Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 2 of 160
Found at i:109822 original size:2 final size:2
Alignment explanation
Indices: 109815--109847 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
109805 TCGTTTACAA
*
109815 AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
109848 ATACAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:110034 original size:80 final size:80
Alignment explanation
Indices: 109944--110098 Score: 301
Period size: 80 Copynumber: 1.9 Consensus size: 80
109934 TATCATTTTC
*
109944 GAGATCTCGTCTTCTATGGTTTTTTATTTGTTTTATTTTTTATTTACCTTGTGCCTTCTCTGTAA
1 GAGATCTCGTCTTCTATGGTTTTTTATTTGTTTTATTTTTAATTTACCTTGTGCCTTCTCTGTAA
110009 TTGAATTAGGACTTG
66 TTGAATTAGGACTTG
110024 GAGATCTCGTCTTCTATGGTTTTTTATTTGTTTTATTTTTAATTTACCTTGTGCCTTCTCTGTAA
1 GAGATCTCGTCTTCTATGGTTTTTTATTTGTTTTATTTTTAATTTACCTTGTGCCTTCTCTGTAA
110089 TTGAATTAGG
66 TTGAATTAGG
110099 GCTTTTCTTC
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 74 1.00
ACGTcount: A:0.17, C:0.14, G:0.16, T:0.54
Consensus pattern (80 bp):
GAGATCTCGTCTTCTATGGTTTTTTATTTGTTTTATTTTTAATTTACCTTGTGCCTTCTCTGTAA
TTGAATTAGGACTTG
Found at i:121731 original size:25 final size:25
Alignment explanation
Indices: 121674--121733 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
121664 CAAATTTAGA
**
121674 AAAAAATTTATCATCTTGGAATTTT
1 AAAAAATTTATCATCTTAAAATTTT
*
121699 ATAGAAATTTATCAT-TTAAAATTTCT
1 A-AAAAATTTATCATCTTAAAATTT-T
121725 AAAAAATTT
1 AAAAAATTT
121734 CATCTTTGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
25 15 0.52
26 14 0.48
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (25 bp):
AAAAAATTTATCATCTTAAAATTTT
Found at i:122679 original size:16 final size:16
Alignment explanation
Indices: 122660--122691 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
122650 ATTTTTCTAA
*
122660 TTTTTTGTTTTTTATT
1 TTTTTTATTTTTTATT
122676 TTTTTTATTTTTTATT
1 TTTTTTATTTTTTATT
122692 AACAAAGTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.00, G:0.03, T:0.88
Consensus pattern (16 bp):
TTTTTTATTTTTTATT
Found at i:122906 original size:43 final size:42
Alignment explanation
Indices: 122858--123117 Score: 243
Period size: 43 Copynumber: 6.0 Consensus size: 42
122848 TAAAAACTTT
* * **
122858 TCTAAACAGAGGCTTTACAACTTTCAAGAAATAAATAAGCTAA
1 TCTAAACAGAGGCTTAACAACTTTGAA-AAATAAATAAGCTCC
* * *
122901 TCTAAATAGAGG-TTCAACGACTTCTGAAAAATAAACAAAGCTCC
1 TCTAAACAGAGGCTT-AACAACTT-TGAAAAATAAA-TAAGCTCC
* *
122945 TCTAAACAGAGGCTTAATAACTTTGAAAAATAAATAAAGCTCT
1 TCTAAACAGAGGCTTAACAACTTTGAAAAATAAAT-AAGCTCC
* * * *
122988 TCTAAACAGAGACTCAACAATTTTGAACAATAAATAAAGCTCC
1 TCTAAACAGAGGCTTAACAACTTTGAAAAATAAAT-AAGCTCC
* *
123031 TCTAAGCAGAGGCTCAACAACTTTGAAAAATAAATAAAGCTCC
1 TCTAAACAGAGGCTTAACAACTTTGAAAAATAAAT-AAGCTCC
* * * * * * *
123074 TATAAGCAGATGCTCAATAATTTTGAAAACTAAATAAAGCTCC
1 TCTAAACAGAGGCTTAACAACTTTGAAAAATAAAT-AAGCTCC
123117 T
1 T
123118 ATAAGTAGAG
Statistics
Matches: 185, Mismatches: 27, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
42 2 0.01
43 156 0.84
44 25 0.14
45 2 0.01
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.25
Consensus pattern (42 bp):
TCTAAACAGAGGCTTAACAACTTTGAAAAATAAATAAGCTCC
Found at i:123041 original size:86 final size:84
Alignment explanation
Indices: 122858--123158 Score: 300
Period size: 86 Copynumber: 3.5 Consensus size: 84
122848 TAAAAACTTT
* * * * * *
122858 TCTAAACAGAGGCTTTACAACTTTCAAGAAATAAAT-AAGCTAATCTAAATAGAGGTTCAACGAC
1 TCTAAACAGAGGCTTAACAACTTTGAA-AAATAAATAAAGCTCATCTAAACAGA-GCTCAAC-AA
* *
122922 TTCTGAAAAATAAACAAAGCTCC
63 TTTTG-AAAATAAATAAAGCTCC
* *
122945 TCTAAACAGAGGCTTAATAACTTTGAAAAATAAATAAAGCTCTTCTAAACAGAGACTCAACAATT
1 TCTAAACAGAGGCTTAACAACTTTGAAAAATAAATAAAGCTCATCTAAACAGAG-CTCAACAATT
123010 TTGAACAATAAATAAAGCTCC
65 TTGAA-AATAAATAAAGCTCC
* * * * * *
123031 TCTAAGCAGAGGCTCAACAACTTTGAAAAATAAATAAAGCTCCTATAAGCAGATGCTCAATAATT
1 TCTAAACAGAGGCTTAACAACTTTGAAAAATAAATAAAGCTCATCTAAACAGA-GCTCAACAATT
123096 TTGAAAACTAAATAAAGCTCC
65 TTGAAAA-TAAATAAAGCTCC
* ** * * * *
123117 TATAAGTAGAGG-TTCGATAATTTTAAAAAATAAATAAAGCTC
1 TCTAAACAGAGGCTT-AACAACTTTGAAAAATAAATAAAGCTC
123159 CTTTACAATC
Statistics
Matches: 184, Mismatches: 24, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
85 5 0.03
86 135 0.73
87 44 0.24
ACGTcount: A:0.46, C:0.17, G:0.12, T:0.26
Consensus pattern (84 bp):
TCTAAACAGAGGCTTAACAACTTTGAAAAATAAATAAAGCTCATCTAAACAGAGCTCAACAATTT
TGAAAATAAATAAAGCTCC
Found at i:123099 original size:129 final size:130
Alignment explanation
Indices: 122886--123160 Score: 329
Period size: 129 Copynumber: 2.1 Consensus size: 130
122876 AACTTTCAAG
** ** * * *
122886 AAATAAAT-AAGCTAATCTAAATAGAGGTTCAACGACTTCTGAAAAATAAACAAAGCTCCTCTAA
1 AAATAAATAAAGCTCCTCTAAGCAGAGGCTCAACAACTTCTGAAAAATAAACAAAGCTCCTATAA
* * * *
122950 ACAGAGGCTTAATAACTTTGAAAAATAAATAAAGCTCTTCTAAACAGAGACTCAACAATTTTGAA
66 ACAGAGGCTCAATAACTTTGAAAAATAAATAAAGCTCCTATAAACAGAGACTCAACAATTTTAAA
* *
123015 CAATAAATAAAGCTCCTCTAAGCAGAGGCTCAACAACTT-TGAAAAATAAATAAAGCTCCTATAA
1 AAATAAATAAAGCTCCTCTAAGCAGAGGCTCAACAACTTCTGAAAAATAAACAAAGCTCCTATAA
* * * * ** ** * *
123079 GCAGATGCTCAATAATTTTGAAAACTAAATAAAGCTCCTATAAGTAGAGGTTCGATAATTTTAAA
66 ACAGAGGCTCAATAACTTTGAAAAATAAATAAAGCTCCTATAAACAGAGACTCAACAATTTTAAA
123144 AAATAAATAAAGCTCCT
1 AAATAAATAAAGCTCCT
123161 TTACAATCTT
Statistics
Matches: 121, Mismatches: 24, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
129 97 0.80
130 24 0.20
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.25
Consensus pattern (130 bp):
AAATAAATAAAGCTCCTCTAAGCAGAGGCTCAACAACTTCTGAAAAATAAACAAAGCTCCTATAA
ACAGAGGCTCAATAACTTTGAAAAATAAATAAAGCTCCTATAAACAGAGACTCAACAATTTTAAA
Found at i:123118 original size:43 final size:43
Alignment explanation
Indices: 122925--123160 Score: 301
Period size: 43 Copynumber: 5.5 Consensus size: 43
122915 CAACGACTTC
* * * *
122925 TGAAAAATAAACAAAGCTCCTCTAAACAGAGGCTTAATAACTT
1 TGAAAAATAAATAAAGCTCCTCTAAGCAGAGGCTCAATAATTT
* * * *
122968 TGAAAAATAAATAAAGCTCTTCTAAACAGAGACTCAACAATTT
1 TGAAAAATAAATAAAGCTCCTCTAAGCAGAGGCTCAATAATTT
* * *
123011 TGAACAATAAATAAAGCTCCTCTAAGCAGAGGCTCAACAACTT
1 TGAAAAATAAATAAAGCTCCTCTAAGCAGAGGCTCAATAATTT
* *
123054 TGAAAAATAAATAAAGCTCCTATAAGCAGATGCTCAATAATTT
1 TGAAAAATAAATAAAGCTCCTCTAAGCAGAGGCTCAATAATTT
* * * * *
123097 TGAAAACTAAATAAAGCTCCTATAAGTAGAGGTTCGATAATTT
1 TGAAAAATAAATAAAGCTCCTCTAAGCAGAGGCTCAATAATTT
*
123140 TAAAAAATAAATAAAGCTCCT
1 TGAAAAATAAATAAAGCTCCT
123161 TTACAATCTT
Statistics
Matches: 170, Mismatches: 23, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 170 1.00
ACGTcount: A:0.46, C:0.17, G:0.12, T:0.25
Consensus pattern (43 bp):
TGAAAAATAAATAAAGCTCCTCTAAGCAGAGGCTCAATAATTT
Found at i:123381 original size:31 final size:31
Alignment explanation
Indices: 123321--123383 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
123311 AATTCACCAA
* *
123321 AATTTGATTATCAAAATTTCAGTTTCACAAG
1 AATTTGATTATCAAAATTTCAGATACACAAG
*
123352 AATTTGATTCAT-AAAATTTTAGATACACAAG
1 AATTTGATT-ATCAAAATTTCAGATACACAAG
123383 A
1 A
123384 TTTTTCATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 26 0.93
32 2 0.07
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.37
Consensus pattern (31 bp):
AATTTGATTATCAAAATTTCAGATACACAAG
Found at i:123928 original size:21 final size:22
Alignment explanation
Indices: 123902--123947 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
123892 AAAGATTCTT
123902 ATTTG-AAACTAAAAAATTTTC
1 ATTTGAAAACTAAAAAATTTTC
*
123923 ATTTGAAAACTCAAAAATTTTC
1 ATTTGAAAACTAAAAAATTTTC
123945 ATT
1 ATT
123948 GGATACTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.39
Consensus pattern (22 bp):
ATTTGAAAACTAAAAAATTTTC
Found at i:123938 original size:22 final size:22
Alignment explanation
Indices: 123889--123985 Score: 85
Period size: 21 Copynumber: 4.5 Consensus size: 22
123879 GGTTTCACAT
*
123889 CTCAAAGATTCTT-ATTTG-AAA
1 CTCAAAAATT-TTCATTTGAAAA
*
123910 CTAAAAAATTTTCATTTGAAAA
1 CTCAAAAATTTTCATTTGAAAA
* *
123932 CTCAAAAATTTTCA-TTGGATA
1 CTCAAAAATTTTCATTTGAAAA
* * *
123953 CTCAAAGATTCTCATCTGAAAA
1 CTCAAAAATTTTCATTTGAAAA
*
123975 CT-TAAAATTTT
1 CTCAAAAATTTT
123986 ATCTTAAGAG
Statistics
Matches: 60, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
20 2 0.03
21 36 0.60
22 22 0.37
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.37
Consensus pattern (22 bp):
CTCAAAAATTTTCATTTGAAAA
Found at i:124895 original size:21 final size:22
Alignment explanation
Indices: 124854--124895 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
124844 TTAATCTAGA
*
124854 ATTATTTTTCAAAACTCATTTC
1 ATTATCTTTCAAAACTCATTTC
*
124876 ATTATCTTTCGAAA-TCATTT
1 ATTATCTTTCAAAACTCATTT
124896 TAAGCTCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.31, C:0.17, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTATCTTTCAAAACTCATTTC
Found at i:125071 original size:26 final size:26
Alignment explanation
Indices: 125037--125102 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
125027 AGTATTCCTT
*
125037 TTTTATTTTTCATTTTTCACTTTTCTC
1 TTTT-TTTTTCATTTTTCACTTTTCTA
* * * *
125064 TTTTTTTTTCCTTTTTTATTTTTTTA
1 TTTTTTTTTCATTTTTCACTTTTCTA
125090 TTTTTTTTTCATT
1 TTTTTTTTTCATT
125103 ATTGATATCT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 29 0.88
27 4 0.12
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (26 bp):
TTTTTTTTTCATTTTTCACTTTTCTA
Found at i:125077 original size:18 final size:19
Alignment explanation
Indices: 125049--125088 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
125039 TTATTTTTCA
*
125049 TTTTTCACTTTTCTCTTTT
1 TTTTTCACTTTTCTATTTT
*
125068 TTTTTC-CTTTTTTATTTT
1 TTTTTCACTTTTCTATTTT
125086 TTT
1 TTT
125089 ATTTTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTCACTTTTCTATTTT
Found at i:129865 original size:19 final size:19
Alignment explanation
Indices: 129841--129882 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
129831 AACCTGCTAA
* *
129841 AAAATTCAACTAACATTGG
1 AAAATTCAACAAAAATTGG
*
129860 AAAATTCATCAAAAATTGG
1 AAAATTCAACAAAAATTGG
129879 AAAA
1 AAAA
129883 AGTCATTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.55, C:0.12, G:0.10, T:0.24
Consensus pattern (19 bp):
AAAATTCAACAAAAATTGG
Found at i:130203 original size:13 final size:14
Alignment explanation
Indices: 130172--130209 Score: 60
Period size: 13 Copynumber: 2.7 Consensus size: 14
130162 CCATCCTAAA
130172 ATTTTTCTATTTTTC
1 ATTTTT-TATTTTTC
130187 ATTTTTTATTTTT-
1 ATTTTTTATTTTTC
130200 ATTTTTTATT
1 ATTTTTTATT
130210 AACAAAGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 10 0.43
14 7 0.30
15 6 0.26
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (14 bp):
ATTTTTTATTTTTC
Found at i:130206 original size:7 final size:7
Alignment explanation
Indices: 130172--130209 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
130162 CCATCCTAAA
130172 ATTTTTCT
1 ATTTTT-T
*
130180 ATTTTTC
1 ATTTTTT
130187 ATTTTTT
1 ATTTTTT
130194 A-TTTTT
1 ATTTTTT
130200 ATTTTTT
1 ATTTTTT
130207 ATT
1 ATT
130210 AACAAAGTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
6 6 0.22
7 15 0.56
8 6 0.22
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (7 bp):
ATTTTTT
Found at i:132265 original size:9 final size:9
Alignment explanation
Indices: 132253--132279 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
132243 CCATGAATAA
132253 ATCATATAT
1 ATCATATAT
132262 ATCATATAT
1 ATCATATAT
132271 ATCATATAT
1 ATCATATAT
132280 TATATTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (9 bp):
ATCATATAT
Found at i:133186 original size:16 final size:16
Alignment explanation
Indices: 133165--133195 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
133155 AAATAAAAAT
133165 AAAAATTTATTTTTAA
1 AAAAATTTATTTTTAA
133181 AAAAATTTATTTTTA
1 AAAAATTTATTTTTA
133196 TTTTGTATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AAAAATTTATTTTTAA
Found at i:142355 original size:14 final size:14
Alignment explanation
Indices: 142336--142366 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
142326 AAAATTTTCA
142336 ATTGTTTCTTCTAT
1 ATTGTTTCTTCTAT
142350 ATTGTTTCTTCTAT
1 ATTGTTTCTTCTAT
142364 ATT
1 ATT
142367 CTTTTTATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.13, G:0.06, T:0.65
Consensus pattern (14 bp):
ATTGTTTCTTCTAT
Found at i:144935 original size:240 final size:240
Alignment explanation
Indices: 144512--144992 Score: 962
Period size: 240 Copynumber: 2.0 Consensus size: 240
144502 TGGGCGAACC
144512 AAATTTACTGATGCTAACAAATTTCTTGGGACATAGGTTCCTGTATTTATTTATTCCTTCAAATA
1 AAATTTACTGATGCTAACAAATTTCTTGGGACATAGGTTCCTGTATTTATTTATTCCTTCAAATA
144577 CTTGATATCATTGAAGATTTTATTCTTAGAATAGTTGTTAAGTTTTGGACCTAGTCATCTGCAAT
66 CTTGATATCATTGAAGATTTTATTCTTAGAATAGTTGTTAAGTTTTGGACCTAGTCATCTGCAAT
144642 GAGTAATGTTGACTAGTCAAATATTATACCTACTTAGAGATCAACTGTAAAATATTGACAATTAG
131 GAGTAATGTTGACTAGTCAAATATTATACCTACTTAGAGATCAACTGTAAAATATTGACAATTAG
144707 AGGCGAACCTTAATTATCATGCTGAGTTTGCATTTCTGAAAATTT
196 AGGCGAACCTTAATTATCATGCTGAGTTTGCATTTCTGAAAATTT
144752 AAATTTACTGATGCTAACAAATTTCTTGGGACATAGGTTCCTGTATTTATTTATTCCTTCAAATA
1 AAATTTACTGATGCTAACAAATTTCTTGGGACATAGGTTCCTGTATTTATTTATTCCTTCAAATA
144817 CTTGATATCATTGAAGATTTTATTCTTAGAATAGTTGTTAAGTTTTGGACCTAGTCATCTGCAAT
66 CTTGATATCATTGAAGATTTTATTCTTAGAATAGTTGTTAAGTTTTGGACCTAGTCATCTGCAAT
144882 GAGTAATGTTGACTAGTCAAATATTATACCTACTTAGAGATCAACTGTAAAATATTGACAATTAG
131 GAGTAATGTTGACTAGTCAAATATTATACCTACTTAGAGATCAACTGTAAAATATTGACAATTAG
144947 AGGCGAACCTTAATTATCATGCTGAGTTTGCATTTCTGAAAATTT
196 AGGCGAACCTTAATTATCATGCTGAGTTTGCATTTCTGAAAATTT
144992 A
1 A
144993 TTACTTAGCT
Statistics
Matches: 241, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
240 241 1.00
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (240 bp):
AAATTTACTGATGCTAACAAATTTCTTGGGACATAGGTTCCTGTATTTATTTATTCCTTCAAATA
CTTGATATCATTGAAGATTTTATTCTTAGAATAGTTGTTAAGTTTTGGACCTAGTCATCTGCAAT
GAGTAATGTTGACTAGTCAAATATTATACCTACTTAGAGATCAACTGTAAAATATTGACAATTAG
AGGCGAACCTTAATTATCATGCTGAGTTTGCATTTCTGAAAATTT
Found at i:159722 original size:44 final size:44
Alignment explanation
Indices: 159674--159763 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
159664 ATGCCAAGTG
159674 CAAGGTGTTGACTATATACAAGATAGTTTAAGACCTAAAAGTAA
1 CAAGGTGTTGACTATATACAAGATAGTTTAAGACCTAAAAGTAA
159718 CAAGGTGTTGACTATATACAAGATAGTTTAAGACCTAAAAGTAA
1 CAAGGTGTTGACTATATACAAGATAGTTTAAGACCTAAAAGTAA
159762 CA
1 CA
159764 TCAGAAGAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (44 bp):
CAAGGTGTTGACTATATACAAGATAGTTTAAGACCTAAAAGTAA
Found at i:173751 original size:2 final size:2
Alignment explanation
Indices: 173739--173767 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
173729 TTTATACCTC
173739 AT AT A- 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
173768 CAATCATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:182059 original size:10 final size:11
Alignment explanation
Indices: 182046--182083 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 11
182036 TAAAAGCAAT
182046 TATATTATAT-
1 TATATTATATA
*
182056 TATATTACATA
1 TATATTATATA
182067 TATATATATATA
1 TATAT-TATATA
182079 TATAT
1 TATAT
182084 CTAAAGCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.38
11 5 0.21
12 10 0.42
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (11 bp):
TATATTATATA
Found at i:183880 original size:8 final size:8
Alignment explanation
Indices: 183861--183891 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
183851 CCTGCCCAAA
183861 TTTTCTTCC
1 TTTTC-TCC
183870 TTTTCTCC
1 TTTTCTCC
183878 TTTTCTCC
1 TTTTCTCC
183886 TTTTCT
1 TTTTCT
183892 TTTTGGTCGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.77
9 5 0.23
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (8 bp):
TTTTCTCC
Found at i:196326 original size:19 final size:19
Alignment explanation
Indices: 196295--196331 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
196285 ATACGATAGA
196295 TTAATTATTATTTTAAAAT
1 TTAATTATTATTTTAAAAT
196314 TTAA-TATTAATTTTAAAA
1 TTAATTATT-ATTTTAAAA
196332 AATAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTAATTATTATTTTAAAAT
Found at i:196500 original size:20 final size:19
Alignment explanation
Indices: 196462--196500 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
196452 AGAAACCAAT
* *
196462 TTATTAAAGAATTTGAATA
1 TTATTAAAAAATTTAAATA
196481 TTATTAAAAAAATTTAAATA
1 TTATT-AAAAAATTTAAATA
196501 CAAAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
TTATTAAAAAATTTAAATA
Found at i:197662 original size:3 final size:3
Alignment explanation
Indices: 197654--197679 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
197644 TGACAGCAAC
197654 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
197680 AAATAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:201376 original size:26 final size:28
Alignment explanation
Indices: 201331--201385 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 28
201321 CCATCAAACC
201331 CTTTTTTTTTTTCGTAATTTTCTTATTTA
1 CTTTTTTTTTTTC-TAATTTTCTTATTTA
*
201360 CTTTTTTTTTTT-T-ATTTTTTTATTTA
1 CTTTTTTTTTTTCTAATTTTCTTATTTA
201386 TTAAATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 12 0.48
27 1 0.04
29 12 0.48
ACGTcount: A:0.13, C:0.07, G:0.02, T:0.78
Consensus pattern (28 bp):
CTTTTTTTTTTTCTAATTTTCTTATTTA
Found at i:201456 original size:14 final size:16
Alignment explanation
Indices: 201425--201456 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
201415 AATATTCAAT
201425 TATTATTAATTAATTA
1 TATTATTAATTAATTA
201441 TATTA-TAA-TAATTA
1 TATTATTAATTAATTA
201455 TA
1 TA
201457 AATGATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTATTAATTAATTA
Found at i:204760 original size:22 final size:21
Alignment explanation
Indices: 204519--204750 Score: 121
Period size: 21 Copynumber: 10.7 Consensus size: 21
204509 TGTTAAAATA
* *
204519 AAAATTATATAAAAAAATTATT
1 AAAATTATAT-TAAAAATTATC
*
204541 AAAAATATATCT-AAAATTATC
1 AAAATTATAT-TAAAAATTATC
* **
204562 AAAATTATTTTAATGATTATC
1 AAAATTATATTAAAAATTATC
* * *
204583 AAAATTATATCATAAGTTATC
1 AAAATTATATTAAAAATTATC
* * *
204604 AAAATCATATTTAAAATAACTAAAATT
1 AAAATTATA-TT-AAA-AA-T--TATC
* ** *
204631 AAAATTTTATTAATGATTATT
1 AAAATTATATTAAAAATTATC
* **
204652 AAAATTATATCAATGATTAGT-
1 AAAATTATATTAAAAATTA-TC
* *
204673 TAAATTATATCATAAAATT-TC
1 AAAATTATATTA-AAAATTATC
*
204694 AAAATAATA-TAAAAAGTTATC
1 AAAATTATATTAAAAA-TTATC
*
204715 AAAGTTATATTAAAAATTATC
1 AAAATTATATTAAAAATTATC
*
204736 AAAATTTTATTAAAA
1 AAAATTATATTAAAA
204751 TGCTATCAAA
Statistics
Matches: 160, Mismatches: 37, Indels: 27
0.71 0.17 0.12
Matches are distributed among these distances:
19 4 0.03
20 5 0.03
21 111 0.69
22 21 0.13
23 3 0.02
24 2 0.01
25 3 0.02
26 2 0.01
27 9 0.06
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (21 bp):
AAAATTATATTAAAAATTATC
Found at i:204761 original size:21 final size:20
Alignment explanation
Indices: 204703--204763 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 20
204693 CAAAATAATA
*
204703 TAAAAAGTTATCAAAGTTATAT
1 TAAAAA-TTATCAAA-TTTTAT
204725 TAAAAATTATCAAAATTTTAT
1 TAAAAATTATC-AAATTTTAT
204746 T-AAAATGCTATCAAATTT
1 TAAAAAT--TATCAAATTT
204764 CTAACAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
20 5 0.14
21 17 0.49
22 13 0.37
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (20 bp):
TAAAAATTATCAAATTTTAT
Found at i:206375 original size:188 final size:190
Alignment explanation
Indices: 206052--206422 Score: 534
Period size: 188 Copynumber: 2.0 Consensus size: 190
206042 TTGATTAGAA
* **
206052 AAAATACATATATATTAATTCTTAAATAATTATCATAATCTTTTTAACATATATGATATTAATTT
1 AAAATACATATATATTAATTATTAAATAATTATCATAATCTCCTTAACATATATGATATTAATTT
** *
206117 TTTATTAACTTTTATTAATAATAAATATGACAAATGATACCTTTAACAATAAAAAAAAGATAAAT
66 TTTATTAACTTTTATTAATAATAAATACAACAAATGATACATTTAACAATAAAAAAAAGATAAAT
206182 ATTTTATTTGATTATT-ATATTATATATAAAATATCATCAAT-AAAAAATATTAATGAAG
131 ATTTTATTTGATTATTGATATTATATATAAAATATCATCAATAAAAAAATATTAATGAAG
* * *
206240 AAAATTCATATATATTAATTATTGAATAATTATCATAATCTCCTTGACATATATGATGA-TAATT
1 AAAATACATATATATTAATTATTAAATAATTATCATAATCTCCTTAACATATATGAT-ATTAATT
* * * *
206304 TTTTATTAATTTTTATTAATAATAAATACCAACAAATGATGCATTTAACAA-CAAAAGAAGATAA
65 TTTTATTAACTTTTATTAATAATAAATA-CAACAAATGATACATTTAACAATAAAAAAAAGATAA
* * * * *
206368 ATATTTTATTTGATTGTTGTTTTTATTTATAAAATATCATTAATAAAAAAATATT
129 ATATTTTATTTGATTATTGATATTATATATAAAATATCATCAATAAAAAAATATT
206423 GAGGATTATT
Statistics
Matches: 161, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
188 111 0.69
189 40 0.25
190 10 0.06
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (190 bp):
AAAATACATATATATTAATTATTAAATAATTATCATAATCTCCTTAACATATATGATATTAATTT
TTTATTAACTTTTATTAATAATAAATACAACAAATGATACATTTAACAATAAAAAAAAGATAAAT
ATTTTATTTGATTATTGATATTATATATAAAATATCATCAATAAAAAAATATTAATGAAG
Found at i:206941 original size:62 final size:62
Alignment explanation
Indices: 206875--206995 Score: 147
Period size: 61 Copynumber: 2.0 Consensus size: 62
206865 TTTTAAGACG
* * *
206875 TTTTTGGGTAGAAAATGTTTTAAATAATACTGA-TCAATTTTTT-TATAGGATTATTTAAATAA
1 TTTTTGGGTA-AAAATATCTTAAATAAT-CTGATTCAATTTTTTATAGAGGATTATTTAAATAA
* * * *
206937 TTTTTGGTTAAAAATATCTTAAATAATTTTATTTAATTTTTTATAGAGGATTATTTAAA
1 TTTTTGGGTAAAAATATCTTAAATAATCTGATTCAATTTTTTATAGAGGATTATTTAAA
206996 GCTTTGTTTG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
60 2 0.04
61 24 0.48
62 24 0.48
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.50
Consensus pattern (62 bp):
TTTTTGGGTAAAAATATCTTAAATAATCTGATTCAATTTTTTATAGAGGATTATTTAAATAA
Found at i:206959 original size:61 final size:63
Alignment explanation
Indices: 206875--207027 Score: 159
Period size: 62 Copynumber: 2.4 Consensus size: 63
206865 TTTTAAGACG
* * * *
206875 TTTTTGGGTAGAAAATGTTTTAAATAATACTGA-TCAATTTTTT-TATAGGATTATTTAAATAA
1 TTTTTGGCTA-AAAATATTTTAAATAATACTGATTCAATTTTTTATAGAGGATTATTTAAAGAA
* * * * * **
206937 TTTTTGGTTAAAAATATCTTAAATAAT-TTTATTTAATTTTTTATAGAGGATTATTTAAAGCT
1 TTTTTGGCTAAAAATATTTTAAATAATACTGATTCAATTTTTTATAGAGGATTATTTAAAGAA
*
206999 TTGTTTGGCCAAAAATATTTTAAATAATA
1 TT-TTTGGCTAAAAATATTTTAAATAATA
207028 TAAAAAAATT
Statistics
Matches: 74, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
60 2 0.03
61 24 0.32
62 26 0.35
63 22 0.30
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (63 bp):
TTTTTGGCTAAAAATATTTTAAATAATACTGATTCAATTTTTTATAGAGGATTATTTAAAGAA
Found at i:207022 original size:63 final size:61
Alignment explanation
Indices: 206910--207026 Score: 153
Period size: 63 Copynumber: 1.9 Consensus size: 61
206900 AATACTGATC
* * **
206910 AATTTTTTTATAGGATTATTTAAATAATTTTTGGTTAAAAATATCTTAAATAATTTTATTT
1 AATTTTTTTAGAGGATTATTTAAAGAATTTTTGGCCAAAAATATCTTAAATAATTTTATTT
** *
206971 AATTTTTTATAGAGGATTATTTAAAGCTTTGTTTGGCCAAAAATATTTTAAATAAT
1 AATTTTTT-TAGAGGATTATTTAAAGAATT-TTTGGCCAAAAATATCTTAAATAAT
207027 ATAAAAAAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
61 8 0.17
62 17 0.36
63 22 0.47
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (61 bp):
AATTTTTTTAGAGGATTATTTAAAGAATTTTTGGCCAAAAATATCTTAAATAATTTTATTT
Found at i:212982 original size:52 final size:51
Alignment explanation
Indices: 212896--213045 Score: 144
Period size: 52 Copynumber: 2.9 Consensus size: 51
212886 GGACAAGAAG
* *
212896 ACTTGCAAAAGAAGAATTTCAAGAA--AAAGAGGATTCTTAATAGGTAAATTTC
1 ACTTGCAAGAGAAGAATTT-AA-AAGGAAAG-GGATTCTTAATAGGCAAATTTC
** *
212948 ACTTGCAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGCATGTTTG
1 ACTTGCAAGAGAAGAATT-TAAAAGGAAAGGGATTCTTAATAGGCAAATTTC
* * * * *
213000 ACTTACAGGAGAAGAATTATAAGAGGAGA-GGATTCTTAATGGGCAA
1 ACTTGCAAGAGAAGAATT-TAAAAGGAAAGGGATTCTTAATAGGCAA
213046 GTTTGTATGG
Statistics
Matches: 83, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
51 17 0.20
52 61 0.73
53 5 0.06
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.25
Consensus pattern (51 bp):
ACTTGCAAGAGAAGAATTTAAAAGGAAAGGGATTCTTAATAGGCAAATTTC
Found at i:213050 original size:51 final size:51
Alignment explanation
Indices: 212923--213050 Score: 157
Period size: 52 Copynumber: 2.5 Consensus size: 51
212913 TTCAAGAAAA
* * * * *
212923 AGAGGATTCTTAATAGGTAAATTTCACTTGCAAGAGAAGAATTCTAAAAGG
1 AGAGGATTCTTAATAGGCAAGTTTGACTTACAAGAGAAGAATTATAAAAGG
* * * *
212974 AAAGGGATTCTTAATAGGCATGTTTGACTTACAGGAGAAGAATTATAAGAGG
1 AGA-GGATTCTTAATAGGCAAGTTTGACTTACAAGAGAAGAATTATAAAAGG
*
213026 AGAGGATTCTTAATGGGCAAGTTTG
1 AGAGGATTCTTAATAGGCAAGTTTG
213051 TATGGTTATA
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
51 22 0.34
52 42 0.66
ACGTcount: A:0.38, C:0.09, G:0.26, T:0.28
Consensus pattern (51 bp):
AGAGGATTCTTAATAGGCAAGTTTGACTTACAAGAGAAGAATTATAAAAGG
Found at i:214397 original size:203 final size:203
Alignment explanation
Indices: 214153--214558 Score: 731
Period size: 203 Copynumber: 2.0 Consensus size: 203
214143 TATTGAGACT
* *
214153 CTACGTCTTATAGGTGTATATGTTTGTTTATGAGTGGACTAGAGAAGACTGAGAGGGTCCACATA
1 CTACGTCTTATAGGTGTATATATTTGTTTATGAGTGGACTAGAGAAGACTGAGAGAGTCCACATA
* *
214218 AGTATGATGTATGGGAGCATATGAGTATGTGTTTGGTTATGTTGAAAGAGTGCACAAGGGTTTGG
66 AGTATGATGTATGAGAGCATATGAGTATGTGTTTGGTTATGTTGAAAGAGTGCACAACGGTTTGG
214283 GTTTGTGTTTGTTTGGGTTGAGAATACTCTATAGGACTAGATGAGATTGAGAGTGTCTTATGAGT
131 GTTTGTGTTTGTTTGGGTTGAGAATACTCTATAGGACTAGATGAGATTGAGAGTGTCTTATGAGT
214348 ATTGATTG
196 ATTGATTG
* * *
214356 CTACGTCTTATAGGTGTGTATATTTGTTTATGAGTGGACTAGAGGAGATTGAGAGAGTCCACATA
1 CTACGTCTTATAGGTGTATATATTTGTTTATGAGTGGACTAGAGAAGACTGAGAGAGTCCACATA
* *
214421 GGTATGATGTATGAGAGCATATGGGTATGTGTTTGGTTATGTTGAAAGAGTGCACAACGGTTTGG
66 AGTATGATGTATGAGAGCATATGAGTATGTGTTTGGTTATGTTGAAAGAGTGCACAACGGTTTGG
214486 GTTTGTGTTTGTTTGGGTTGAGAATACTCTATAGGACTAGATGAGATTGAGAGTGTCTTATGAGT
131 GTTTGTGTTTGTTTGGGTTGAGAATACTCTATAGGACTAGATGAGATTGAGAGTGTCTTATGAGT
214551 ATTGATTG
196 ATTGATTG
214559 TTGAGTGAGG
Statistics
Matches: 194, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
203 194 1.00
ACGTcount: A:0.25, C:0.07, G:0.31, T:0.36
Consensus pattern (203 bp):
CTACGTCTTATAGGTGTATATATTTGTTTATGAGTGGACTAGAGAAGACTGAGAGAGTCCACATA
AGTATGATGTATGAGAGCATATGAGTATGTGTTTGGTTATGTTGAAAGAGTGCACAACGGTTTGG
GTTTGTGTTTGTTTGGGTTGAGAATACTCTATAGGACTAGATGAGATTGAGAGTGTCTTATGAGT
ATTGATTG
Found at i:219879 original size:213 final size:212
Alignment explanation
Indices: 219475--219893 Score: 473
Period size: 213 Copynumber: 2.0 Consensus size: 212
219465 AATTTTGAAG
* * * *
219475 AAAAAAAATTTAATTATATTGAAGATTTTTTATAAATATTTTAATACATTGGTAATATTTTACAA
1 AAAAAAAATTTAATTATATTGAAAATTTTTTATAAATACTTGAATACACTGGTAATATTTTACAA
* * * *
219540 AAAATCTTTCACCTAGGGATTTCTTAAAGTATCTTTACTCGAAATACTTTTAGAATCCAATCATT
66 AAAATCTTTCACCTAGAGATTTCGTAAAGTATCTCTACTCGAAATACTTTTAGAATCCAATCATC
* *
219605 GGATAAAATTTCTTTTCTTCCCATTTTTATTACTTATTTAATTTATTAATCAATTTTTATTTAT-
131 GGATAAAATTTCTTTTCTTCCCAATTTTATTACTTATTTAATTTATTAATCAATATTTATTTATA
219669 TACTATTTTATAAAAAA
196 TACTATTTTATAAAAAA
* * *
219686 AAAAGAAAATTATTATTGTATTGAAAATTTTTTATAAATACTTGAATACACTGGTAGTATTTTA-
1 AAAA-AAAATT-TAATTATATTGAAAATTTTTTATAAATACTTGAATACACTGGTAATATTTTAC
*
219750 AAAATAATCTTCTCACCTAGAGATTTCGT-AGGTAT-TACTACTCGAAATA-TCTTT-GAATCTC
64 AAAA-AATCTT-TCACCTAGAGATTTCGTAAAGTATCT-CTACTCGAAATACT-TTTAGAATC-C
** * *
219811 -ATTGTCGGATAAAATTTCTTTTCTTCTCCTACATTTT-TTA-TTAGTTTAGTATTATT-ATTAA
124 AATCATCGGATAAAATTTCTTTTCTTC-CC-A-ATTTTATTACTTA-TTTAAT-TTATTAATCAA
* *
219872 -ATTTATTTTTATATTATTTTAT
184 TATTTATTTATATACTATTTTAT
219894 GTTTTAAGTT
Statistics
Matches: 175, Mismatches: 20, Indels: 23
0.80 0.09 0.11
Matches are distributed among these distances:
211 4 0.02
212 40 0.23
213 84 0.48
214 38 0.22
215 9 0.05
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.47
Consensus pattern (212 bp):
AAAAAAAATTTAATTATATTGAAAATTTTTTATAAATACTTGAATACACTGGTAATATTTTACAA
AAAATCTTTCACCTAGAGATTTCGTAAAGTATCTCTACTCGAAATACTTTTAGAATCCAATCATC
GGATAAAATTTCTTTTCTTCCCAATTTTATTACTTATTTAATTTATTAATCAATATTTATTTATA
TACTATTTTATAAAAAA
Found at i:221383 original size:50 final size:49
Alignment explanation
Indices: 221312--221513 Score: 268
Period size: 48 Copynumber: 4.2 Consensus size: 49
221302 AAAAGGTTCC
*
221312 TCTCAGCAGAGG-TTAACAACTTTAAAAAATCTCATCTTGAAAAAGCTCA
1 TCTCAACAGAGGCTTAACAACTTT-AAAAATCTCATCTTGAAAAAGCTCA
* * * * * *
221361 TCTCAGCAGAGACTTCACAACTTTAAAAGT-TTATCTTGAAAAGGCTCA
1 TCTCAACAGAGGCTTAACAACTTTAAAAATCTCATCTTGAAAAAGCTCA
*
221409 TCTCAACAGAGGCTTAACAACTTTAAAAATCTCATCTTGAAAAAGGCTCC
1 TCTCAACAGAGGCTTAACAACTTTAAAAATCTCATCTTGAAAAA-GCTCA
* *
221459 TCTCAACAGAGGCTCAACAACTTT-AAAATCTCAT-TTGAAAAAACTCA
1 TCTCAACAGAGGCTTAACAACTTTAAAAATCTCATCTTGAAAAAGCTCA
221506 TCTCAACA
1 TCTCAACA
221514 ACGTTAAAAA
Statistics
Matches: 135, Mismatches: 15, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
47 11 0.08
48 50 0.37
49 37 0.27
50 37 0.27
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (49 bp):
TCTCAACAGAGGCTTAACAACTTTAAAAATCTCATCTTGAAAAAGCTCA
Found at i:221497 original size:97 final size:97
Alignment explanation
Indices: 221302--221513 Score: 279
Period size: 97 Copynumber: 2.2 Consensus size: 97
221292 TAAAATCTAA
* * * *
221302 AAAAGGTTCCTCTCAGCAGAGGTTAACAACTTTAAAAAATCTCATCTTGAAAAAGCTCATCTCAG
1 AAAAGGCTCATCTCAACAGAGGTTAACAACTTTAAAAAATCTCATCTTGAAAAAGCTCATCTCAA
*
221367 CAGAGACTTCACAACTTTAAAAGTTTATCTTG
66 CAGAGACTTCACAACTTTAAAAGTTCATCTTG
*
221399 AAAAGGCTCATCTCAACAGAGGCTTAACAACTTT-AAAAATCTCATCTTGAAAAAGGCTCCTCTC
1 AAAAGGCTCATCTCAACAGAGG-TTAACAACTTTAAAAAATCTCATCTTGAAAAA-GCTCATCTC
*
221463 AACAGAGGC-TCAACAACTTTAAAA-TCTCAT-TTG
64 AACAGAGACTTC-ACAACTTTAAAAGT-TCATCTTG
**
221496 AAAAAACTCATCTCAACA
1 AAAAGGCTCATCTCAACA
221514 ACGTTAAAAA
Statistics
Matches: 102, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
97 61 0.60
98 41 0.40
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (97 bp):
AAAAGGCTCATCTCAACAGAGGTTAACAACTTTAAAAAATCTCATCTTGAAAAAGCTCATCTCAA
CAGAGACTTCACAACTTTAAAAGTTCATCTTG
Found at i:221567 original size:84 final size:88
Alignment explanation
Indices: 221424--221963 Score: 258
Period size: 96 Copynumber: 5.9 Consensus size: 88
221414 ACAGAGGCTT
*
221424 AACAACTTTAAAAATCTCATCTTGAAAAAGGCTCCTCTCAACAGAGGCTCAACAACTTTAAAATC
1 AACAACGTTAAAAATCTCATCTTGAAAAAGGCTCCTCTCAACAGAGGCTCAACAACTTTAAAATC
221489 TCAT-TT-GAAAAAACTCATCTC
66 TCATCTTAGAAAAAACTCATCTC
* * **
221510 AACAACGTTAAAAATCTCA-CTTGAAAAA-GTTCTTCTCAGTAGAGGCTCAACAACTTTAAAATC
1 AACAACGTTAAAAATCTCATCTTGAAAAAGGCTCCTCTCAACAGAGGCTCAACAACTTTAAAATC
** *
221573 TCATCTTAGAAAAGCTCTTCTTAGCAGAGGGTC
66 TCATCTTAGAAAA-AAC-TC--ATC------TC
* * * *
221606 AACAACTTTAAAAAT-T-TTCTT--AAAATGCTCCTCTCAACAGAGGCTCAACAATTTTAAAA--
1 AACAACGTTAAAAATCTCATCTTGAAAAAGGCTCCTCTCAACAGAGGCTCAACAACTTTAAAATC
* *
221665 TC-TCTT-GAAAAAATTCCTCTC
66 TCATCTTAGAAAAAACTCATCTC
* * * *
221686 AACAGAGGTTCAACAACTTTAAAATCTTATCTTGAAAAA-GCTCCTCTCAACAGAGGCTCGACGA
1 AACA-ACGTT-----A----AAAATCTCATCTTGAAAAAGGCTCCTCTCAACAGAGGCTCAACAA
* * **
221750 TTTTAAAATCTCAT-TTGGAAAAGCTCTTCTTAGTAGAGGCTC
56 CTTTAAAATCTCATCTTAGAAAA-AAC-TC--A-T-----CTC
* * * *
221792 AACAACTTTAAAAATTTCATCTTG-AAAATGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAT-
1 AACAACGTTAAAAATCTCATCTTGAAAAAGGCTCCTCTCAACAGAGGCTCAACAACTTTAAAATC
* *
221855 T--T-TTAAAAAAAAAACTCTTCTCAAC
66 TCATCTT--AGAAAAAACTCATCT---C
* * * **
221880 AGAGGCTCAACAACTTTAAAATCTCATCTTGAAAAA-GCTCATCTCAGTAGAGGCTCAACAACTT
1 A-A----CAAC--GTTAAAAATCTCATCTTGAAAAAGGCTCCTCTCAACAGAGGCTCAACAACTT
221944 TAAAATCTCATCTT-GAAAAA
59 TAAAATCTCATCTTAGAAAAA
221964 GCTTCTCTCA
Statistics
Matches: 346, Mismatches: 48, Indels: 110
0.69 0.10 0.22
Matches are distributed among these distances:
80 6 0.02
81 3 0.01
84 35 0.10
85 13 0.04
86 25 0.07
87 1 0.00
88 6 0.02
89 1 0.00
90 13 0.04
91 5 0.01
92 6 0.02
93 44 0.13
94 33 0.10
95 64 0.18
96 74 0.21
98 3 0.01
99 2 0.01
100 1 0.00
101 1 0.00
105 3 0.01
106 7 0.02
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.29
Consensus pattern (88 bp):
AACAACGTTAAAAATCTCATCTTGAAAAAGGCTCCTCTCAACAGAGGCTCAACAACTTTAAAATC
TCATCTTAGAAAAAACTCATCTC
Found at i:221790 original size:47 final size:48
Alignment explanation
Indices: 221507--221996 Score: 516
Period size: 48 Copynumber: 10.3 Consensus size: 48
221497 AAAAACTCAT
* * *
221507 CTCAACAACGTTAAAAATCTCA-CTTGAAAAAGTTCTTCTCAGTAGAGG
1 CTCAACAAC-TTTAAAATCTCATCTTGAAAAAGCTCTTCTCAGCAGAGG
*
221555 CTCAACAACTTTAAAATCTCATCTT-AGAAAAGCTCTTCTTAGCAGAGG
1 CTCAACAACTTTAAAATCTCATCTTGA-AAAAGCTCTTCTCAGCAGAGG
* * * * *
221603 GTCAACAACTTTAAAAAT-T-TTCTT-AAAATGCTCCTCTCAACAGAGG
1 CTCAACAACTTT-AAAATCTCATCTTGAAAAAGCTCTTCTCAGCAGAGG
* ** * *
221649 CTCAACAATTTTAAAA--TC-TCTTGAAAAAATTCCTCTCAACAGAGG
1 CTCAACAACTTTAAAATCTCATCTTGAAAAAGCTCTTCTCAGCAGAGG
* * * *
221694 TTCAACAACTTTAAAATCTTATCTTGAAAAAGCTCCTCTCAACAGAGG
1 CTCAACAACTTTAAAATCTCATCTTGAAAAAGCTCTTCTCAGCAGAGG
* * * * * *
221742 CTCGACGATTTTAAAATCTCAT-TTGGAAAAGCTCTTCTTAGTAGAGG
1 CTCAACAACTTTAAAATCTCATCTTGAAAAAGCTCTTCTCAGCAGAGG
* * *
221789 CTCAACAACTTTAAAAATTTCATCTTGAAAATGCTCCTCTCAGCAGAGG
1 CTCAACAACTTT-AAAATCTCATCTTGAAAAAGCTCTTCTCAGCAGAGG
** **** * *
221838 CTCAACAACTTTAAAAT-TTTTAAAAAAAAAACTCTTCTCAACAGAGG
1 CTCAACAACTTTAAAATCTCATCTTGAAAAAGCTCTTCTCAGCAGAGG
* *
221885 CTCAACAACTTTAAAATCTCATCTTGAAAAAGCTCATCTCAGTAGAGG
1 CTCAACAACTTTAAAATCTCATCTTGAAAAAGCTCTTCTCAGCAGAGG
221933 CTCAACAACTTTAAAATCTCATCTTGAAAAAGCT-TCTCTCAGCAGAGG
1 CTCAACAACTTTAAAATCTCATCTTGAAAAAGCTCT-TCTCAGCAGAGG
*
221981 CTCAACAATTTTAAAA
1 CTCAACAACTTTAAAA
221997 AATCATCTAT
Statistics
Matches: 368, Mismatches: 62, Indels: 24
0.81 0.14 0.05
Matches are distributed among these distances:
44 5 0.01
45 37 0.10
46 27 0.07
47 84 0.23
48 178 0.48
49 37 0.10
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.29
Consensus pattern (48 bp):
CTCAACAACTTTAAAATCTCATCTTGAAAAAGCTCTTCTCAGCAGAGG
Found at i:232607 original size:16 final size:17
Alignment explanation
Indices: 232569--232607 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
232559 AAGAAAAAAA
232569 TATTTTTTGTTTTTTAG
1 TATTTTTTGTTTTTTAG
* *
232586 TGTTTTTT-TTTTTTTG
1 TATTTTTTGTTTTTTAG
232602 TATTTT
1 TATTTT
232608 GAGATTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.08, C:0.00, G:0.10, T:0.82
Consensus pattern (17 bp):
TATTTTTTGTTTTTTAG
Found at i:232607 original size:24 final size:26
Alignment explanation
Indices: 232571--232629 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
232561 GAAAAAAATA
*
232571 TTTTTTGT-TTTTTAG-TGTTTTT-TT
1 TTTTTTGTATTTTGAGAT-TTTTTATT
232595 TTTTTTGTATTTTGAGATTTTTTATT
1 TTTTTTGTATTTTGAGATTTTTTATT
232621 TTGTTTTGT
1 TT-TTTTGT
232630 TTTGTATTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 8 0.27
25 11 0.37
26 5 0.17
27 6 0.20
ACGTcount: A:0.08, C:0.00, G:0.14, T:0.78
Consensus pattern (26 bp):
TTTTTTGTATTTTGAGATTTTTTATT
Found at i:234269 original size:209 final size:208
Alignment explanation
Indices: 233805--234269 Score: 529
Period size: 209 Copynumber: 2.2 Consensus size: 208
233795 TGTTAAAAAT
*
233805 TTTATTATT-TTATTAATATTTATTTTTA-ATTGAAATTTTGA-AGAAAAAAGAATTTAATTATA
1 TTTAATATTATTATTAA-ATTTATTTTTATATT---ATTTT-ATA-AAAAAAGAATTTAATTATA
* * * * *
233867 TTGAAGATTTTTTATAAATATTCCAATACACTAGTAATATTTTATAAAAAATCTTCTCACCTAGG
60 TTGAAAATTTTTTATAAATACTCAAATACACTAGTAATATTTTAAAAAAAATCTTCTCACCTAGA
* ** *
233932 GATTTCTTAAAGCATCTTTACTCGAAATACTTTTAGAATCTCATCATTGGATAAAATTTCTTTTC
125 GATTTCATAAAGCATCACTACTCGAAATACTTTTAGAATCTCATCATCGGATAAAATTTCTTTTC
233997 TTCTCATTTTTATTACTTA
190 TTCTCATTTTTATTACTTA
* * * ** *
234016 TTTAAT-TTATTAATCAATTT-TTATTTATTACTATTTTATAAAAAAAGAATTTTTCTTGTATTG
1 TTTAATATTATTATTAAATTTATT-TTTA-TATTATTTTATAAAAAAAGAA-TTTAATTATATTG
*
234079 AAAATTTTTTTATAAATACTCAAATACACTAGTAGTA-TTTAAAAAAAATCTTCTCACCTAGAGA
63 AAAA-TTTTTTATAAATACTCAAATACACTAGTAATATTTTAAAAAAAATCTTCTCACCTAGAGA
* *
234143 TTTCAT-AGGCATCACTACTCGAAATA-TCTTT-GAATCTCATCGTCGGATAAAATTTCTTTTCT
127 TTTCATAAAGCATCACTACTCGAAATACT-TTTAGAATCTCATCATCGGATAAAATTTCTTTTCT
234205 TCTCCTATATTTT-TTA-TTA
191 TCT-C-AT-TTTTATTACTTA
* *
234224 GTTTAGTATTATTATTAAATTTATTTTTATATTATTTTTTAAAAAA
1 -TTTAATATTATTATTAAATTTATTTTTATATTATTTTATAAAAAA
234270 TTTATTTTAA
Statistics
Matches: 216, Mismatches: 24, Indels: 30
0.80 0.09 0.11
Matches are distributed among these distances:
207 33 0.15
208 34 0.16
209 76 0.35
210 59 0.27
211 12 0.06
212 2 0.01
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.47
Consensus pattern (208 bp):
TTTAATATTATTATTAAATTTATTTTTATATTATTTTATAAAAAAAGAATTTAATTATATTGAAA
ATTTTTTATAAATACTCAAATACACTAGTAATATTTTAAAAAAAATCTTCTCACCTAGAGATTTC
ATAAAGCATCACTACTCGAAATACTTTTAGAATCTCATCATCGGATAAAATTTCTTTTCTTCTCA
TTTTTATTACTTA
Found at i:234369 original size:16 final size:16
Alignment explanation
Indices: 234342--234383 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
234332 AACAAATATA
* *
234342 AATATTTTAATATACAT
1 AATATATTAATA-AAAT
234359 AA-ATATTAATAAAAT
1 AATATATTAATAAAAT
234374 AATATATTAA
1 AATATATTAA
234384 AAATAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 5 0.23
16 15 0.68
17 2 0.09
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
AATATATTAATAAAAT
Found at i:235338 original size:29 final size:29
Alignment explanation
Indices: 235271--235326 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
235261 GAGTGTAAGA
235271 TAAGGTATGATGATCAGAAAGATGTGGAG
1 TAAGGTATGATGATCAGAAAGATGTGGAG
*
235300 T-AGAGTATGATGATCAGAAGGATGTGG
1 TAAG-GTATGATGATCAGAAAGATGTGG
235327 GCTAAGGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.36, C:0.04, G:0.36, T:0.25
Consensus pattern (29 bp):
TAAGGTATGATGATCAGAAAGATGTGGAG
Found at i:247571 original size:11 final size:10
Alignment explanation
Indices: 247551--247576 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
247541 GATACCAAGC
247551 TTTTTCTTTT
1 TTTTTCTTTT
247561 TTTTTCTTTT
1 TTTTTCTTTT
247571 TTTTTC
1 TTTTTC
247577 CTCCATGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:249532 original size:54 final size:52
Alignment explanation
Indices: 249445--249645 Score: 154
Period size: 54 Copynumber: 3.7 Consensus size: 52
249435 TACTTTTGCA
** *
249445 TAAGAAAAATTGATACTTTCAACTTTTTTTTAAAGCATTTGAGAGTTT-TTA-TTT
1 TAAG-AAAATTGATACTTTCAACTTTTCCTTAAAACATTT---AGTTTATTATTTT
* **
249499 TAAGTAAAATTGATACTTTCAACTTTTCCTTAAAATATTTTTTTTATTATTTT
1 TAAG-AAAATTGATACTTTCAACTTTTCCTTAAAACATTTAGTTTATTATTTT
* * * ** *
249552 TAAAGAAAATTGATACTTTCAACTTTTTCTCAAAATGCTTTTTTTTTTAATTTAATTT
1 T-AAGAAAATTGATACTTTCAACTTTTCCTTAAAA--C-ATTTAGTTT-A-TTATTTT
*
249610 TAAGGAAAAATTGATACTTTCAACTTTTCCTAAAAA
1 TAA-G-AAAATTGATACTTTCAACTTTTCCTTAAAA
249646 TATATTTTTT
Statistics
Matches: 123, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
51 3 0.02
52 3 0.02
53 32 0.26
54 38 0.31
56 8 0.07
57 3 0.02
58 8 0.07
59 28 0.23
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.48
Consensus pattern (52 bp):
TAAGAAAATTGATACTTTCAACTTTTCCTTAAAACATTTAGTTTATTATTTT
Found at i:249576 original size:53 final size:55
Alignment explanation
Indices: 249495--249697 Score: 198
Period size: 60 Copynumber: 3.6 Consensus size: 55
249485 GAGAGTTTTT
* *
249495 ATTTT-AAGTAAAATTGATACTTTCAACTTTTCCTTAAAATATTTTTTTTA-TTA
1 ATTTTAAAGAAAAATTGATACTTTCAACTTTTCCTAAAAATATTTTTTTTATTTA
* * * *
249548 TTTTTAAAG-AAAATTGATACTTTCAACTTTTTCTCAAAATGCTTTTTTTTTTAATTTA
1 ATTTTAAAGAAAAATTGATACTTTCAACTTTTCCT-AAAA--ATATTTTTTTT-ATTTA
* * *
249606 ATTTTAAGGAAAAATTGATACTTTCAACTTTTCCTAAAAATATATTTTTTAAATCTTTTT
1 ATTTTAAAGAAAAATTGATACTTTCAACTTTTCCTAAAAATAT-TTTTTT---T-ATTTA
*
249666 ATCTTT-AAGAAAAATTAATACTTTCAACTTTT
1 AT-TTTAAAGAAAAATTGATACTTTCAACTTTT
249698 TTCTAAATAC
Statistics
Matches: 123, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
53 28 0.23
54 6 0.05
56 11 0.09
57 7 0.06
58 14 0.11
59 24 0.20
60 30 0.24
61 3 0.02
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.50
Consensus pattern (55 bp):
ATTTTAAAGAAAAATTGATACTTTCAACTTTTCCTAAAAATATTTTTTTTATTTA
Found at i:249622 original size:59 final size:56
Alignment explanation
Indices: 249495--249697 Score: 207
Period size: 53 Copynumber: 3.6 Consensus size: 56
249485 GAGAGTTTTT
* * *
249495 ATTTTAAGTAAAATTGATACTTTCAACTTTTCCTTAAAA-TATTTTTTTT-A-TTA
1 ATTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAATTTTTTTTTTTAATTTA
* *
249548 TTTTTAA-AGAAAATTGATACTTTCAACTTTTTCTCAAAATGCTTTTTTTTTTAATTTA
1 ATTTTAAGA-AAAATTGATACTTTCAACTTTTCCTCAAAAT--TTTTTTTTTTAATTTA
* * * * *
249606 ATTTTAAGGAAAAATTGATACTTTCAACTTTTCCTAAAAATATATTTTTTAAATCTTTTT
1 ATTTTAA-GAAAAATTGATACTTTCAACTTTTCCTCAAAATTTTTTTTTTTAA---TTTA
*
249666 ATCTTTAAGAAAAATTAATACTTTCAACTTTT
1 AT-TTTAAGAAAAATTGATACTTTCAACTTTT
249698 TTCTAAATAC
Statistics
Matches: 125, Mismatches: 13, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
53 34 0.27
56 9 0.07
57 10 0.08
58 9 0.07
59 29 0.23
60 29 0.23
61 5 0.04
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.50
Consensus pattern (56 bp):
ATTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAATTTTTTTTTTTAATTTA
Found at i:249733 original size:112 final size:108
Alignment explanation
Indices: 249445--249731 Score: 294
Period size: 112 Copynumber: 2.6 Consensus size: 108
249435 TACTTTTGCA
* * * *
249445 TAAGAAAAATTGATACTTTCAACTTTTTTTTAAA-GCATTTGAGAGTTTTTATTTTAAGTAAAAT
1 TAAGAAAAATTGATACTTTCAACTTTTTTCTAAATGCTTTTGAAAATTTTTATTTTAAG-AAAAT
*
249509 TGATACTTTCAACTTTTCCTTAAAATATTTTTTTTATTATTTTT
65 TGATACTTTCAACTTTTCCTAAAAATATTTTTTTTATTATTTTT
* * *** *
249553 AAAG-AAAATTGATACTTTCAACTTTTTCTCAAAATGCTTTTTTTTTTAA-TTTAATTTTAAGGA
1 TAAGAAAAATTGATACTTTCAACTTTTT-TCTAAATGC---TTTTGAAAATTTTTATTTTAA-G-
* *
249616 AAAATTGATACTTTCAACTTTTCCTAAAAATATATTTTTTAAATCTTTTTATCTT
60 AAAATTGATACTTTCAACTTTTCCTAAAAATAT-TTTTTT---TATTATT-T-TT
* *
249671 TAAGAAAAATTAATACTTTCAACTTTTTTCTAAATACTTTTGAAAATTTTTATTTT-AGAAA
1 TAAGAAAAATTGATACTTTCAACTTTTTTCTAAATGCTTTTGAAAATTTTTATTTTAAGAAA
249732 TTTTTTTTTT
Statistics
Matches: 144, Mismatches: 21, Indels: 23
0.77 0.11 0.12
Matches are distributed among these distances:
107 23 0.16
108 7 0.05
109 2 0.01
111 10 0.07
112 37 0.26
113 9 0.06
114 1 0.01
115 7 0.05
116 13 0.09
117 1 0.01
118 12 0.08
119 22 0.15
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.49
Consensus pattern (108 bp):
TAAGAAAAATTGATACTTTCAACTTTTTTCTAAATGCTTTTGAAAATTTTTATTTTAAGAAAATT
GATACTTTCAACTTTTCCTAAAAATATTTTTTTTATTATTTTT
Found at i:250706 original size:21 final size:21
Alignment explanation
Indices: 250657--250746 Score: 103
Period size: 21 Copynumber: 4.2 Consensus size: 21
250647 TAATAATAGT
*
250657 AATAATAATAGATAAA-AATATA
1 AATATTAATAGATAAATAA-A-A
* *
250679 TATATTAATAGCTAAATAAAA
1 AATATTAATAGATAAATAAAA
*
250700 AATATTAATAGAAAAATAAAA
1 AATATTAATAGATAAATAAAA
250721 AA-ATTAATAGATAAATAATAA
1 AATATTAATAGATAAATAA-AA
250742 AATAT
1 AATAT
250747 ATGTATTAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
20 15 0.26
21 25 0.43
22 16 0.28
23 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (21 bp):
AATATTAATAGATAAATAAAA
Found at i:250726 original size:20 final size:20
Alignment explanation
Indices: 250682--250744 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
250672 AAATATATAT
*
250682 ATTAATAGCTAAATAAAAAA
1 ATTAATAGATAAATAAAAAA
*
250702 TATTAATAGAAAAATAAAAAA
1 -ATTAATAGATAAATAAAAAA
*
250723 ATTAATAGATAAATAATAAA
1 ATTAATAGATAAATAAAAAA
250743 AT
1 AT
250745 ATATGTATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
20 20 0.53
21 18 0.47
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.27
Consensus pattern (20 bp):
ATTAATAGATAAATAAAAAA
Found at i:250743 original size:28 final size:30
Alignment explanation
Indices: 250711--250779 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 30
250701 ATATTAATAG
*
250711 AAAAATAAAAAAATTAATAGATAAAT-AAT
1 AAAAATAAAAAAATTAATAAATAAATAAAT
* ***
250740 -AAAATATATGTATTAATAAATAAATAAAT
1 AAAAATAAAAAAATTAATAAATAAATAAAT
250769 AAAAATAAAAA
1 AAAAATAAAAA
250780 TAAAACTGCA
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
28 20 0.67
29 3 0.10
30 7 0.23
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (30 bp):
AAAAATAAAAAAATTAATAAATAAATAAAT
Found at i:250974 original size:25 final size:25
Alignment explanation
Indices: 250932--250980 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
250922 CTACTTGACC
* *
250932 CTTTTTTCGTTTTTTTTTTTTTTTA
1 CTTTTTTCGTTGTCTTTTTTTTTTA
*
250957 CTTTTTTTGTTGTCTTTTTTTTTT
1 CTTTTTTCGTTGTCTTTTTTTTTT
250981 TGTTAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.02, C:0.08, G:0.06, T:0.84
Consensus pattern (25 bp):
CTTTTTTCGTTGTCTTTTTTTTTTA
Found at i:251045 original size:44 final size:42
Alignment explanation
Indices: 250997--251298 Score: 180
Period size: 42 Copynumber: 7.2 Consensus size: 42
250987 AATTTTAATT
*
250997 AAAGCTCCTCTAAGCAGAGGCTCAACGACTTTTGAAAAATAAAA
1 AAAGCTCCTCTAAACAGAGGCTCAACGACTTTTGAAAAAT--AA
* * * * * *
251041 AAAGCTCATTTAATCAGAGGCTTAACGACTTTGGAAAAGTAA
1 AAAGCTCCTCTAAACAGAGGCTCAACGACTTTTGAAAAATAA
** * * *
251083 ATTGCTCCTCTAAATAGAGGCTC-ACTGACTTTTGGAAAGTAA
1 AAAGCTCCTCTAAACAGAGGCTCAAC-GACTTTTGAAAAATAA
**** * * **** *
251125 TTTTCTCCTCTAAACAAAGGCACTGTAACTTTTGAAAAGTAA
1 AAAGCTCCTCTAAACAGAGGCTCAACGACTTTTGAAAAATAA
** * * * *
251167 ATTGCTCCTCTAAATAGAGGCAACCACAAC-TTTGAAAAATAA
1 AAAGCTCCTCTAAACAGAGGC-TCAACGACTTTTGAAAAATAA
* * * **
251209 AATGCTCCTCTAAACAGAGGCAACTACGAC-TTTGGGAAATAA
1 AAAGCTCCTCTAAACAGAGGC-TCAACGACTTTTGAAAAATAA
** **
251251 ATTGCTCCTCTAAACAGAGGCTCAATAAC-TTTGAAAAATAA
1 AAAGCTCCTCTAAACAGAGGCTCAACGACTTTTGAAAAATAA
*
251292 ATAGCTC
1 AAAGCTC
251299 ATCGACAATC
Statistics
Matches: 209, Mismatches: 46, Indels: 9
0.79 0.17 0.03
Matches are distributed among these distances:
41 22 0.11
42 148 0.71
43 5 0.02
44 34 0.16
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.26
Consensus pattern (42 bp):
AAAGCTCCTCTAAACAGAGGCTCAACGACTTTTGAAAAATAA
Found at i:251122 original size:42 final size:41
Alignment explanation
Indices: 251070--251271 Score: 187
Period size: 42 Copynumber: 4.8 Consensus size: 41
251060 GCTTAACGAC
*
251070 TTTGGAAAAGTAAATTGCTCCTCTAAATAGAGGCTCACTGACT
1 TTTGG-AAAGTAAATTGCTCCTCTAAACAGAGGC-CACTGACT
* * *
251113 TTTGGAAAGTAATTTTCTCCTCTAAACAAAGG-CACTGTAACT
1 TTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCCACTG--ACT
* * *
251155 TTTGAAAAGTAAATTGCTCCTCTAAATAGAGGCAACCAC-AAC-
1 TTTGGAAAGTAAATTGCTCCTCTAAACAGAGG---CCACTGACT
* * * *
251197 TTTGAAAAATAAAATGCTCCTCTAAACAGAGGCAACTACGACT
1 TTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCCACT--GACT
*
251240 TTGGGAAA-TAAATTGCTCCTCTAAACAGAGGC
1 TTTGGAAAGTAAATTGCTCCTCTAAACAGAGGC
251272 TCAATAACTT
Statistics
Matches: 131, Mismatches: 18, Indels: 21
0.77 0.11 0.12
Matches are distributed among these distances:
39 3 0.02
40 5 0.04
42 107 0.82
43 13 0.10
46 3 0.02
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (41 bp):
TTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCCACTGACT
Found at i:251179 original size:84 final size:83
Alignment explanation
Indices: 251068--251292 Score: 256
Period size: 84 Copynumber: 2.7 Consensus size: 83
251058 AGGCTTAACG
* * * ** *
251068 ACTTTGGAAAAGTAAATTGCTCCTCTAAATAGAGGCTCACTGACTTTTGGAAAGTAATTTTCTCC
1 ACTTTGGAAAAGTAAATTGCTCCTCTAAATAGAGGCTCAC-AAC-TTTGAAAAATAAAATGCTCC
**
251133 TCTAAACAAAGGC-ACTGTA
64 TCTAAACAAAGGCAACTACA
* *
251152 ACTTTTGAAAAGTAAATTGCTCCTCTAAATAGAGGCAACCACAACTTTGAAAAATAAAATGCTCC
1 ACTTTGGAAAAGTAAATTGCTCCTCTAAATAGAGGC--TCACAACTTTGAAAAATAAAATGCTCC
* *
251217 TCTAAACAGAGGCAACTACG
64 TCTAAACAAAGGCAACTACA
* * *
251237 ACTTTGGGAAA-TAAATTGCTCCTCTAAACAGAGGCTCAATAACTTTGAAAAATAAA
1 ACTTTGGAAAAGTAAATTGCTCCTCTAAATAGAGGCTC-ACAACTTTGAAAAATAAA
251293 TAGCTCATCG
Statistics
Matches: 120, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
82 1 0.01
83 17 0.14
84 85 0.71
85 14 0.12
86 3 0.03
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (83 bp):
ACTTTGGAAAAGTAAATTGCTCCTCTAAATAGAGGCTCACAACTTTGAAAAATAAAATGCTCCTC
TAAACAAAGGCAACTACA
Found at i:251228 original size:126 final size:125
Alignment explanation
Indices: 251068--251298 Score: 295
Period size: 126 Copynumber: 1.8 Consensus size: 125
251058 AGGCTTAACG
* * * * * * *
251068 ACTTTGGAAAAGTAAATTGCTCCTCTAAATAGAGGCTCACT-GACTTTTGGAAAGTAATTTTCTC
1 ACTTTGGAAAAATAAAATGCTCCTCTAAACAGAGGC-AACTAGACTTTGGGAAA-TAAATTGCTC
** * *
251132 CTCTAAACAAAGGCACTGTAACTTTTGAAAAGTAAATTGCTCCTCTAAATAGAGGCAACCACA
64 CTCTAAACAAAGGCACAATAAC-TTTGAAAAATAAATAGCTCCTCTAAATAGAGGCAACCACA
251195 ACTTT-GAAAAATAAAATGCTCCTCTAAACAGAGGCAACTACGACTTTGGGAAATAAATTGCTCC
1 ACTTTGGAAAAATAAAATGCTCCTCTAAACAGAGGCAACTA-GACTTTGGGAAATAAATTGCTCC
* *
251259 TCTAAACAGAGGCTCAATAACTTTGAAAAATAAATAGCTC
65 TCTAAACAAAGGCACAATAACTTTGAAAAATAAATAGCTC
251299 ATCGACAATC
Statistics
Matches: 89, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
125 20 0.22
126 53 0.60
127 16 0.18
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.27
Consensus pattern (125 bp):
ACTTTGGAAAAATAAAATGCTCCTCTAAACAGAGGCAACTAGACTTTGGGAAATAAATTGCTCCT
CTAAACAAAGGCACAATAACTTTGAAAAATAAATAGCTCCTCTAAATAGAGGCAACCACA
Found at i:262877 original size:54 final size:52
Alignment explanation
Indices: 262790--262998 Score: 158
Period size: 54 Copynumber: 3.9 Consensus size: 52
262780 TGCTTTTGCA
* *
262790 TAAAGAAAATTGATACTTTTAAC-TTTTCTTTAAAGCATTTGGGAGTTTTT-A-TTT
1 TAAAGAAAATTGATACTTTCAACTTTTTC-TTAAAACATTT----GTTTTTAATTTT
* *
262844 T-AAGAAAAATTGATACTTTCAACTTTTTCTTAAAATATTTTTTTTTAATTTT
1 TAAAG-AAAATTGATACTTTCAACTTTTTCTTAAAACATTTGTTTTTAATTTT
* ** * *
262896 TAAAGAAAATTGGTACTTTCAACTTTTTCTTAAAATGTTTTTTTTTTTATTTAATT
1 TAAAGAAAATTGATACTTTCAACTTTTTCTTAAAA--CATTTGTTTTTAATT--TT
* * *
262952 TCAAGGAAAAATTGATACTTTCAACTTTTTTCTAAAAATATTT-TTTT
1 T-AAAG-AAAATTGATACTTTCAAC-TTTTTCTTAAAACATTTGTTTT
262999 AAAATCTTTT
Statistics
Matches: 132, Mismatches: 11, Indels: 22
0.80 0.07 0.13
Matches are distributed among these distances:
50 5 0.04
51 1 0.01
52 33 0.25
53 6 0.05
54 40 0.30
55 5 0.04
56 7 0.05
57 7 0.05
58 17 0.13
59 11 0.08
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.51
Consensus pattern (52 bp):
TAAAGAAAATTGATACTTTCAACTTTTTCTTAAAACATTTGTTTTTAATTTT
Found at i:262878 original size:26 final size:26
Alignment explanation
Indices: 262849--262931 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
262839 TATTTTAAGA
262849 AAAATTGATACTTTCAACTTTTTCTT
1 AAAATTGATACTTTCAACTTTTTCTT
* ** * ***
262875 AAAATAT-TTTTTTTTAA-TTTTTAAAG
1 AAAAT-TGATACTTTCAACTTTTT-CTT
*
262901 AAAATTGGTACTTTCAACTTTTTCTT
1 AAAATTGATACTTTCAACTTTTTCTT
262927 AAAAT
1 AAAAT
262932 GTTTTTTTTT
Statistics
Matches: 39, Mismatches: 14, Indels: 8
0.64 0.23 0.13
Matches are distributed among these distances:
25 6 0.15
26 27 0.69
27 6 0.15
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.51
Consensus pattern (26 bp):
AAAATTGATACTTTCAACTTTTTCTT
Found at i:262916 original size:52 final size:53
Alignment explanation
Indices: 262841--262998 Score: 203
Period size: 52 Copynumber: 2.9 Consensus size: 53
262831 GGAGTTTTTA
262841 TTTT-AAGAAAAATTGATACTTTCAACTTTTTCTTAAAATATTTTTTTTTAAT
1 TTTTAAAGAAAAATTGATACTTTCAACTTTTTCTTAAAATATTTTTTTTTAAT
* * *
262893 TTTTAAAG-AAAATTGGTACTTTCAACTTTTTCTTAAAATGTTTTTTTTTTTATT
1 TTTTAAAGAAAAATTGATACTTTCAACTTTTTCTTAAAA--TATTTTTTTTTAAT
* *
262947 TAATTTCAAGGAAAAATTGATACTTTCAACTTTTTTCTAAAAATATTTTTTT
1 T--TTT-AAAGAAAAATTGATACTTTCAAC-TTTTTCTTAAAATATTTTTTT
262999 AAAATCTTTT
Statistics
Matches: 91, Mismatches: 7, Indels: 11
0.83 0.06 0.10
Matches are distributed among these distances:
52 33 0.36
53 3 0.03
54 13 0.14
56 3 0.03
57 11 0.12
58 17 0.19
59 11 0.12
ACGTcount: A:0.33, C:0.08, G:0.06, T:0.53
Consensus pattern (53 bp):
TTTTAAAGAAAAATTGATACTTTCAACTTTTTCTTAAAATATTTTTTTTTAAT
Found at i:263188 original size:13 final size:13
Alignment explanation
Indices: 263163--263241 Score: 56
Period size: 13 Copynumber: 5.9 Consensus size: 13
263153 AAAATATTGA
*
263163 AAAATAAGA-AAT
1 AAAATAATATAAT
263175 AAAATAATATAAT
1 AAAATAATATAAT
*
263188 AAAATAATAAAAAT
1 AAAATAAT-ATAAT
*
263202 ACCAAATAATTTTAA-
1 A--AAATAA-TATAAT
*
263217 ATAATAATAATAAT
1 AAAATAAT-ATAAT
263231 AAAATAA-ATAA
1 AAAATAATATAA
263242 ATAATTTAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
12 13 0.25
13 19 0.36
14 11 0.21
15 1 0.02
16 8 0.15
17 1 0.02
ACGTcount: A:0.70, C:0.03, G:0.01, T:0.27
Consensus pattern (13 bp):
AAAATAATATAAT
Found at i:263200 original size:34 final size:34
Alignment explanation
Indices: 263153--263234 Score: 85
Period size: 34 Copynumber: 2.4 Consensus size: 34
263143 TATTTTAGAA
* *
263153 AAAATATTGAAAAATAAGAAATAA-AATAATATAAT
1 AAAATAAT-AAAAATAACAAATAATAATAA-ATAAT
* **
263188 AAAATAATAAAAATACCAAATAATTTTAAATAAT
1 AAAATAATAAAAATAACAAATAATAATAAATAAT
263222 AATAATAATAAAA
1 AA-AATAATAAAA
263235 TAAATAAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
34 20 0.50
35 20 0.50
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (34 bp):
AAAATAATAAAAATAACAAATAATAATAAATAAT
Found at i:263233 original size:16 final size:15
Alignment explanation
Indices: 263165--263238 Score: 64
Period size: 16 Copynumber: 4.9 Consensus size: 15
263155 AATATTGAAA
*
263165 AATAAGAAATAAAAT
1 AATAATAAATAAAAT
263180 AAT-AT-AATAAAAT
1 AATAATAAATAAAAT
263193 AATAA-AAATACCAAAT
1 AATAATAAATA--AAAT
**
263209 AATTTTAAATAATAAT
1 AATAATAAATAA-AAT
263225 AATAATAAAATAAA
1 AATAAT-AAATAAA
263239 TAAATAATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
13 11 0.23
14 6 0.13
15 4 0.09
16 15 0.32
17 11 0.23
ACGTcount: A:0.69, C:0.03, G:0.01, T:0.27
Consensus pattern (15 bp):
AATAATAAATAAAAT
Found at i:263251 original size:34 final size:34
Alignment explanation
Indices: 263183--263248 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
263173 ATAAAATAAT
*
263183 ATAATAAAATAATAAAAATACCAAATAATTTTAA
1 ATAATAAAATAATAAAAATAACAAATAATTTTAA
*
263217 ATAATAATAATAAT-AAAATAAATAAATAATTT
1 ATAATAA-AATAATAAAAAT-AACAAATAATTT
263249 AAAAAAACCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 12 0.43
35 16 0.57
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (34 bp):
ATAATAAAATAATAAAAATAACAAATAATTTTAA
Found at i:263255 original size:21 final size:21
Alignment explanation
Indices: 263214--263255 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
263204 CAAATAATTT
*
263214 TAAATAATAATAATAATAAAA
1 TAAATAATAATAATAAAAAAA
*
263235 TAAATAAATAAT-TTAAAAAAA
1 TAAAT-AATAATAATAAAAAAA
263256 CCTTGAAACG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAATAATAATAATAAAAAAA
Found at i:263522 original size:21 final size:20
Alignment explanation
Indices: 263498--263540 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
263488 TTTCTTCATA
263498 TTTTCCCTATCTTTT-TCTCTC
1 TTTTCCCT-TCTTTTCTC-CTC
263519 TTTTCCCTTCTTTTCTCCTC
1 TTTTCCCTTCTTTTCTCCTC
263539 TT
1 TT
263541 CTCTCTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTCCCTTCTTTTCTCCTC
Found at i:263539 original size:20 final size:21
Alignment explanation
Indices: 263498--263540 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
263488 TTTCTTCATA
263498 TTTTCCCTATCTTTTTCTCTC
1 TTTTCCCTATCTTTTTCTCTC
263519 TTTTCCCT-TC-TTTTCTCCTC
1 TTTTCCCTATCTTTTTCT-CTC
263539 TT
1 TT
263541 CTCTCTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.29
20 7 0.33
21 8 0.38
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTCCCTATCTTTTTCTCTC
Found at i:263998 original size:3 final size:3
Alignment explanation
Indices: 263992--264053 Score: 52
Period size: 3 Copynumber: 18.7 Consensus size: 3
263982 TCAAAAAAAA
*
263992 AAT AAT AAT AAT AAT AAT AAAT ACAT ATT AAT AAAT AAAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT A-AT AAT AAT -AAT -AAT -AAT AAT
*
264039 AAT AAAT AAA AAT AA
1 AAT -AAT AAT AAT AA
264054 AACTACAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
3 31 0.61
4 20 0.39
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:264025 original size:14 final size:13
Alignment explanation
Indices: 263992--264053 Score: 63
Period size: 14 Copynumber: 4.6 Consensus size: 13
263982 TCAAAAAAAA
263992 AATAATAAT-AAT
1 AATAATAATAAAT
*
264004 AATAATAAATACAT
1 AATAAT-AATAAAT
*
264018 ATTAATAAATAAAT
1 AATAAT-AATAAAT
264032 AAATAATAATAAAT
1 -AATAATAATAAAT
*
264046 AAAAATAA
1 AATAATAA
264054 AACTACAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
12 6 0.14
13 10 0.24
14 21 0.50
15 5 0.12
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATAAAT
Found at i:264030 original size:18 final size:17
Alignment explanation
Indices: 263991--264053 Score: 78
Period size: 18 Copynumber: 3.8 Consensus size: 17
263981 GTCAAAAAAA
263991 AAAT-AATAATAATAAT
1 AAATAAATAATAATAAT
*
264007 -AATAAATACATATTAAT
1 AAATAAATA-ATAATAAT
264024 AAATAAATAAATAATAAT
1 AAATAAAT-AATAATAAT
264042 AAATAAA-AATAA
1 AAATAAATAATAA
264054 AACTACAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
15 3 0.07
16 9 0.22
17 7 0.17
18 21 0.51
19 1 0.02
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATAAATAATAATAAT
Found at i:269593 original size:30 final size:30
Alignment explanation
Indices: 269559--269615 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
269549 AACTCTTAAT
269559 TTTTAATTTATATCCAAATTAATCTTTCAC
1 TTTTAATTTATATCCAAATTAATCTTTCAC
*
269589 TTTTAATTTATATCTAAATTAATCTTT
1 TTTTAATTTATATCCAAATTAATCTTT
269616 TTATTTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.54
Consensus pattern (30 bp):
TTTTAATTTATATCCAAATTAATCTTTCAC
Found at i:287854 original size:22 final size:22
Alignment explanation
Indices: 287808--287861 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
287798 ATTTTGAGGT
* ***
287808 TTTTGGATTTTATGGTTTGGCA
1 TTTTGGATTTTAGGGTTTCAAA
287830 TTTTGGATTTTAGGGTTTCAAA
1 TTTTGGATTTTAGGGTTTCAAA
*
287852 TTTAGGATTT
1 TTTTGGATTT
287862 GGATGTTTAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.19, C:0.04, G:0.24, T:0.54
Consensus pattern (22 bp):
TTTTGGATTTTAGGGTTTCAAA
Found at i:287903 original size:7 final size:7
Alignment explanation
Indices: 287893--287950 Score: 57
Period size: 7 Copynumber: 8.3 Consensus size: 7
287883 TAGAACTTAG
287893 AGGGTTT
1 AGGGTTT
287900 AGGGTTT
1 AGGGTTT
*
287907 A-GTTTT
1 AGGGTTT
287913 AGGGTTTAT
1 AGGG-TT-T
287922 AGGGTTT
1 AGGGTTT
287929 AGGGTTT
1 AGGGTTT
*
287936 A-GTTTT
1 AGGGTTT
*
287942 ATGGTTT
1 AGGGTTT
287949 AG
1 AG
287951 AGGGTTTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
6 10 0.24
7 23 0.55
8 4 0.10
9 5 0.12
ACGTcount: A:0.17, C:0.00, G:0.34, T:0.48
Consensus pattern (7 bp):
AGGGTTT
Found at i:287915 original size:13 final size:13
Alignment explanation
Indices: 287897--287950 Score: 63
Period size: 13 Copynumber: 3.9 Consensus size: 13
287887 ACTTAGAGGG
287897 TTTAGGGTTTAGT
1 TTTAGGGTTTAGT
*
287910 TTTAGGGTTTATAGGG
1 TTTAGGG-TT-TA-GT
287926 TTTAGGGTTTAGT
1 TTTAGGGTTTAGT
*
287939 TTTATGGTTTAG
1 TTTAGGGTTTAG
287951 AGGGTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
13 19 0.54
14 4 0.11
15 4 0.11
16 8 0.23
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.52
Consensus pattern (13 bp):
TTTAGGGTTTAGT
Found at i:287964 original size:29 final size:29
Alignment explanation
Indices: 287866--287958 Score: 123
Period size: 29 Copynumber: 3.2 Consensus size: 29
287856 GGATTTGGAT
* ***
287866 GTTTAGGGTTTCGATTTTAGAACTTAGAGG
1 GTTTAGGGTTTAG-TTTTAGGGTTTAGAGG
*
287896 GTTTAGGGTTTAGTTTTAGGGTTTATAGG
1 GTTTAGGGTTTAGTTTTAGGGTTTAGAGG
*
287925 GTTTAGGGTTTAGTTTTATGGTTTAGAGG
1 GTTTAGGGTTTAGTTTTAGGGTTTAGAGG
287954 GTTTA
1 GTTTA
287959 AAGTTTTGAT
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
29 44 0.79
30 12 0.21
ACGTcount: A:0.19, C:0.02, G:0.32, T:0.46
Consensus pattern (29 bp):
GTTTAGGGTTTAGTTTTAGGGTTTAGAGG
Found at i:288206 original size:3 final size:3
Alignment explanation
Indices: 288200--288247 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
288190 TTTTATGAAA
288200 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
288248 TATCCTTTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:288463 original size:11 final size:11
Alignment explanation
Indices: 288380--288472 Score: 57
Period size: 11 Copynumber: 8.2 Consensus size: 11
288370 ATTGTTAAAT
288380 TTTTATTATT-
1 TTTTATTATTA
*
288390 TTTTA-GATTA
1 TTTTATTATTA
*
288400 TTATATTATTA
1 TTTTATTATTA
**
288411 TTTTAAGCATT-
1 TTTT-ATTATTA
*
288422 TTTAGTATTTTTA
1 TTT--TATTATTA
288435 TATTTATTATCCTA
1 T-TTTATTAT--TA
*
288449 TTTTATTGTTA
1 TTTTATTATTA
288460 TTTTATTATTA
1 TTTTATTATTA
288471 TT
1 TT
288473 AAAAACAATC
Statistics
Matches: 62, Mismatches: 12, Indels: 17
0.68 0.13 0.19
Matches are distributed among these distances:
9 3 0.05
10 9 0.15
11 24 0.39
12 12 0.19
13 9 0.15
14 5 0.08
ACGTcount: A:0.26, C:0.03, G:0.04, T:0.67
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:288573 original size:11 final size:11
Alignment explanation
Indices: 288557--288595 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
288547 CTAATAATAT
288557 AAAAATTAGAA-
1 AAAAATTA-AAG
288568 AAAAATTAAAG
1 AAAAATTAAAG
288579 AAAAATTAAAG
1 AAAAATTAAAG
288590 AAAAAT
1 AAAAAT
288596 ACTTGAACTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 2 0.07
11 25 0.93
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (11 bp):
AAAAATTAAAG
Found at i:292943 original size:3 final size:3
Alignment explanation
Indices: 292937--292968 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
292927 ACTTCTTCTC
292937 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
292969 AATATATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:296949 original size:30 final size:31
Alignment explanation
Indices: 296840--296950 Score: 119
Period size: 30 Copynumber: 3.7 Consensus size: 31
296830 TTCATTACTT
296840 TACTTAAATAAA-TCTTTATATTTTT-A-TTA
1 TACTTAAATAAACTCTTTA-ATTTTTAATTTA
*
296869 TA-TCTAAATAAACTC-TTAATCTTTAATTTA
1 TACT-TAAATAAACTCTTTAATTTTTAATTTA
* * *
296899 TATTTAAAT-AAGTCATTAATTTTTAATTTA
1 TACTTAAATAAACTCTTTAATTTTTAATTTA
296929 TACTTAAATAAACT-TTTAATTT
1 TACTTAAATAAACTCTTTAATTT
296951 AAATTAATTT
Statistics
Matches: 69, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
28 6 0.09
29 18 0.26
30 41 0.59
31 4 0.06
ACGTcount: A:0.40, C:0.08, G:0.01, T:0.51
Consensus pattern (31 bp):
TACTTAAATAAACTCTTTAATTTTTAATTTA
Found at i:296954 original size:17 final size:17
Alignment explanation
Indices: 296932--296976 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
296922 TAATTTATAC
296932 TTAAATAAACTTTTAAT
1 TTAAATAAACTTTTAAT
**
296949 TTAAATTAATTTTTTAAT
1 TTAAA-TAAACTTTTAAT
296967 TTAAAATAAA
1 TT-AAATAAA
296977 AACTTATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 5 0.22
18 15 0.65
19 3 0.13
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
TTAAATAAACTTTTAAT
Found at i:296965 original size:60 final size:59
Alignment explanation
Indices: 296843--296958 Score: 139
Period size: 59 Copynumber: 2.0 Consensus size: 59
296833 ATTACTTTAC
* * *
296843 TTAAATAAATCTTTATATTTTTATTATATCTAAATAAACTCTTAATCTTTAATTTATAT
1 TTAAATAAATCATTATATTTTTATTATATCTAAATAAACTCTTAATCTTAAATTAATAT
* *
296902 TTAAATAAGTCATTA-ATTTTTAATT-TATACTTAAATAAACTTTTAAT-TTAAATTAAT
1 TTAAATAAATCATTATATTTTT-ATTATAT-C-TAAATAAACTCTTAATCTTAAATTAAT
296959 TTTTTAATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
58 9 0.18
59 25 0.51
60 15 0.31
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.51
Consensus pattern (59 bp):
TTAAATAAATCATTATATTTTTATTATATCTAAATAAACTCTTAATCTTAAATTAATAT
Found at i:297003 original size:30 final size:29
Alignment explanation
Indices: 296969--297056 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
296959 TTTTTAATTT
* *
296969 AAAATAAAAACTTATTTAGATAGAAATAAA
1 AAAATAAAAAATTATTTAAATA-AAATAAA
*
296999 AAAATAAAAAATTATTTAAATATAATAAA
1 AAAATAAAAAATTATTTAAATAAAATAAA
* * * *
297028 TATATAAAAATTTATTTTAA-AAAATAAA
1 AAAATAAAAAATTATTTAAATAAAATAAA
297056 A
1 A
297057 TAATCTGAAG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
28 7 0.14
29 22 0.45
30 20 0.41
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (29 bp):
AAAATAAAAAATTATTTAAATAAAATAAA
Found at i:297025 original size:29 final size:28
Alignment explanation
Indices: 296969--297056 Score: 88
Period size: 30 Copynumber: 3.0 Consensus size: 28
296959 TTTTTAATTT
* *
296969 AAAATAAAAACTTATTTAGATAGAAATAAA
1 AAAATAAAAAATTATTTA-A-ATAAATAAA
296999 AAAATAAAAAATTATTTAAATATAATAAA
1 AAAATAAAAAATTATTTAAATA-AATAAA
* * *
297028 TATATAAAAATTTATTTTAAA-AAATAAA
1 AAAATAAAAAATTA-TTTAAATAAATAAA
297056 A
1 A
297057 TAATCTGAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
28 8 0.16
29 19 0.38
30 23 0.46
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (28 bp):
AAAATAAAAAATTATTTAAATAAATAAA
Found at i:301714 original size:24 final size:21
Alignment explanation
Indices: 301671--301728 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 21
301661 TATTAATTTA
*
301671 ATATAATAAATAAATGTTATC
1 ATATAATAAATAAATATTATC
*
301692 ATATAATAAATAAATTTTATTATT
1 ATATAATAAATAAA---TATTATC
301716 ATATAATAAATAA
1 ATATAATAAATAA
301729 TCCATATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 14 0.44
24 18 0.56
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
ATATAATAAATAAATATTATC
Found at i:301721 original size:21 final size:21
Alignment explanation
Indices: 301671--301711 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
301661 TATTAATTTA
301671 ATATAATAAATAAATGTTATC
1 ATATAATAAATAAATGTTATC
*
301692 ATATAATAAATAAATTTTAT
1 ATATAATAAATAAATGTTAT
301712 TATTATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
ATATAATAAATAAATGTTATC
Found at i:301742 original size:27 final size:24
Alignment explanation
Indices: 301661--301742 Score: 64
Period size: 24 Copynumber: 3.4 Consensus size: 24
301651 AAAATTATTT
301661 TATTAAT-TTAATATAATAAATAAA
1 TATTAATATT-ATATAATAAATAAA
* *
301685 T-GT--TATCATATAATAAATAAA
1 TATTAATATTATATAATAAATAAA
* *
301706 TTTTATTATTATATAATAAATAATCCA
1 TATTAATATTATATAATAAATAA---A
301733 TATTAATATT
1 TATTAATATT
301743 TTGATTGAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
21 16 0.36
22 2 0.04
23 1 0.02
24 17 0.38
27 9 0.20
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (24 bp):
TATTAATATTATATAATAAATAAA
Found at i:301780 original size:12 final size:12
Alignment explanation
Indices: 301763--301821 Score: 54
Period size: 11 Copynumber: 5.2 Consensus size: 12
301753 TAAAATTTTA
301763 AATATTATAAAT
1 AATATTATAAAT
301775 AATATTA-AAA-
1 AATATTATAAAT
301785 AATA-TATAAAT
1 AATATTATAAAT
*
301796 AAT-TTATCAAT
1 AATATTATAAAT
* *
301807 ACATTTTTTAAAT
1 A-ATATTATAAAT
301820 AA
1 AA
301822 AACCCCTTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
9 2 0.05
10 7 0.18
11 13 0.33
12 10 0.26
13 7 0.18
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (12 bp):
AATATTATAAAT
Found at i:303204 original size:2 final size:2
Alignment explanation
Indices: 303197--303221 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
303187 CATGTTTTTA
303197 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 A
303222 GCACAGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:310926 original size:40 final size:39
Alignment explanation
Indices: 310853--310936 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 39
310843 AAAAAGGGTG
310853 AAAATAAAAAAAAAGTATTAATTTAATAGTTAAATT-AT
1 AAAATAAAAAAAAAGTATTAATTTAATAGTTAAATTAAT
* * *
310891 AAAATAAAATAATAATTATTTATTTTAATTA-TTAAATTAAT
1 AAAATAAAA-AAAAAGTA-TTAATTTAA-TAGTTAAATTAAT
310932 AAAAT
1 AAAAT
310937 TTTCATCTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
38 9 0.23
39 6 0.15
40 15 0.38
41 9 0.23
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.39
Consensus pattern (39 bp):
AAAATAAAAAAAAAGTATTAATTTAATAGTTAAATTAAT
Found at i:312495 original size:3 final size:3
Alignment explanation
Indices: 312487--312511 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
312477 AACCAGATTT
312487 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
312512 ACTGAAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:320696 original size:23 final size:23
Alignment explanation
Indices: 320670--320713 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
320660 AGATAATTTA
*
320670 AGATAATTTAATAGGAAGCTTTG
1 AGATAATTTAATAAGAAGCTTTG
320693 AGATAATTTAATAAGAAGCTT
1 AGATAATTTAATAAGAAGCTT
320714 ACAGTAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.05, G:0.18, T:0.34
Consensus pattern (23 bp):
AGATAATTTAATAAGAAGCTTTG
Found at i:323704 original size:86 final size:87
Alignment explanation
Indices: 323573--323744 Score: 249
Period size: 86 Copynumber: 2.0 Consensus size: 87
323563 TTAATAAGAA
* * *
323573 AAACGATGTCAATAAAGAAATCAGAATTGATGCAAATAAACTATATTACTAATGAAATGATGATA
1 AAACGATGTCAATAAAGAAATCAGAATTGATGCAAATAAACTATATTAATAAAGAAATAATGATA
*
323638 CA-AAAGAAACTAAAGGACAAAT
66 CATAAA-AAACTAAAGAACAAAT
* * *
323660 AAACTATGTCAATAAAGAAAT-GGAATTTATGCAAATAAACTATATTAATAAAGAAATAATGATA
1 AAACGATGTCAATAAAGAAATCAGAATTGATGCAAATAAACTATATTAATAAAGAAATAATGATA
*
323724 CATATAAAACTAAAGAACAAA
66 CATAAAAAACTAAAGAACAAA
323745 ATCAGAACAC
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
86 54 0.71
87 22 0.29
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.23
Consensus pattern (87 bp):
AAACGATGTCAATAAAGAAATCAGAATTGATGCAAATAAACTATATTAATAAAGAAATAATGATA
CATAAAAAACTAAAGAACAAAT
Found at i:324795 original size:15 final size:16
Alignment explanation
Indices: 324772--324804 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
324762 AAACAAAACC
*
324772 AGAAGAAAAAA-ATTA
1 AGAAAAAAAAACATTA
324787 AGAAAAAAAAACATTA
1 AGAAAAAAAAACATTA
324803 AG
1 AG
324805 TGAAAGGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.73, C:0.03, G:0.12, T:0.12
Consensus pattern (16 bp):
AGAAAAAAAAACATTA
Found at i:325491 original size:14 final size:14
Alignment explanation
Indices: 325431--325483 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
325421 AAGTAATTTT
325431 ATTTATTAATTAAA
1 ATTTATTAATTAAA
*
325445 ATATT-TTAAATCTGTAA
1 AT-TTATT-AAT-T-AAA
325462 ATTTATTAATTAAA
1 ATTTATTAATTAAA
325476 ATTTATTA
1 ATTTATTA
325484 TTTCAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 14 0.44
15 6 0.19
16 6 0.19
17 6 0.19
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (14 bp):
ATTTATTAATTAAA
Found at i:338124 original size:17 final size:18
Alignment explanation
Indices: 338088--338127 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
338078 TAACAAACAT
*
338088 AATTAAATAATTAATAAA
1 AATTAAATAAGTAATAAA
*
338106 AATTAAAT-AGTAATCAA
1 AATTAAATAAGTAATAAA
338123 AATTA
1 AATTA
338128 TTAATATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (18 bp):
AATTAAATAAGTAATAAA
Found at i:348129 original size:18 final size:18
Alignment explanation
Indices: 348108--348154 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
348098 ATGAAAGTGG
*
348108 TTCTGATGAGGATGATGA
1 TTCTGATGAGGAAGATGA
* *
348126 TTCTGAGGATGAAGATGA
1 TTCTGATGAGGAAGATGA
*
348144 GTCTGATGAGG
1 TTCTGATGAGG
348155 TTTCTTTTTG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.28, C:0.06, G:0.36, T:0.30
Consensus pattern (18 bp):
TTCTGATGAGGAAGATGA
Found at i:357088 original size:23 final size:24
Alignment explanation
Indices: 357053--357098 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
357043 TTGCAGAGGA
*
357053 AAATGTTATATATATT-AATATTT
1 AAATGTTAGATATATTAAATATTT
*
357076 AAATTTTAGATATATTAAATATT
1 AAATGTTAGATATATTAAATATT
357099 ACTTTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (24 bp):
AAATGTTAGATATATTAAATATTT
Found at i:359640 original size:23 final size:23
Alignment explanation
Indices: 359610--359655 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
359600 TAGTAACTAA
359610 GAATTTTGAGGGAGTCTTAGGCT
1 GAATTTTGAGGGAGTCTTAGGCT
359633 GAATTTTGAGGGAGTCTTAGGCT
1 GAATTTTGAGGGAGTCTTAGGCT
359656 CGTAGCATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.09, G:0.35, T:0.35
Consensus pattern (23 bp):
GAATTTTGAGGGAGTCTTAGGCT
Found at i:360878 original size:34 final size:34
Alignment explanation
Indices: 360830--360911 Score: 155
Period size: 34 Copynumber: 2.4 Consensus size: 34
360820 ATGTGATCAT
360830 AAAATATTAAAATTTTAATTTTAATTTTAATAATC
1 AAAA-ATTAAAATTTTAATTTTAATTTTAATAATC
360865 AAAAATTAAAATTTTAATTTTAATTTTAATAATC
1 AAAAATTAAAATTTTAATTTTAATTTTAATAATC
360899 AAAAATTAAAATT
1 AAAAATTAAAATT
360912 CGAATATTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
34 43 0.91
35 4 0.09
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (34 bp):
AAAAATTAAAATTTTAATTTTAATTTTAATAATC
Found at i:366972 original size:20 final size:20
Alignment explanation
Indices: 366947--366984 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
366937 GTAATTAATG
366947 TTATTATTGTTGTTTAAGAT
1 TTATTATTGTTGTTTAAGAT
366967 TTATTATTGTTGTTTAAG
1 TTATTATTGTTGTTTAAG
366985 TCTCGTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.61
Consensus pattern (20 bp):
TTATTATTGTTGTTTAAGAT
Found at i:368667 original size:3 final size:3
Alignment explanation
Indices: 368659--368703 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
368649 AGGTTCAACA
368659 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
368704 TTGAAATAGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:370002 original size:2 final size:2
Alignment explanation
Indices: 369997--370023 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
369987 TTTCAAATTT
369997 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
370024 TTGTTGGGGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:370116 original size:2 final size:2
Alignment explanation
Indices: 370109--370151 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
370099 AAAAGAAGTT
*
370109 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
370151 T
1 T
370152 CAAATCCCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:380014 original size:55 final size:55
Alignment explanation
Indices: 379948--380057 Score: 193
Period size: 55 Copynumber: 2.0 Consensus size: 55
379938 GATATTATTC
* *
379948 CCAAATATATTAACTAAACGTTGGAAATTTATTTATTATGGTCTGTTGTTAATTT
1 CCAAATATATTAACTAAACGTTGGAAATTTATTTATTATGGTCTGGTGCTAATTT
*
380003 CCAAATATATTAACTAAATGTTGGAAATTTATTTATTATGGTCTGGTGCTAATTT
1 CCAAATATATTAACTAAACGTTGGAAATTTATTTATTATGGTCTGGTGCTAATTT
380058 TTTTGGAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.45
Consensus pattern (55 bp):
CCAAATATATTAACTAAACGTTGGAAATTTATTTATTATGGTCTGGTGCTAATTT
Found at i:380488 original size:24 final size:24
Alignment explanation
Indices: 380438--380491 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
380428 AAATAATAAT
*
380438 AAAAATTATTGTAACTGTGATTAA
1 AAAAATTATTGTAACTATGATTAA
* *
380462 AAAAATTATTGTAATTATTATTTAA
1 AAAAATTATTGTAACTATGA-TTAA
380487 AAAAA
1 AAAAA
380492 ATTTAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 17 0.65
25 9 0.35
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (24 bp):
AAAAATTATTGTAACTATGATTAA
Found at i:389089 original size:22 final size:20
Alignment explanation
Indices: 389048--389091 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
389038 CACACTCAAT
*
389048 AACAGAAAAGCAAAGAACTA
1 AACAGAAAAACAAAGAACTA
*
389068 AACAGATAAAACATAGATACTA
1 AACAGA-AAAACAAAGA-ACTA
389090 AA
1 AA
389092 AGTGCTATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 8 0.40
22 6 0.30
ACGTcount: A:0.64, C:0.14, G:0.11, T:0.11
Consensus pattern (20 bp):
AACAGAAAAACAAAGAACTA
Found at i:394607 original size:38 final size:38
Alignment explanation
Indices: 394547--394623 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 38
394537 TAAGCAATAC
* *
394547 ATGGCAAAACTCCCCATTAATTTACGCATCCTAATCCA
1 ATGGCAAAACTCCCCATCAATTTACGCATCATAATCCA
*
394585 ATGGCAAAACTCTCCC-TCAATTTATGCATCATAATCCA
1 ATGGCAAAACTC-CCCATCAATTTACGCATCATAATCCA
394623 A
1 A
394624 CACAACTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
38 32 0.91
39 3 0.09
ACGTcount: A:0.35, C:0.30, G:0.08, T:0.27
Consensus pattern (38 bp):
ATGGCAAAACTCCCCATCAATTTACGCATCATAATCCA
Found at i:400610 original size:16 final size:15
Alignment explanation
Indices: 400583--400615 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
400573 TTAATTTTAA
400583 AATATAAATAATTAT
1 AATATAAATAATTAT
400598 AATATAGAATAATTAT
1 AATATA-AATAATTAT
400614 AA
1 AA
400616 ATTTAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (15 bp):
AATATAAATAATTAT
Found at i:403017 original size:5 final size:5
Alignment explanation
Indices: 403009--403043 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
402999 TCCAACCAAA
*
403009 AAAAG AAAAGG AAAAG AGAAG AAAAG AAAAG AAAA
1 AAAAG AAAA-G AAAAG AAAAG AAAAG AAAAG AAAA
403044 TATATAATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:430758 original size:11 final size:11
Alignment explanation
Indices: 430742--430768 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
430732 ACATAGAGAG
430742 CTTATAACTTT
1 CTTATAACTTT
430753 CTTATAACTTT
1 CTTATAACTTT
430764 CTTAT
1 CTTAT
430769 TCATTCTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.19, G:0.00, T:0.56
Consensus pattern (11 bp):
CTTATAACTTT
Found at i:442560 original size:20 final size:20
Alignment explanation
Indices: 442521--442560 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
442511 TAGATTATCA
*
442521 AAAATTAATATTTAATCATT
1 AAAATTAAAATTTAATCATT
442541 AAAATTAAAAATTTAA-CATT
1 AAAATT-AAAATTTAATCATT
442561 TTATCAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAATTAAAATTTAATCATT
Found at i:443580 original size:17 final size:17
Alignment explanation
Indices: 443540--443580 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
443530 TAAAATTAAG
443540 ATAAGA-TA-AAATAAA
1 ATAAGATTATAAATAAA
*
443555 ATAATATTATAAATAAA
1 ATAAGATTATAAATAAA
*
443572 ATTAGATTA
1 ATAAGATTA
443581 AATAATATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
15 5 0.24
16 2 0.10
17 14 0.67
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (17 bp):
ATAAGATTATAAATAAA
Found at i:443786 original size:26 final size:25
Alignment explanation
Indices: 443726--443787 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 25
443716 TGTAAATTTA
*
443726 ATAT-AATAAAATAAAAATAATCTT
1 ATATCAATAAAAAAAAAATAATCTT
* *
443750 -TTTCACTTAAAAAAATAAATAATCTT
1 ATATCA-ATAAAAAAA-AAATAATCTT
443776 ATATCAATAAAA
1 ATATCAATAAAA
443788 TATTAAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
23 2 0.07
24 1 0.03
25 7 0.24
26 15 0.52
27 4 0.14
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (25 bp):
ATATCAATAAAAAAAAAATAATCTT
Found at i:443794 original size:26 final size:25
Alignment explanation
Indices: 443726--443795 Score: 63
Period size: 26 Copynumber: 2.8 Consensus size: 25
443716 TGTAAATTTA
*
443726 ATAT-AATAAAATAAAAATAATCTT
1 ATATCAATAAAATATAAATAATCTT
* * *
443750 -TTTCACTTAAAAAAATAAATAATCTT
1 ATATCA-AT-AAAATATAAATAATCTT
443776 ATATCAATAAAATATTAAAT
1 ATATCAATAAAATA-TAAAT
443796 TTTCTTACAA
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
23 2 0.06
24 1 0.03
25 6 0.18
26 21 0.62
27 4 0.12
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (25 bp):
ATATCAATAAAATATAAATAATCTT
Done.