GTTTGAGTTTGAGTTT
20030968 GTTTGAGTTTGAGTTT
1 GTTTGAGTTTGAGTTT
20030984 TGGTTCAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.31, T:0.56
Consensus pattern (16 bp):
GTTTGAGTTTGAGTTT
Found at i:20031003 original size:7 final size:7
Alignment explanation
Indices: 20030993--20031049 Score: 62
Period size: 7 Copynumber: 8.1 Consensus size: 7
20030983 TTGGTTCAGT
20030993 GTTTAAG
1 GTTTAAG
*
20031000 GTTTAGG
1 GTTTAAG
*
20031007 GTTTATG
1 GTTTAAG
*
20031014 GTTTTGAG
1 G-TTTAAG
20031022 GTTTAAG
1 GTTTAAG
*
20031029 GTTTGA-
1 GTTTAAG
20031035 GTTTAAG
1 GTTTAAG
20031042 GTTTAAG
1 GTTTAAG
20031049 G
1 G
20031050 GTATGGTTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
6 5 0.12
7 31 0.76
8 5 0.12
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (7 bp):
GTTTAAG
Found at i:20031010 original size:14 final size:14
Alignment explanation
Indices: 20030993--20031051 Score: 66
Period size: 15 Copynumber: 4.1 Consensus size: 14
20030983 TTGGTTCAGT
20030993 GTTTAAGGTTTAGG
1 GTTTAAGGTTTAGG
* *
20031007 GTTTATGGTTTTGAG
1 GTTTAAGGTTTAG-G
*
20031022 GTTTAAGGTTT-GA
1 GTTTAAGGTTTAGG
20031035 GTTTAAGGTTTAAGG
1 GTTTAAGGTTT-AGG
20031050 GT
1 GT
20031052 ATGGTTTATG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
13 11 0.30
14 12 0.32
15 14 0.38
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.46
Consensus pattern (14 bp):
GTTTAAGGTTTAGG
Found at i:20031058 original size:20 final size:20
Alignment explanation
Indices: 20030993--20031059 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 20
20030983 TTGGTTCAGT
20030993 GTTTAAGGTTT-AGGGTTTATG
1 GTTTAAGGTTTAAGGG--TATG
* *
20031014 GTTTTGAGGTTTAA-GGTTTG
1 G-TTTAAGGTTTAAGGGTATG
20031034 AGTTTAAGGTTTAAGGGTATG
1 -GTTTAAGGTTTAAGGGTATG
20031055 GTTTA
1 GTTTA
20031060 TGGGGTATGA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
20 19 0.50
21 7 0.18
22 11 0.29
23 1 0.03
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (20 bp):
GTTTAAGGTTTAAGGGTATG
Found at i:20031127 original size:21 final size:21
Alignment explanation
Indices: 20031103--20031143 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20031093 TTAAGGTTTA
* * *
20031103 GGTTTTGGGTTTTATATTTTG
1 GGTTTAGGATTTTAGATTTTG
20031124 GGTTTAGGATTTTAGATTTT
1 GGTTTAGGATTTTAGATTTT
20031144 AGATTCATGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.27, T:0.59
Consensus pattern (21 bp):
GGTTTAGGATTTTAGATTTTG
Found at i:20031135 original size:14 final size:14
Alignment explanation
Indices: 20031070--20031136 Score: 50
Period size: 14 Copynumber: 4.9 Consensus size: 14
20031060 TGGGGTATGA
*
20031070 GTTTAGGGTTTT-G
1 GTTTAGGATTTTGG
* **
20031083 ATTTAAGGATTTAAG
1 GTTT-AGGATTTTGG
20031098 GTTTAGG-TTTTGG
1 GTTTAGGATTTTGG
*
20031111 GTTTTA-TATTTTGG
1 G-TTTAGGATTTTGG
20031125 GTTTAGGATTTT
1 GTTTAGGATTTT
20031137 AGATTTTAGA
Statistics
Matches: 41, Mismatches: 8, Indels: 9
0.71 0.14 0.16
Matches are distributed among these distances:
13 12 0.29
14 25 0.61
15 4 0.10
ACGTcount: A:0.18, C:0.00, G:0.28, T:0.54
Consensus pattern (14 bp):
GTTTAGGATTTTGG
Found at i:20032168 original size:182 final size:179
Alignment explanation
Indices: 20031861--20033265 Score: 1786
Period size: 182 Copynumber: 7.7 Consensus size: 179
20031851 AAGGAGTCAG
* * *
20031861 AACATACATCTGTTTCAATACTATCTTCTGCTTCAACGATAGCAGCACCAATATTTG-CTCATGA
1 AACATACATCTGTTTCAATACTATCTTCTGCTTCAACGATAGCAGCAACAATA-TTGACTCCTCA
* * *
20031925 GGAGTCAAATGTGTTGGTGTTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTT
65 GGAG-CCAA--TATTGGTGCTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTT
* * * * * * *
20031990 TCCCGCTTCAGGAGAGGTA-TTAACATAT-TAAAGTGTCTCTCTTGAAGCAGGAA
127 TCCTGCTTCAAGAGAGGCACTTTA-ATATCTTAA-TGCCTCTCCTGAAGCAGGAA
* *
20032043 AACATACATCTGTTTCAATACTATCTTCTGCTTCAACGATAGCAGCAACAATATTGGCTCCTGAG
1 AACATACATCTGTTTCAATACTATCTTCTGCTTCAACGATAGCAGCAACAATATTGACTCCTCAG
* *
20032108 GAGTCAGATGTATTGGTGCTGCTATCATTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTT
66 GAGCCA-A--TATTGGTGCTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTT
*
20032173 CCTGCTTCAAGAGAGGCACTTTAATATCTTAATGCCTCTCCTGAAGCGGGAA
128 CCTGCTTCAAGAGAGGCACTTTAATATCTTAATGCCTCTCCTGAAGCAGGAA
* * *
20032225 AACATACATCTGTTTCAATACAATCTTCTGCTTCAACGATAGCAGCACCAACACATCTGACTCCT
1 AACATACATCTGTTTCAATACTATCTTCTGCTTCAACGATAGCAGCAAC-A-ATAT-TGACTCCT
* * * * *
20032290 CAAGAGCCAATATTGGTGTTGCTATCATTAAAGCAGAAGATAGTATTGAAACAGATGTACGTTTT
63 CAGGAGCCAATATTGGTGCTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTT
* * **
20032355 CCTGCTTCAAGAGAGGTA-TTAAGATAT-AAAAGTGCCTCTCCTGAAGCAGGAA
128 CCTGCTTCAAGAGAGGCACTTTA-ATATCTTAA-TGCCTCTCCTGAAGCAGGAA
* * * * *
20032407 AACATATATTTGTTTCAATACTATCTTCTGCTTCAACGATAGTAGC-ACAAATATTGGCTCCTGA
1 AACATACATCTGTTTCAATACTATCTTCTGCTTCAACGATAGCAGCAAC-AATATTGACTCCTCA
* * * *
20032471 GGAGTCATATCTATTGGTGCTGCTATCGTTAAAGCAAAAAGATAGTATTGAAACAAATGTATGTT
65 GGAGCCA-A--TATTGGTGCTGCTATCGTTGAAGC-AGAAGATAGTATTGAAACAGATGTATGTT
* * *
20032536 TTCCTGCTTCAGGAGAGGCACTTTAATATCTTAATACCTCTCCTGAAACAGGAA
126 TTCCTGCTTCAAGAGAGGCACTTTAATATCTTAATGCCTCTCCTGAAGCAGGAA
* * * * * *
20032590 AACACACATCTGTTTCAATACTATCCTCTGCTTCAATGATAGCAGCACCAATATTGGCTCCTGAG
1 AACATACATCTGTTTCAATACTATCTTCTGCTTCAACGATAGCAGCAACAATATTGACTCCTCAG
* *
20032655 GAGTCAGATGTATTGGTGTTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTT
66 GAGCCA-A--TATTGGTGCTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTT
* * * * * * *
20032720 CATGATTCAGGAGAGGTA-TTAAGATAT-TAAAGTGCCTCTCTTGAAGCAGGAA
128 CCTGCTTCAAGAGAGGCACTTTA-ATATCTTAA-TGCCTCTCCTGAAGCAGGAA
*
20032772 AACATACATCTGTTTCAATACTATCTTCTGCTTCAATGATAGCAGC-ACTAATACATCTGACTCC
1 AACATACATCTGTTTCAATACTATCTTCTGCTTCAACGATAGCAGCAAC-AAT--AT-TGACTCC
*
20032836 TCAGGAGCCAATATTGGTGCTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGCTT
62 TCAGGAGCCAATATTGGTGCTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTT
* *
20032901 TCTTGCTTCAAGAGAGGCACTTTAATATCTTAATACCTCTCCTGAAGCAGGAA
127 TCCTGCTTCAAGAGAGGCACTTTAATATCTTAATGCCTCTCCTGAAGCAGGAA
* *
20032954 AACATACATCTGTTTCAATACTATCTTCTGCTTCAATGATAGCAGCACCAATACATCTGACTCCT
1 AACATACATCTGTTTCAATACTATCTTCTGCTTCAACGATAGCAGCAACAAT--AT-TGACTCCT
*
20033019 CAGGAGCCAATATTGTTGCTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTT
63 CAGGAGCCAATATTGGTGCTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTT
* * * *
20033084 CCTGCTTCAAGAGAGACACTTTAATATGTTAATACCTCTCCTGAAGCGGGAA
128 CCTGCTTCAAGAGAGGCACTTTAATATCTTAATGCCTCTCCTGAAGCAGGAA
*
20033136 AACATACATCTGTTTCAATACTATCTTCTGCTTCAACGATAGCAACACCAACACAT-TTGACTCC
1 AACATACATCTGTTTCAATACTATCTTCTGCTTCAACGATAG---CAGCAACA-ATATTGACTCC
* *
20033200 TCATGAGCCAATATTGGTGCTACTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTT
62 TCAGGAGCCAATATTGGTGCTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTT
20033265 T
127 T
20033266 GACTCCTTCA
Statistics
Matches: 1092, Mismatches: 102, Indels: 58
0.87 0.08 0.05
Matches are distributed among these distances:
179 13 0.01
180 4 0.00
181 19 0.02
182 841 0.77
183 167 0.15
184 13 0.01
185 33 0.03
186 2 0.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (179 bp):
AACATACATCTGTTTCAATACTATCTTCTGCTTCAACGATAGCAGCAACAATATTGACTCCTCAG
GAGCCAATATTGGTGCTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTTCCT
GCTTCAAGAGAGGCACTTTAATATCTTAATGCCTCTCCTGAAGCAGGAA
Found at i:20033045 original size:364 final size:362
Alignment explanation
Indices: 20031861--20033265 Score: 1995
Period size: 364 Copynumber: 3.9 Consensus size: 362
20031851 AAGGAGTCAG
* * *
20031861 AACATACATCTGTTTCAATACTATCTTCTGCTTCAACGATAGCAGCACCAATATTTG-CTCATGA
1 AACATACATCTGTTTCAATACTATCTTCTGCTTCAACGATAGCAGCACCAATATCTGACTCCTCA
* *
20031925 GGAGTCAAATGTGTTGGTGTTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTT
66 GGAG-CCAA--TATTGGTGTTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTT
* * * * *
20031990 TCCCGCTTCAGGAGAGGTATTAACATATTAAAGTGTCTCTCTTGAAGCAGGAAAACATACATCTG
128 TCCTGCTTCAAGAGAGGTATTAAGATATTAAAGTGCCTCTCCTGAAGCAGGAAAACATACATCTG
* * *
20032055 TTTCAATACTATCTTCTGCTTCAACGATAGCAGCAACAAT--ATTGGCTCCTGAGGAGTCAGATG
193 TTTCAATACTATCTTCTGCTTCAACGATAGCAGC-ACAATACATTGACTCCTCAGGAGCCAGAT-
*
20032118 TATTGGTGCTGCTATCATTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTTCCTGCTTCAA
256 TATTGGTGCTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTTCCTGCTTCAA
* *
20032183 GAGAGGCACTTTAATATCTTAATGCCTCTCCTGAAGCGGGAA
321 GAGAGGCACTTTAATATCTTAATACCTCTCCTGAAGCAGGAA
* *
20032225 AACATACATCTGTTTCAATACAATCTTCTGCTTCAACGATAGCAGCACCAACACATCTGACTCCT
1 AACATACATCTGTTTCAATACTATCTTCTGCTTCAACGATAGCAGCACC-A-ATATCTGACTCCT
* * * *
20032290 CAAGAGCCAATATTGGTGTTGCTATCATTAAAGCAGAAGATAGTATTGAAACAGATGTACGTTTT
64 CAGGAGCCAATATTGGTGTTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTT
* * *
20032355 CCTGCTTCAAGAGAGGTATTAAGATATAAAAGTGCCTCTCCTGAAGCAGGAAAACATATATTTGT
129 CCTGCTTCAAGAGAGGTATTAAGATATTAAAGTGCCTCTCCTGAAGCAGGAAAACATACATCTGT
* * * * * *
20032420 TTCAATACTATCTTCTGCTTCAACGATAGTAGCACAA-ATATTGGCTCCTGAGGAGTCATATCTA
194 TTCAATACTATCTTCTGCTTCAACGATAGCAGCACAATACATTGACTCCTCAGGAGCCAGAT-TA
* * * *
20032484 TTGGTGCTGCTATCGTTAAAGCAAAAAGATAGTATTGAAACAAATGTATGTTTTCCTGCTTCAGG
258 TTGGTGCTGCTATCGTTGAAGC-AGAAGATAGTATTGAAACAGATGTATGTTTTCCTGCTTCAAG
*
20032549 AGAGGCACTTTAATATCTTAATACCTCTCCTGAAACAGGAA
322 AGAGGCACTTTAATATCTTAATACCTCTCCTGAAGCAGGAA
* * * * *
20032590 AACACACATCTGTTTCAATACTATCCTCTGCTTCAATGATAGCAGCACCAATAT-TGGCTCCTGA
1 AACATACATCTGTTTCAATACTATCTTCTGCTTCAACGATAGCAGCACCAATATCTGACTCCTCA
*
20032654 GGAGTCAGATGTATTGGTGTTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTT
66 GGAGCCA-A--TATTGGTGTTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTT
* * * *
20032719 TCATGATTCAGGAGAGGTATTAAGATATTAAAGTGCCTCTCTTGAAGCAGGAAAACATACATCTG
128 TCCTGCTTCAAGAGAGGTATTAAGATATTAAAGTGCCTCTCCTGAAGCAGGAAAACATACATCTG
*
20032784 TTTCAATACTATCTTCTGCTTCAATGATAGCAGCACTAATACATCTGACTCCTCAGGAGCCA-A-
193 TTTCAATACTATCTTCTGCTTCAACGATAGCAGCAC-AATACAT-TGACTCCTCAGGAGCCAGAT
* *
20032847 TATTGGTGCTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGCTTTCTTGCTTCAA
256 TATTGGTGCTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTTCCTGCTTCAA
20032912 GAGAGGCACTTTAATATCTTAATACCTCTCCTGAAGCAGGAA
321 GAGAGGCACTTTAATATCTTAATACCTCTCCTGAAGCAGGAA
*
20032954 AACATACATCTGTTTCAATACTATCTTCTGCTTCAATGATAGCAGCACCAATACATCTGACTCCT
1 AACATACATCTGTTTCAATACTATCTTCTGCTTCAACGATAGCAGCACCAAT--ATCTGACTCCT
* *
20033019 CAGGAGCCAATATTGTTGCTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTT
64 CAGGAGCCAATATTGGTGTTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTT
** * * * *
20033084 CCTGCTTCAAGAGAGACACTTTA-ATATGTTAA-TACCTCTCCTGAAGCGGGAAAACATACATCT
129 CCTGCTTCAAGAGAGGTA-TTAAGATAT-TAAAGTGCCTCTCCTGAAGCAGGAAAACATACATCT
* * *
20033147 GTTTCAATACTATCTTCTGCTTCAACGATAGCAACACCAACACATTTGACTCCTCATGAGCCA-A
192 GTTTCAATACTATCTTCTGCTTCAACGATAGCAGCA-CAATACA-TTGACTCCTCAGGAGCCAGA
*
20033211 -TATTGGTGCTACTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTT
255 TTATTGGTGCTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTT
20033266 GACTCCTTCA
Statistics
Matches: 937, Mismatches: 85, Indels: 38
0.88 0.08 0.04
Matches are distributed among these distances:
362 13 0.01
363 8 0.01
364 566 0.60
365 297 0.32
366 13 0.01
367 26 0.03
368 14 0.01
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (362 bp):
AACATACATCTGTTTCAATACTATCTTCTGCTTCAACGATAGCAGCACCAATATCTGACTCCTCA
GGAGCCAATATTGGTGTTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTTCC
TGCTTCAAGAGAGGTATTAAGATATTAAAGTGCCTCTCCTGAAGCAGGAAAACATACATCTGTTT
CAATACTATCTTCTGCTTCAACGATAGCAGCACAATACATTGACTCCTCAGGAGCCAGATTATTG
GTGCTGCTATCGTTGAAGCAGAAGATAGTATTGAAACAGATGTATGTTTTCCTGCTTCAAGAGAG
GCACTTTAATATCTTAATACCTCTCCTGAAGCAGGAA
Found at i:20036554 original size:2 final size:2
Alignment explanation
Indices: 20036549--20036575 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20036539 GGATTTGTAG
20036549 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
20036576 GAGGTTTTTG
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:20046025 original size:20 final size:20
Alignment explanation
Indices: 20045985--20046025 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
20045975 ATGCTATTAT
* *
20045985 TGTTCATGACATGATCTCAC
1 TGTTCATGACATGACCCCAC
*
20046005 TGTTCATGACTTGACCCCAC
1 TGTTCATGACATGACCCCAC
20046025 T
1 T
20046026 ATTTTTAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.34
Consensus pattern (20 bp):
TGTTCATGACATGACCCCAC
Found at i:20051137 original size:331 final size:333
Alignment explanation
Indices: 20050473--20051145 Score: 1176
Period size: 331 Copynumber: 2.0 Consensus size: 333
20050463 GAAGAATAAA
* *
20050473 TAAAATTTATTTTTAGTTGGAATCGAATTTTTATAAGTAAAAATCATAGTTAAGGGCTTATTTAA
1 TAAAATTTATTTCTAGTTGGAATCGAATTTTTATAAGTAAAAATCATAGTTAAAGGCTTATTTAA
* * *
20050538 TTATAAAAATAAGTTAATGGTTTGTTTAAATACAATGTAATGAATTGAAGGGGAATAAAATAATA
66 TTACAAAAATAAGTTAAGGGTTTGTTTAAATACAATGCAATGAATTGAAGGGGAAT-AAATAATA
* *
20050603 ATAATAATAATAAGAGCTTACAAGGTAGGTTTTGGGTTAGAAACATATTTTTTTTAAAATTAACC
130 ATAATAATAATAAGAGCTTACAAGGTAGGTTTTGGGTTACAAAAATATTTTTTTTAAAATTAACC
20050668 ACATTCTGGTTGCAATTGATTTTTTTACAAAAATATTTTTTTATAGAAATTAGTTAATAGTTCTC
195 ACATTCTGGTTGCAATTGATTTTTTTACAAAAATATTTTTTTATAGAAATTAGTTAATAGTTCTC
20050733 TCTTTTTTTTGTGTTGAAGGAAAATAAAAGAAAATAGTAAATAAGAAGGACTTACAATGCAATTA
260 TCTTTTTTTTGTGTTGAAGGAAAATAAAAGAAAATAGTAAATAAGAAGGACTTACAATGCAATTA
*
20050798 ATCATATTT
325 ACCATATTT
20050807 TAAAATTTATTTCTAGTTGGAATCGAATTTTTATAAGTAAAAATCATAGGTTAAAGGCTTA-TTA
1 TAAAATTTATTTCTAGTTGGAATCGAATTTTTATAAGTAAAAATCATA-GTTAAAGGCTTATTTA
*
20050871 ATTACAAAAATAAGTTAAGGGTTTGTTTAAATACAATGCAGTGAATTGAAGGGGAAT-AA-AATA
65 ATTACAAAAATAAGTTAAGGGTTTGTTTAAATACAATGCAATGAATTGAAGGGGAATAAATAATA
20050934 ATAATAATAATAAGAGCTTACAAGGTAGGTTTTGGGTTACAAAAATA-TTTTTTTAAAATTAA-C
130 ATAATAATAATAAGAGCTTACAAGGTAGGTTTTGGGTTACAAAAATATTTTTTTTAAAATTAACC
*
20050997 ACATTTTGGTTGCAATTGATTTTTTTACAAAAATATTTTTTTATAGAAATTAGTTAATAGTTTTC
195 ACATTCTGGTTGCAATTGATTTTTTTACAAAAATATTTTTTTATAGAAATTAGTTAATAG--TTC
*
20051062 TCTTTTTTTTTTGTGTTGAAGGAAAATAAAAGAAAATAGTAAATAAGAAGGACTTACAATGCAAT
258 TCTCTTTTTTTTGTGTTGAAGGAAAATAAAAGAAAATAGTAAATAAGAAGGACTTACAATGCAAT
20051127 TAACCATATTT
323 TAACCATATTT
20051138 TAAAATTT
1 TAAAATTT
20051146 GCTACCGCCA
Statistics
Matches: 325, Mismatches: 11, Indels: 9
0.94 0.03 0.03
Matches are distributed among these distances:
329 60 0.18
330 15 0.05
331 134 0.41
332 2 0.01
334 103 0.32
335 11 0.03
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (333 bp):
TAAAATTTATTTCTAGTTGGAATCGAATTTTTATAAGTAAAAATCATAGTTAAAGGCTTATTTAA
TTACAAAAATAAGTTAAGGGTTTGTTTAAATACAATGCAATGAATTGAAGGGGAATAAATAATAA
TAATAATAATAAGAGCTTACAAGGTAGGTTTTGGGTTACAAAAATATTTTTTTTAAAATTAACCA
CATTCTGGTTGCAATTGATTTTTTTACAAAAATATTTTTTTATAGAAATTAGTTAATAGTTCTCT
CTTTTTTTTGTGTTGAAGGAAAATAAAAGAAAATAGTAAATAAGAAGGACTTACAATGCAATTAA
CCATATTT
Found at i:20060565 original size:21 final size:21
Alignment explanation
Indices: 20060536--20060575 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
20060526 TGATAATTGT
*
20060536 TATTGTTATTAAATATAATAG
1 TATTATTATTAAATATAATAG
20060557 TATTATTATTAAATATAAT
1 TATTATTATTAAATATAAT
20060576 TTAATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (21 bp):
TATTATTATTAAATATAATAG
Found at i:20060612 original size:11 final size:10
Alignment explanation
Indices: 20060568--20060625 Score: 53
Period size: 11 Copynumber: 5.4 Consensus size: 10
20060558 ATTATTATTA
20060568 AATATAATTT
1 AATATAATTT
* *
20060578 AATAAAAATAT
1 AAT-ATAATTT
20060589 AATAAATAATTT
1 AAT--ATAATTT
*
20060601 AATCATATTTT
1 AAT-ATAATTT
20060612 AATATAATTT
1 AATATAATTT
20060622 AATA
1 AATA
20060626 AAAATAATAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
10 13 0.33
11 17 0.44
12 9 0.23
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (10 bp):
AATATAATTT
Found at i:20060616 original size:44 final size:46
Alignment explanation
Indices: 20060568--20060666 Score: 157
Period size: 45 Copynumber: 2.2 Consensus size: 46
20060558 ATTATTATTA
* *
20060568 AATATAATTTAATAAAAAT-ATAATAAATAATTTAATCATATT-TT
1 AATATAATTTAATAAAAATAATAATAAATAATTTAATAACATTCTT
*
20060612 AATATAATTTAATAAAAATAATAATATATAATTTAATAACATTCTT
1 AATATAATTTAATAAAAATAATAATAAATAATTTAATAACATTCTT
20060658 AATATAATT
1 AATATAATT
20060667 ATTTTTATTA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
44 19 0.38
45 20 0.40
46 11 0.22
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (46 bp):
AATATAATTTAATAAAAATAATAATAAATAATTTAATAACATTCTT
Found at i:20060663 original size:24 final size:23
Alignment explanation
Indices: 20060565--20060650 Score: 88
Period size: 24 Copynumber: 3.8 Consensus size: 23
20060555 AGTATTATTA
20060565 TTAA-ATATAATTTAATAAAAAT
1 TTAATATATAATTTAATAAAAAT
* * * *
20060587 ATAATAAATAATTTAAT-CATAT
1 TTAATATATAATTTAATAAAAAT
*
20060609 TTTA-ATATAATTTAATAAAAAT
1 TTAATATATAATTTAATAAAAAT
*
20060631 AATAATATATAATTTAATAA
1 -TTAATATATAATTTAATAA
20060651 CATTCTTAAT
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
21 11 0.22
22 11 0.22
23 13 0.27
24 14 0.29
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (23 bp):
TTAATATATAATTTAATAAAAAT
Found at i:20060800 original size:23 final size:23
Alignment explanation
Indices: 20060755--20060798 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
20060745 TTTTGAAATA
20060755 AAATATTTATATTATAATATTTC
1 AAATATTTATATTATAATATTTC
* *
20060778 AAATATTT-TATTTTTATATTT
1 AAATATTTATATTATAATATTT
20060799 TCTAAGTCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
AAATATTTATATTATAATATTTC
Found at i:20063555 original size:20 final size:19
Alignment explanation
Indices: 20063513--20063564 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
20063503 TTATATTTTT
*
20063513 AAAATTCAAAATATTTATA
1 AAAATTCAAAATATATATA
*
20063532 AAAATTCTAAATATATATTAA
1 AAAATTCAAAATATATA-T-A
20063553 AAAATT-AAAATA
1 AAAATTCAAAATA
20063565 ATGTAAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 15 0.54
20 6 0.21
21 7 0.25
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAATTCAAAATATATATA
Found at i:20063555 original size:21 final size:19
Alignment explanation
Indices: 20063513--20063564 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
20063503 TTATATTTTT
20063513 AAAATTCAAAATATTTATA
1 AAAATTCAAAATATTTATA
20063532 AAAATTCTAAATATATATTA-A
1 AAAATTC-AAA-ATAT-TTATA
20063553 AAAATT-AAAATA
1 AAAATTCAAAATA
20063565 ATGTAAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
18 3 0.10
19 10 0.33
20 3 0.10
21 11 0.37
22 3 0.10
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAATTCAAAATATTTATA
Found at i:20069272 original size:28 final size:29
Alignment explanation
Indices: 20069240--20069295 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
20069230 TTTCATTATT
* *
20069240 TAAAATTAATTC-CATCAAGTGAAAGGAA
1 TAAAAGTAATTCACAACAAGTGAAAGGAA
**
20069268 TAAAAGTCTTTCACAACAAGTGAAAGGA
1 TAAAAGTAATTCACAACAAGTGAAAGGA
20069296 CTTTTTGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 9 0.39
29 14 0.61
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.23
Consensus pattern (29 bp):
TAAAAGTAATTCACAACAAGTGAAAGGAA
Found at i:20071647 original size:2 final size:2
Alignment explanation
Indices: 20071640--20071668 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20071630 AAACAAAACA
20071640 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 A
20071669 GACATGGTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20075856 original size:24 final size:23
Alignment explanation
Indices: 20075801--20075863 Score: 90
Period size: 24 Copynumber: 2.7 Consensus size: 23
20075791 AACTTAATCA
20075801 AACATGTTCACGAACATTAAATG
1 AACATGTTCACGAACATTAAATG
* * *
20075824 AACAAGTTCATGAACATATAATTG
1 AACATGTTCACGAACAT-TAAATG
20075848 AACATGTTCACGAACA
1 AACATGTTCACGAACA
20075864 ATGTTAATGA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 15 0.44
24 19 0.56
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.25
Consensus pattern (23 bp):
AACATGTTCACGAACATTAAATG
Found at i:20075970 original size:11 final size:12
Alignment explanation
Indices: 20075953--20075985 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
20075943 ATCATTAATA
20075953 AATAAACGAGTC
1 AATAAACGAGTC
*
20075965 -ATAAACAAGTC
1 AATAAACGAGTC
20075976 AATAAACGAG
1 AATAAACGAG
20075986 CTTGTTTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.55, C:0.15, G:0.15, T:0.15
Consensus pattern (12 bp):
AATAAACGAGTC
Found at i:20079172 original size:22 final size:22
Alignment explanation
Indices: 20079147--20079190 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
20079137 GAAGTCTACT
20079147 GGGAAATAACGAAGATAAAGGA
1 GGGAAATAACGAAGATAAAGGA
20079169 GGGAAATAACGAAGATAAAGGA
1 GGGAAATAACGAAGATAAAGGA
20079191 AGTCCATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.05, G:0.32, T:0.09
Consensus pattern (22 bp):
GGGAAATAACGAAGATAAAGGA
Found at i:20081137 original size:25 final size:25
Alignment explanation
Indices: 20081084--20081129 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
20081074 GTTGGATCCA
20081084 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAATTCTAAAAAGATAATTTG
*
20081109 AATTAAA-TCTAAACA-ATAATT
1 AATTAAATTCTAAAAAGATAATT
20081130 CTCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (25 bp):
AATTAAATTCTAAAAAGATAATTTG
Found at i:20081216 original size:13 final size:13
Alignment explanation
Indices: 20081195--20081228 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
20081185 ATAATATAAT
20081195 AATAATAATCCTA
1 AATAATAATCCTA
*
20081208 AATATTAATCCTA
1 AATAATAATCCTA
*
20081221 AAAAATAA
1 AATAATAA
20081229 AGTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:20082192 original size:17 final size:17
Alignment explanation
Indices: 20082168--20082206 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
20082158 CTTTTTCTTC
*
20082168 TCTTTTTTCTCAA-TTT
1 TCTTTTTTTTCAATTTT
20082184 TCTTTTTTTTCAATTTT
1 TCTTTTTTTTCAATTTT
20082201 TCTTTT
1 TCTTTT
20082207 CGACCTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.74
Consensus pattern (17 bp):
TCTTTTTTTTCAATTTT
Found at i:20086067 original size:13 final size:13
Alignment explanation
Indices: 20086042--20086087 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
20086032 GTAAAAGGGA
20086042 AAAAAATTGAAAT
1 AAAAAATTGAAAT
20086055 AGAAAAATT-AAAT
1 A-AAAAATTGAAAT
20086068 AAAAAA-TGCAAAT
1 AAAAAATTG-AAAT
20086081 AATAAAA
1 AA-AAAA
20086088 CAAAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
11 1 0.03
12 5 0.17
13 12 0.41
14 11 0.38
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.20
Consensus pattern (13 bp):
AAAAAATTGAAAT
Found at i:20087197 original size:25 final size:23
Alignment explanation
Indices: 20087169--20087221 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 23
20087159 ACTCTAGTTG
20087169 AATTCAAATTAAATTCTAAAAAGAT
1 AATTCAAATTAAA-TCTAAAAA-AT
** *
20087194 AATTTGAATTAAATCTAAACAAT
1 AATTCAAATTAAATCTAAAAAAT
20087217 AATTC
1 AATTC
20087222 CCTAATTGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 6 0.25
24 7 0.29
25 11 0.46
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (23 bp):
AATTCAAATTAAATCTAAAAAAT
Found at i:20088659 original size:129 final size:129
Alignment explanation
Indices: 20088366--20088752 Score: 607
Period size: 129 Copynumber: 3.0 Consensus size: 129
20088356 TAGATTCTAT
* * *
20088366 AGAGAGATATTTACTTTCCTACTAAAAGTAAGAAAATTGTTTCTGGTTCTGTGTTTGATTCGTGT
1 AGAGAGAGATTTACTTTCCTACTAAAAGTAAGAAAATTATTTTTGGTTCTGTGTTTGATTCGT-T
* * * *
20088431 -TTATTTGAGCCCACACTCAAAGCGATTCGTGGTACAAG-ATAGCGAAGAAGGTCGTTCGGTTGA
65 ATTGTTCGAGCCCACACTCGAAGCGATTCGTGGTACGAGAATAGCGAAGAAGGTCGTTCGGTTGA
* *
20088494 AGAGAGAGATTTACTTTTCTTCTAAAAGTAAGAAAATTATTTTTGGTTCTGTGTTTGATTCGTTA
1 AGAGAGAGATTTACTTTCCTACTAAAAGTAAGAAAATTATTTTTGGTTCTGTGTTTGATTCGTTA
*
20088559 TTGTTCGAGCCCACACTCGAAGCGATTCATGGTACGAGAATAGCGAAGAAGGTCGTTCGGTTGA
66 TTGTTCGAGCCCACACTCGAAGCGATTCGTGGTACGAGAATAGCGAAGAAGGTCGTTCGGTTGA
* *
20088623 AGAGAGAGATTTACTTTCCTACCAAAAGTAAGAAAATTATTTTTGGTTCTGTGTTTGATTCGTGA
1 AGAGAGAGATTTACTTTCCTACTAAAAGTAAGAAAATTATTTTTGGTTCTGTGTTTGATTCGTTA
* * * *
20088688 TTGTTCGAGCCCACATTCGAAGCGATTCGTGGTACGATAATAGCGAAGAAGATTGTTCGGTTGA
66 TTGTTCGAGCCCACACTCGAAGCGATTCGTGGTACGAGAATAGCGAAGAAGGTCGTTCGGTTGA
20088752 A
1 A
20088753 AGCCAAGAAC
Statistics
Matches: 238, Mismatches: 19, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
127 1 0.00
128 91 0.38
129 146 0.61
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (129 bp):
AGAGAGAGATTTACTTTCCTACTAAAAGTAAGAAAATTATTTTTGGTTCTGTGTTTGATTCGTTA
TTGTTCGAGCCCACACTCGAAGCGATTCGTGGTACGAGAATAGCGAAGAAGGTCGTTCGGTTGA
Found at i:20101705 original size:18 final size:18
Alignment explanation
Indices: 20101684--20101718 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
20101674 TTTTTAAAAT
20101684 ATTTTTAGAAT-ATTTATG
1 ATTTTT-GAATGATTTATG
20101702 ATTTTTGAATGATTTAT
1 ATTTTTGAATGATTTAT
20101719 TTAATCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.57
Consensus pattern (18 bp):
ATTTTTGAATGATTTATG
Found at i:20102261 original size:17 final size:18
Alignment explanation
Indices: 20102228--20102262 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
20102218 TTAATAACAC
20102228 AAATATAAAATATTATAA
1 AAATATAAAATATTATAA
20102246 AAATATAAAA-ATTATAA
1 AAATATAAAATATTATAA
20102263 TTGTTACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATATAAAATATTATAA
Found at i:20102438 original size:18 final size:18
Alignment explanation
Indices: 20102410--20102457 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
20102400 TAGTTTTATT
20102410 ATATATTTTTATAATCTTT-
1 ATAT-TTTTTATAAT-TTTA
*
20102429 GTATTTTTTAATAATTTTA
1 ATATTTTTT-ATAATTTTA
20102448 ATATTTTTTA
1 ATATTTTTTA
20102458 ATATTGTTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
ATATTTTTTATAATTTTA
Found at i:20102456 original size:10 final size:10
Alignment explanation
Indices: 20102430--20102462 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
20102420 ATAATCTTTG
20102430 TATTTTTTAA
1 TATTTTTTAA
*
20102440 TA-ATTTTAA
1 TATTTTTTAA
20102449 TATTTTTTAA
1 TATTTTTTAA
20102459 TATT
1 TATT
20102463 GTTCCAACTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TATTTTTTAA
Found at i:20104290 original size:18 final size:18
Alignment explanation
Indices: 20104269--20104303 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
20104259 TTTTTAAAAT
20104269 ATTTTTAGAAT-ATTTATG
1 ATTTTT-GAATGATTTATG
20104287 ATTTTTGAATGATTTAT
1 ATTTTTGAATGATTTAT
20104304 TTATTAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.57
Consensus pattern (18 bp):
ATTTTTGAATGATTTATG
Found at i:20105045 original size:19 final size:19
Alignment explanation
Indices: 20105020--20105070 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
20105010 GTTTTATTAT
*
20105020 ATATTTTTTTATAATCTTT-
1 ATATTTTTTAATAAT-TTTA
*
20105039 GTATTTTTTAATAATTTTA
1 ATATTTTTTAATAATTTTA
20105058 ATATTTTTTAATA
1 ATATTTTTTAATA
20105071 TTGTTCCAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 3 0.11
19 25 0.89
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (19 bp):
ATATTTTTTAATAATTTTA
Found at i:20105066 original size:10 final size:10
Alignment explanation
Indices: 20105040--20105072 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
20105030 ATAATCTTTG
20105040 TATTTTTTAA
1 TATTTTTTAA
*
20105050 TA-ATTTTAA
1 TATTTTTTAA
20105059 TATTTTTTAA
1 TATTTTTTAA
20105069 TATT
1 TATT
20105073 GTTCCAACTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TATTTTTTAA
Found at i:20109106 original size:26 final size:24
Alignment explanation
Indices: 20109077--20109127 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 24
20109067 TTTGAAAGTA
20109077 AAAAATTAAATATGATGATAATTAAT
1 AAAAATTAAATATG-TGA-AATTAAT
*
20109103 AAAAATTAAATGTGTGAAATTAAT
1 AAAAATTAAATATGTGAAATTAAT
20109127 A
1 A
20109128 TTATATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 8 0.33
25 3 0.12
26 13 0.54
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (24 bp):
AAAAATTAAATATGTGAAATTAAT
Found at i:20109169 original size:19 final size:23
Alignment explanation
Indices: 20109119--20109162 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
20109109 TAAATGTGTG
20109119 AAATTAATATTATATATATTTATA
1 AAATTAATATTATATATA-TTATA
*
20109143 AAAATAATATTA-ATATATTA
1 AAATTAATATTATATATATTA
20109163 AATTAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 5 0.26
24 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AAATTAATATTATATATATTATA
Found at i:20110178 original size:23 final size:23
Alignment explanation
Indices: 20110151--20110207 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 23
20110141 ATTATCATTT
20110151 AATTAGTAAATATA-TATTTTAA-A
1 AATTA-TAAATATATTA-TTTAATA
*
20110174 AATTATAAAAATATTATTTAATA
1 AATTATAAATATATTATTTAATA
20110197 AATT-TAAATAT
1 AATTATAAATAT
20110208 TAACACTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 18 0.60
23 12 0.40
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
AATTATAAATATATTATTTAATA
Found at i:20111080 original size:17 final size:17
Alignment explanation
Indices: 20111060--20111093 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20111050 AAAAGTGTAG
*
20111060 TAATTTTAAAATTTTAA
1 TAATGTTAAAATTTTAA
*
20111077 TAATGTTAAACTTTTAA
1 TAATGTTAAAATTTTAA
20111094 ATATTTTTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (17 bp):
TAATGTTAAAATTTTAA
Found at i:20117562 original size:41 final size:42
Alignment explanation
Indices: 20117515--20117601 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
20117505 ACTCATCAAC
20117515 AAACTAAACCC-AATATAATTTCATTCTTCAAA-AACACTCAT
1 AAACTAAACCCAAATATAATTTCATTCTT-AAATAACACTCAT
*
20117556 AAACTAAACCCAAATATAATTTTATTCTTAAATAACACTCAT
1 AAACTAAACCCAAATATAATTTCATTCTTAAATAACACTCAT
20117598 AAAC
1 AAAC
20117602 AATTCCTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
41 14 0.33
42 29 0.67
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (42 bp):
AAACTAAACCCAAATATAATTTCATTCTTAAATAACACTCAT
Found at i:20130432 original size:15 final size:15
Alignment explanation
Indices: 20130414--20130452 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
20130404 GACCAAAGTA
20130414 TAATTTTATTTTTAT
1 TAATTTTATTTTTAT
*
20130429 TAATTTAAATTTTTAT
1 TAATTT-TATTTTTAT
*
20130445 AAATTTTA
1 TAATTTTA
20130453 AAGAGTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TAATTTTATTTTTAT
Found at i:20137716 original size:12 final size:12
Alignment explanation
Indices: 20137699--20137723 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20137689 ACCAGCACTT
20137699 TCCGTCTTTCTC
1 TCCGTCTTTCTC
20137711 TCCGTCTTTCTC
1 TCCGTCTTTCTC
20137723 T
1 T
20137724 TTCTTTTTTT
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:0.00, C:0.40, G:0.08, T:0.52
Consensus pattern (12 bp):
TCCGTCTTTCTC
Found at i:20142466 original size:79 final size:79
Alignment explanation
Indices: 20142334--20142538 Score: 284
Period size: 79 Copynumber: 2.6 Consensus size: 79
20142324 ACAAATATGA
* * * *
20142334 CACCCAGTGCTTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTAGTTAGATTAACCAACGACGT
1 CACCCAGTGCCTAGCGGATAAACCGCAAATGTAAGCCCAGCTCTAGTTAGATTAACCAACAACAT
*
20142399 CCGTCAAATCCTGG
66 CCATCAAATCCTGG
* * * * *
20142413 CACCCAGTGCCTAGCGGATAAACCGCGATTGTAAGCCCAGCTCTAGTTGGATTAACCAATAATAT
1 CACCCAGTGCCTAGCGGATAAACCGCAAATGTAAGCCCAGCTCTAGTTAGATTAACCAACAACAT
20142478 CCATCAAATCCTGG
66 CCATCAAATCCTGG
* ** *
20142492 CACCCAGTGCCTAACGGATAAACCGCAAATGTGTGCCCAGCACTAGT
1 CACCCAGTGCCTAGCGGATAAACCGCAAATGTAAGCCCAGCTCTAGT
20142539 CAGTTAAACT
Statistics
Matches: 110, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 110 1.00
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.20
Consensus pattern (79 bp):
CACCCAGTGCCTAGCGGATAAACCGCAAATGTAAGCCCAGCTCTAGTTAGATTAACCAACAACAT
CCATCAAATCCTGG
Found at i:20144487 original size:42 final size:42
Alignment explanation
Indices: 20144439--20144526 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 42
20144429 ACCCATCAAC
* *
20144439 AAACTAAACCCAAATATAATTTCATTCTTCAAA-AACACTCCT
1 AAACTAAACCCAAATATAATTTCATTCCT-AAATAACACTCAT
*
20144481 AAACTAAACCCAAATATAATTTTATTCCTAAATAACACTCAT
1 AAACTAAACCCAAATATAATTTCATTCCTAAATAACACTCAT
20144523 AAAC
1 AAAC
20144527 AACTCCTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
41 3 0.07
42 39 0.93
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (42 bp):
AAACTAAACCCAAATATAATTTCATTCCTAAATAACACTCAT
Found at i:20152469 original size:26 final size:26
Alignment explanation
Indices: 20152436--20152486 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
20152426 ACTTATATAT
*
20152436 TTTAATTAGTAATTAATT-TTAATTTA
1 TTTAATTA-AAATTAATTGTTAATTTA
20152462 TTTAATTAAAATTAATTGTTAATTT
1 TTTAATTAAAATTAATTGTTAATTT
20152487 TATATATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (26 bp):
TTTAATTAAAATTAATTGTTAATTTA
Found at i:20159166 original size:30 final size:30
Alignment explanation
Indices: 20159106--20159168 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
20159096 AATTTATATC
* **
20159106 TTTATAATTTTTAAAAAATTAATTTAAATT
1 TTTATAATTTTTAAAAAATCAAAATAAATT
*
20159136 TTTAT-ATTTTTAAAAGATCAAAATATAATT
1 TTTATAATTTTTAAAAAATCAAAATA-AATT
20159166 TTT
1 TTT
20159169 TTTTTATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (30 bp):
TTTATAATTTTTAAAAAATCAAAATAAATT
Found at i:20166874 original size:29 final size:29
Alignment explanation
Indices: 20166832--20166889 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
20166822 TCCTCGATCA
20166832 CTTTAGCGTGTATTTGAGTGATTAAATCT
1 CTTTAGCGTGTATTTGAGTGATTAAATCT
*
20166861 CTTTAGCTTGTATTTGAGTGATTAAATCT
1 CTTTAGCGTGTATTTGAGTGATTAAATCT
20166890 TTATTGTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.24, C:0.10, G:0.19, T:0.47
Consensus pattern (29 bp):
CTTTAGCGTGTATTTGAGTGATTAAATCT
Found at i:20167417 original size:7 final size:7
Alignment explanation
Indices: 20167405--20167437 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
20167395 TTATGTCTGT
20167405 ATATTGC
1 ATATTGC
20167412 ATATTGC
1 ATATTGC
20167419 ATATTGC
1 ATATTGC
20167426 ATATTGC
1 ATATTGC
*
20167433 TTATT
1 ATATT
20167438 TTTATTTGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.48
Consensus pattern (7 bp):
ATATTGC
Found at i:20173180 original size:24 final size:24
Alignment explanation
Indices: 20173144--20173190 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
20173134 AGAAATAATC
* *
20173144 TTTCAGTTAAACTTTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
*
20173168 TTTCAATTGAACTCTGTTTATTT
1 TTTCAATTAAACTCTGTTTATTT
20173191 ATTTGAACTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.21, C:0.11, G:0.11, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:20175169 original size:24 final size:24
Alignment explanation
Indices: 20175126--20175172 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
20175116 TAAAACTTTG
*
20175126 TTTATTTGTTTCAATTAAACTCTA
1 TTTATTTGTTTCAATCAAACTCTA
* *
20175150 TTTATTTGTTTGAGTCAAACTCT
1 TTTATTTGTTTCAATCAAACTCT
20175173 TATTACTCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.53
Consensus pattern (24 bp):
TTTATTTGTTTCAATCAAACTCTA
Found at i:20176087 original size:17 final size:17
Alignment explanation
Indices: 20176017--20176081 Score: 69
Period size: 17 Copynumber: 3.8 Consensus size: 17
20176007 TTATTAATTA
20176017 TATATATATATTTAATTT
1 TATATATATATTT-ATTT
* * *
20176035 TATAAATATTTTTGTTT
1 TATATATATATTTATTT
*
20176052 TAGT-TATTTATTTATTT
1 TA-TATATATATTTATTT
20176069 TATATATATATTT
1 TATATATATATTT
20176082 GGTTTAATAC
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
16 1 0.03
17 24 0.65
18 12 0.32
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
TATATATATATTTATTT
Found at i:20178637 original size:15 final size:15
Alignment explanation
Indices: 20178595--20178642 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
20178585 AATTTTATAA
20178595 TTTAA-ACTTAATTT
1 TTTAACACTTAATTT
*
20178609 TTTAACA-TTTATTT
1 TTTAACACTTAATTT
**
20178623 TTTCTCACTTAATTT
1 TTTAACACTTAATTT
20178638 TTTAA
1 TTTAA
20178643 TTTATCATAC
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
14 16 0.62
15 10 0.38
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTAACACTTAATTT
Found at i:20179141 original size:18 final size:19
Alignment explanation
Indices: 20179096--20179157 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
20179086 TATACACATT
20179096 AAAAATATA-AAAA--TAG
1 AAAAATATATAAAATCTAG
*
20179112 AAATAAATATATACAAATTTAG
1 -AA-AAATATATA-AAATCTAG
20179134 AAAAATATATAAAATCTAG
1 AAAAATATATAAAATCTAG
20179153 AAAAA
1 AAAAA
20179158 AAAATAAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
17 2 0.05
18 7 0.18
19 13 0.33
20 12 0.31
21 2 0.05
22 3 0.08
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (19 bp):
AAAAATATATAAAATCTAG
Found at i:20179148 original size:47 final size:46
Alignment explanation
Indices: 20179097--20179186 Score: 110
Period size: 46 Copynumber: 1.9 Consensus size: 46
20179087 ATACACATTA
* * * *
20179097 AAAATATA-AAAATAGAAATAAATATATACAAATTTAGAAAAATATAT
1 AAAATATAGAAAA-AAAAATAAAT-TATAAAAAATTACAAAAATATAT
*
20179144 AAAATCTAGAAAAAAAAATAAATTATAAAAAATTACAAAAATA
1 AAAATATAGAAAAAAAAATAAATTATAAAAAATTACAAAAATA
20179187 CAATAATTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
46 17 0.46
47 16 0.43
48 4 0.11
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.24
Consensus pattern (46 bp):
AAAATATAGAAAAAAAAATAAATTATAAAAAATTACAAAAATATAT
Found at i:20179157 original size:20 final size:19
Alignment explanation
Indices: 20179096--20179176 Score: 73
Period size: 20 Copynumber: 4.3 Consensus size: 19
20179086 TATACACATT
20179096 AAAAATATA-AAAA-TAGA
1 AAAAATATATAAAATTAGA
20179113 AATAAATATATACAAATTTAG-
1 AA-AAATATATA-AAA-TTAGA
20179134 AAAAATATATAAAATCTAGA
1 AAAAATATATAAAAT-TAGA
* *
20179154 AAAAA-AAAT-AAATTATA
1 AAAAATATATAAAATTAGA
20179171 AAAAAT
1 AAAAAT
20179177 TACAAAAATA
Statistics
Matches: 54, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
17 10 0.19
18 12 0.22
19 10 0.19
20 17 0.31
21 2 0.04
22 3 0.06
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (19 bp):
AAAAATATATAAAATTAGA
Found at i:20179164 original size:19 final size:19
Alignment explanation
Indices: 20179126--20179165 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
20179116 AAATATATAC
* * *
20179126 AAATTTAGAAAAATATATA
1 AAATCTAGAAAAAAAAATA
20179145 AAATCTAGAAAAAAAAATA
1 AAATCTAGAAAAAAAAATA
20179164 AA
1 AA
20179166 TTATAAAAAA
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:0.70, C:0.03, G:0.05, T:0.23
Consensus pattern (19 bp):
AAATCTAGAAAAAAAAATA
Found at i:20179397 original size:22 final size:23
Alignment explanation
Indices: 20179365--20179426 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
20179355 TTATTTTGAC
* *
20179365 TTTTTAAAA-TTTATAAATAATT
1 TTTTTAAAATTTTATAAAAAATA
*
20179387 TTTTTAGAATTTTATAAAAAATA
1 TTTTTAAAATTTTATAAAAAATA
20179410 -TTTTAAAACTTTT-TAAA
1 TTTTTAAAA-TTTTATAAA
20179427 TATATATATG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
22 19 0.56
23 15 0.44
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTTTTAAAATTTTATAAAAAATA
Found at i:20179433 original size:23 final size:21
Alignment explanation
Indices: 20179366--20179433 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 21
20179356 TATTTTGACT
* *
20179366 TTTTAAAATTTATAAATAATTT
1 TTTTAAAATTTTTAAATAA-TA
* *
20179388 TTTTAGAATTTTATAAAAAATA
1 TTTTAAAATTTT-TAAATAATA
20179410 TTTTAAAACTTTTTAAATATATA
1 TTTTAAAA-TTTTTAAATA-ATA
20179433 T
1 T
20179434 ATGATTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
22 23 0.62
23 14 0.38
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (21 bp):
TTTTAAAATTTTTAAATAATA
Found at i:20190596 original size:7 final size:6
Alignment explanation
Indices: 20190568--20190595 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
20190558 GGCAATGAAG
20190568 GGGGAA GGGGAA GGGGAA GGGGAA GGGG
1 GGGGAA GGGGAA GGGGAA GGGGAA GGGG
20190596 GATTTTCCCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.71, T:0.00
Consensus pattern (6 bp):
GGGGAA
Found at i:20196774 original size:14 final size:14
Alignment explanation
Indices: 20196755--20196783 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
20196745 TCATACTTGC
20196755 TGTGAAGTTGCTCT
1 TGTGAAGTTGCTCT
20196769 TGTGAAGTTGCTCT
1 TGTGAAGTTGCTCT
20196783 T
1 T
20196784 TGTTTGTGAC
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:0.14, C:0.14, G:0.28, T:0.45
Consensus pattern (14 bp):
TGTGAAGTTGCTCT
Found at i:20201621 original size:15 final size:15
Alignment explanation
Indices: 20201601--20201630 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20201591 AACAACTTCG
20201601 ATCATGTCGCATTTT
1 ATCATGTCGCATTTT
*
20201616 ATCATGTCTCATTTT
1 ATCATGTCGCATTTT
20201631 TGTCTATGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.50
Consensus pattern (15 bp):
ATCATGTCGCATTTT
Found at i:20207591 original size:31 final size:31
Alignment explanation
Indices: 20207556--20207620 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
20207546 AATTGTTCAT
* *
20207556 TAAACTATTTAAAACTTTTCATTTAAGTCAC
1 TAAACTATTCAAAACTTTTCATTTAACTCAC
* *
20207587 TAAACTATTCAAAAGTTTTTATTTAACTCAC
1 TAAACTATTCAAAACTTTTCATTTAACTCAC
20207618 TAA
1 TAA
20207621 TATGTTAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.42
Consensus pattern (31 bp):
TAAACTATTCAAAACTTTTCATTTAACTCAC
Done.