Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167949.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_21, 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: 19848060
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Warning! 113000 characters in sequence are not A, C, G, or T
File 132 of 138
Found at i:18805602 original size:117 final size:117
Alignment explanation
Indices: 18805456--18805678 Score: 374
Period size: 117 Copynumber: 1.9 Consensus size: 117
18805446 TAATCCTATC
* * * *
18805456 TTCAAGAATTAAGTGAAAGATGGGTAAAAAAAAAATCAGAAAACAAGTAATGTTTAGATTCAGCT
1 TTCAAGAATTAAGTGAAAGATGGGAAAAAAAAAAATCACAAAACAAGTAATGTTTAGATTCACCA
*
18805521 ACCATTTCCAAAAGCTCCATCACTTTCAAATTGATTTTTTCTAAAACTTATA
66 ACCATTTCCAAAACCTCCATCACTTTCAAATTGATTTTTTCTAAAACTTATA
* *
18805573 TTCAAGAATTAAGTGAAAGATGGGAAAAAAATATATCACAAAACAAGTAATGTTTAGATTCACCA
1 TTCAAGAATTAAGTGAAAGATGGGAAAAAAAAAAATCACAAAACAAGTAATGTTTAGATTCACCA
*
18805638 ACCTTTTCCAAAACCTCCATCACTTTCAAATTGATTTTTTC
66 ACCATTTCCAAAACCTCCATCACTTTCAAATTGATTTTTTC
18805679 ATCACATGCC
Statistics
Matches: 98, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
117 98 1.00
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (117 bp):
TTCAAGAATTAAGTGAAAGATGGGAAAAAAAAAAATCACAAAACAAGTAATGTTTAGATTCACCA
ACCATTTCCAAAACCTCCATCACTTTCAAATTGATTTTTTCTAAAACTTATA
Found at i:18806018 original size:20 final size:21
Alignment explanation
Indices: 18805971--18806016 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
18805961 TATACGATCA
*
18805971 TTTTTGTCCAAGTTACTTCTC
1 TTTTTGTCCAAGTTACCTCTC
*
18805992 TTTTTGTCCAAGTTTCCTCTC
1 TTTTTGTCCAAGTTACCTCTC
18806013 TTTT
1 TTTT
18806017 GTTAAACTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.11, C:0.24, G:0.09, T:0.57
Consensus pattern (21 bp):
TTTTTGTCCAAGTTACCTCTC
Found at i:18810783 original size:23 final size:20
Alignment explanation
Indices: 18810737--18810781 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
18810727 AAAAGCATTG
18810737 TTTTTATATCTAATTATTAT
1 TTTTTATATCTAATTATTAT
*
18810757 TTTTTATTTCTAATTATTAT
1 TTTTTATATCTAATTATTAT
18810777 TTTTT
1 TTTTT
18810782 TTAACATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTTATATCTAATTATTAT
Found at i:18811855 original size:14 final size:15
Alignment explanation
Indices: 18811833--18811872 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
18811823 TGATAAAAAT
18811833 AATTAATAAAAG-AA
1 AATTAATAAAAGTAA
* *
18811847 AATTTATAAATGTAA
1 AATTAATAAAAGTAA
18811862 AATTAATAAAA
1 AATTAATAAAA
18811873 AAATCTACAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (15 bp):
AATTAATAAAAGTAA
Found at i:18812199 original size:16 final size:16
Alignment explanation
Indices: 18812180--18812222 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
18812170 AGTAATTAAT
*
18812180 TATTTTATGAATTTTG
1 TATTTTATGAAATTTG
18812196 TATTTTA--AAATTTG
1 TATTTTATGAAATTTG
*
18812210 TAGTTTATGAAAT
1 TATTTTATGAAAT
18812223 ACTTTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 12 0.52
16 11 0.48
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.56
Consensus pattern (16 bp):
TATTTTATGAAATTTG
Found at i:18813347 original size:23 final size:23
Alignment explanation
Indices: 18813293--18813348 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
18813283 GAATAGTTAA
18813293 AACTAT-TCATTTTGAACAAACTT
1 AACTATCT-ATTTTGAACAAACTT
** * *
18813316 ATTTGTCTATTTTGAACAGACTT
1 AACTATCTATTTTGAACAAACTT
18813339 AACTATCTAT
1 AACTATCTAT
18813349 CTTTATTTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.43
Consensus pattern (23 bp):
AACTATCTATTTTGAACAAACTT
Found at i:18814374 original size:23 final size:21
Alignment explanation
Indices: 18814348--18814389 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
18814338 ATCAAAGAGA
18814348 AAAACCAAAAATATAAAAAAATG
1 AAAA-CAAAAATA-AAAAAAATG
*
18814371 AAAAGAAAAATAAAAAAAA
1 AAAACAAAAATAAAAAAAA
18814390 CCTTTTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 7 0.39
23 4 0.22
ACGTcount: A:0.81, C:0.05, G:0.05, T:0.10
Consensus pattern (21 bp):
AAAACAAAAATAAAAAAAATG
Found at i:18815934 original size:40 final size:40
Alignment explanation
Indices: 18815829--18815941 Score: 97
Period size: 40 Copynumber: 2.9 Consensus size: 40
18815819 GGTTTATTTA
* *
18815829 CATTTGCATCATTG-C-TTCTGCATCATTAAAAAAAAAGTTG
1 CATTTGCATCA-TGACATT-TGCATCATGAAAAAAAAACTTG
* * * * ** * *
18815869 TATGTGCATCATTACATCTATATCATGAGAAAAACACTTG
1 CATTTGCATCATGACATTTGCATCATGAAAAAAAAACTTG
18815909 CATTTGCATCATGACATTTGCATCAT-AAAAAAA
1 CATTTGCATCATGACATTTGCATCATGAAAAAAA
18815942 GAATTCATAT
Statistics
Matches: 54, Mismatches: 17, Indels: 5
0.71 0.22 0.07
Matches are distributed among these distances:
39 7 0.13
40 46 0.85
41 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.33
Consensus pattern (40 bp):
CATTTGCATCATGACATTTGCATCATGAAAAAAAAACTTG
Found at i:18816167 original size:40 final size:40
Alignment explanation
Indices: 18816123--18816272 Score: 151
Period size: 40 Copynumber: 3.7 Consensus size: 40
18816113 ATTGTATTTA
* *
18816123 CATCATGAA-AAAGACATTCGCATTTGCATTATTACATCCG
1 CATCAT-AACAAAGACATTCGCATTTGCATCATTACATCTG
* * *
18816163 CATCATAACAAAGACATTTGCATTTGCAACATTTGCATCTG
1 CATCATAACAAAGACATTCGCATTTGCATCA-TTACATCTG
* * * * *
18816204 CATC-TCGAGAAAGACATTTGCATATGCATCATTACATCTA
1 CATCAT-AACAAAGACATTCGCATTTGCATCATTACATCTG
* *
18816244 CATCATAAGAAAAACATTCGCATTTGCAT
1 CATCATAACAAAGACATTCGCATTTGCAT
18816273 TTGCATATAA
Statistics
Matches: 91, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
39 2 0.02
40 56 0.62
41 33 0.36
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (40 bp):
CATCATAACAAAGACATTCGCATTTGCATCATTACATCTG
Found at i:18816196 original size:15 final size:15
Alignment explanation
Indices: 18816176--18816205 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18816166 CATAACAAAG
*
18816176 ACATTTGCATTTGCA
1 ACATTTGCATCTGCA
18816191 ACATTTGCATCTGCA
1 ACATTTGCATCTGCA
18816206 TCTCGAGAAA
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:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (15 bp):
ACATTTGCATCTGCA
Found at i:18816352 original size:34 final size:34
Alignment explanation
Indices: 18816314--18816390 Score: 102
Period size: 34 Copynumber: 2.2 Consensus size: 34
18816304 ATTGTATCTA
* *
18816314 CATCACATGAAAGACATTTGCATTTGTATCATTG
1 CATCACATGAAAGACATTCGCATGTGTATCATTG
*
18816348 CATCACGA-GAAAGACATTCGTATGTGTATCATTG
1 CATCAC-ATGAAAGACATTCGCATGTGTATCATTG
18816382 CATCTACAT
1 CATC-ACAT
18816391 CACAAGAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
34 34 0.92
35 3 0.08
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (34 bp):
CATCACATGAAAGACATTCGCATGTGTATCATTG
Found at i:18816408 original size:26 final size:26
Alignment explanation
Indices: 18816379--18816431 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
18816369 ATGTGTATCA
18816379 TTGCATCTACATCACAAGAAAGACAT
1 TTGCATCTACATCACAAGAAAGACAT
* **
18816405 TTGCATTTACATCATTAGAAAGACAT
1 TTGCATCTACATCACAAGAAAGACAT
18816431 T
1 T
18816432 CACTTTTGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (26 bp):
TTGCATCTACATCACAAGAAAGACAT
Found at i:18816419 original size:40 final size:40
Alignment explanation
Indices: 18816291--18816420 Score: 128
Period size: 40 Copynumber: 3.4 Consensus size: 40
18816281 AAAAAAGCCA
* *
18816291 TTGCATGTGCATCATTGTATCTACATCACATGAAAGACAT
1 TTGCATGTGCATCATTGCATCTACATCACAAGAAAGACAT
* * *
18816331 TTGCATTTG--T-A-T-CAT-TGCATCACGAGAAAGACAT
1 TTGCATGTGCATCATTGCATCTACATCACAAGAAAGACAT
* * *
18816365 TCGTATGTGTATCATTGCATCTACATCACAAGAAAGACAT
1 TTGCATGTGCATCATTGCATCTACATCACAAGAAAGACAT
* *
18816405 TTGCATTTACATCATT
1 TTGCATGTGCATCATT
18816421 AGAAAGACAT
Statistics
Matches: 69, Mismatches: 15, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
34 22 0.32
35 2 0.03
36 2 0.03
37 2 0.03
38 2 0.03
39 3 0.04
40 36 0.52
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (40 bp):
TTGCATGTGCATCATTGCATCTACATCACAAGAAAGACAT
Found at i:18816419 original size:74 final size:73
Alignment explanation
Indices: 18816192--18816420 Score: 261
Period size: 74 Copynumber: 3.2 Consensus size: 73
18816182 GCATTTGCAA
* * * *
18816192 CATTTGCATC--TGCATCTCGAGAAAGACATTTGCATATGCATCATTACATCTACATCATAAGAA
1 CATTTGCATCATTGCATCACGAGAAAGACA-TTGCATGTGCATCATTGCATCTACATCACAAGAA
* *
18816255 AAACATTCG
65 AGACATTTG
** * * * *
18816264 CATTTGCAT--TTGCAT-ATAAAAAAGCCATTGCATGTGCATCATTGTATCTACATCACATGAAA
1 CATTTGCATCATTGCATCACGAGAAAGACATTGCATGTGCATCATTGCATCTACATCACAAGAAA
18816326 GACATTTG
66 GACATTTG
* * *
18816334 CATTTGTATCATTGCATCACGAGAAAGACATTCGTATGTGTATCATTGCATCTACATCACAAGAA
1 CATTTGCATCATTGCATCACGAGAAAGACATT-GCATGTGCATCATTGCATCTACATCACAAGAA
18816399 AGACATTTG
65 AGACATTTG
*
18816408 CATTTACATCATT
1 CATTTGCATCATT
18816421 AGAAAGACAT
Statistics
Matches: 129, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
70 44 0.34
71 7 0.05
72 20 0.16
73 10 0.08
74 48 0.37
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (73 bp):
CATTTGCATCATTGCATCACGAGAAAGACATTGCATGTGCATCATTGCATCTACATCACAAGAAA
GACATTTG
Found at i:18816443 original size:26 final size:26
Alignment explanation
Indices: 18816386--18816446 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
18816376 TCATTGCATC
** **
18816386 TACATCACAAGAAAGACATTTGCATT
1 TACATCATTAGAAAGACATTCACATT
*
18816412 TACATCATTAGAAAGACATTCACTTT
1 TACATCATTAGAAAGACATTCACATT
*
18816438 TGCATCATT
1 TACATCATT
18816447 GGTCCACATC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.33
Consensus pattern (26 bp):
TACATCATTAGAAAGACATTCACATT
Found at i:18817080 original size:32 final size:34
Alignment explanation
Indices: 18817012--18817080 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 34
18817002 GGCACTGAGA
18817012 TTTTAAGCCCAATTAAGTTGGCATTAGTTGAGATTT
1 TTTTAAGCCCAATTAAGTTGGC--TAGTTGAGATTT
18817048 TTTTAAGCCCAATCTAA-TTGGC-A-TTGAGATTT
1 TTTTAAGCCCAAT-TAAGTTGGCTAGTTGAGATTT
18817080 T
1 T
18817081 AAGTCTAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
32 10 0.31
33 1 0.03
36 18 0.56
37 3 0.09
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (34 bp):
TTTTAAGCCCAATTAAGTTGGCTAGTTGAGATTT
Found at i:18817188 original size:99 final size:99
Alignment explanation
Indices: 18817007--18817225 Score: 259
Period size: 99 Copynumber: 2.2 Consensus size: 99
18816997 TAGCTGGCAC
* *
18817007 TGAGA-TTTTAAGCCCAATTAAGTTGGCATTAGTTGAGATTTTTTTAAGCCCAATCTAATTGGCA
1 TGAGATTTTTAAGCCCAATTAAGTGGGCATTAATTGAGATTTTTTTAAGCCCAATCTAATTGGCA
* * *
18817071 TTGAGATTTTAAGTCTAGTAAAGTTGGCATT-AGA
66 CTGAAATTTAAAGTCTAGTAAAGTTGGCATTGA-A
* * * *
18817105 TGAGATTTTTGAAGGCCAGTTAAGTGGGCATTGAATT-AGA-TTTTTTAAGCTCAATCTAGTTGG
1 TGAGATTTTT-AAGCCCAATTAAGTGGGCATT-AATTGAGATTTTTTTAAGCCCAATCTAATTGG
*
18817168 CACTGAAATATTAAAG-CTAGTTAAGTTGGCATTGAA
64 CACTGAAAT-TTAAAGTCTAGTAAAGTTGGCATTGAA
18817204 TGAGATTTTTTAAAGCCCAATT
1 TGAGA-TTTTT-AAGCCCAATT
18817226 TAGTTGGTAA
Statistics
Matches: 102, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
98 5 0.05
99 54 0.53
100 40 0.39
101 3 0.03
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.37
Consensus pattern (99 bp):
TGAGATTTTTAAGCCCAATTAAGTGGGCATTAATTGAGATTTTTTTAAGCCCAATCTAATTGGCA
CTGAAATTTAAAGTCTAGTAAAGTTGGCATTGAA
Found at i:18817217 original size:35 final size:35
Alignment explanation
Indices: 18817077--18817219 Score: 99
Period size: 35 Copynumber: 4.3 Consensus size: 35
18817067 GGCATTGAGA
*
18817077 TTTT-AAGTCTAGTAAAGTTGGCATT-AGATGAGATT
1 TTTTAAAG-CTAGTTAAGTTGGCATTGA-ATGAGATT
* * * * *
18817112 TTTGAAGGCCAGTTAAGTGGGCATTGAATTAGATT
1 TTTTAAAGCTAGTTAAGTTGGCATTGAATGAGATT
* *
18817147 TTTT-AAGCTCAATCT-AGTTGGCACTG-A--A-A--
1 TTTTAAAGCT-AGT-TAAGTTGGCATTGAATGAGATT
*
18817176 TATTAAAGCTAGTTAAGTTGGCATTGAATGAGATT
1 TTTTAAAGCTAGTTAAGTTGGCATTGAATGAGATT
18817211 TTTTAAAGC
1 TTTTAAAGC
18817220 CCAATTTAGT
Statistics
Matches: 80, Mismatches: 16, Indels: 24
0.67 0.13 0.20
Matches are distributed among these distances:
28 1 0.01
29 15 0.19
30 6 0.08
31 1 0.01
32 2 0.03
33 1 0.01
34 4 0.05
35 46 0.57
36 4 0.05
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.37
Consensus pattern (35 bp):
TTTTAAAGCTAGTTAAGTTGGCATTGAATGAGATT
Found at i:18819066 original size:19 final size:19
Alignment explanation
Indices: 18819029--18819070 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
18819019 GTAATGGAGA
18819029 AAAGAGAAAAAGGAAAAAGG
1 AAAGAGAAAAA-GAAAAAGG
18819049 AAAGAAGAAAAA-AAAAAGG
1 AAAG-AGAAAAAGAAAAAGG
18819068 AAA
1 AAA
18819071 AATGTGCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.48
20 4 0.19
21 7 0.33
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (19 bp):
AAAGAGAAAAAGAAAAAGG
Found at i:18819072 original size:7 final size:7
Alignment explanation
Indices: 18819028--18819072 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
18819018 GGTAATGGAG
18819028 AAAAGAGA
1 AAAAG-GA
18819036 AAAAGGA
1 AAAAGGA
18819043 AAAAGGA
1 AAAAGGA
18819050 AAGAA-GA
1 AA-AAGGA
18819057 AAAA--A
1 AAAAGGA
18819062 AAAAGGA
1 AAAAGGA
18819069 AAAA
1 AAAA
18819073 TGTGCTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.15
6 2 0.06
7 20 0.59
8 7 0.21
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (7 bp):
AAAAGGA
Found at i:18819520 original size:17 final size:17
Alignment explanation
Indices: 18819498--18819538 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
18819488 AAGATTTATT
*
18819498 TAAATAACCAAAATAAA
1 TAAATAACAAAAATAAA
* *
18819515 TAAATAATAAAAATAAG
1 TAAATAACAAAAATAAA
18819532 TAAATAA
1 TAAATAA
18819539 AAACGTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (17 bp):
TAAATAACAAAAATAAA
Found at i:18819729 original size:19 final size:18
Alignment explanation
Indices: 18819705--18819752 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
18819695 TAGATAATCA
*
18819705 CATAATAATAAATAATTAT
1 CATAATAATAAA-AAGTAT
*
18819724 CATAAT-GTAAAAAGTAT
1 CATAATAATAAAAAGTAT
18819741 -ATAATAATAAAA
1 CATAATAATAAAA
18819753 TAGTTGTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 5 0.20
17 10 0.40
18 4 0.16
19 6 0.24
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (18 bp):
CATAATAATAAAAAGTAT
Found at i:18820489 original size:89 final size:89
Alignment explanation
Indices: 18820332--18820510 Score: 218
Period size: 89 Copynumber: 2.0 Consensus size: 89
18820322 TTTGAAAAAT
* *
18820332 TACAAAATATTATTAAACCTCAATTTTTTTTGAAAAATCTATACTTTTAAATGAACAATACTAGT
1 TACAAAATATTATTAAACCTCAA-TTTTTTTGAAAAATCTACACTCTTAAATGAACAATACTAGT
*
18820397 AAAAATGTGTTTGAAAAAAATCAAC
65 AAAAAAGTGTTTGAAAAAAATCAAC
** * * * *
18820422 TACAAAATATTATTGGACCTTAA-TTTTTT-AAAAATCTCTACACTCTTAAATGGACATTGCTAG
1 TACAAAATATTATTAAACCTCAATTTTTTTGAAAAA--TCTACACTCTTAAATGAACAATACTAG
**
18820485 TAAAAAAGTGTTTGAGTAAAATCAAC
64 TAAAAAAGTGTTTGAAAAAAATCAAC
18820511 ATTTTTTCCT
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
87 5 0.07
88 6 0.08
89 45 0.59
90 20 0.26
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (89 bp):
TACAAAATATTATTAAACCTCAATTTTTTTGAAAAATCTACACTCTTAAATGAACAATACTAGTA
AAAAAGTGTTTGAAAAAAATCAAC
Found at i:18822473 original size:8 final size:8
Alignment explanation
Indices: 18822460--18822497 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
18822450 GTTTGAAAAC
18822460 TAAAAATA
1 TAAAAATA
18822468 TAAAAAATA
1 T-AAAAATA
18822477 TAAAAA-A
1 TAAAAATA
*
18822484 TAAAAAAA
1 TAAAAATA
18822492 TAAAAA
1 TAAAAA
18822498 AAACTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 7 0.25
8 13 0.46
9 8 0.29
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (8 bp):
TAAAAATA
Found at i:18822498 original size:8 final size:9
Alignment explanation
Indices: 18822461--18822499 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
18822451 TTTGAAAACT
18822461 AAAAATATA
1 AAAAATATA
18822470 AAAAATATA
1 AAAAATATA
18822479 AAAAATA-A
1 AAAAATATA
18822487 AAAAATA-A
1 AAAAATATA
18822495 AAAAA
1 AAAAA
18822500 ACTTTTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 14 0.47
9 16 0.53
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (9 bp):
AAAAATATA
Found at i:18822498 original size:17 final size:18
Alignment explanation
Indices: 18822461--18822500 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
18822451 TTTGAAAACT
*
18822461 AAAAATATAAAAAATATA
1 AAAAATATAAAAAATAAA
18822479 AAAAATA-AAAAAATAAA
1 AAAAATATAAAAAATAAA
18822496 AAAAA
1 AAAAA
18822501 CTTTTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (18 bp):
AAAAATATAAAAAATAAA
Found at i:18823236 original size:6 final size:7
Alignment explanation
Indices: 18823219--18823252 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
18823209 CCATTGAGAA
*
18823219 AAAAATA
1 AAAAATG
18823226 AAAAATG
1 AAAAATG
18823233 AAAAATG
1 AAAAATG
18823240 AAAAATG
1 AAAAATG
18823247 AAAAAT
1 AAAAAT
18823253 AACCCTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (7 bp):
AAAAATG
Found at i:18824083 original size:40 final size:39
Alignment explanation
Indices: 18823917--18824140 Score: 161
Period size: 40 Copynumber: 5.5 Consensus size: 39
18823907 GGCTTATTTA
* * *
18823917 CATTTGCATCATTGCTTCTGCATCATAAAAAAAAAAAAAATTTG
1 CATTTGCATCATTGCATCTACATCAT----AAGAAAAAAA-TTG
* * * *
18823961 TATTTGCATCATTGCATCTACATCATGAGAAAAATACTTA
1 CATTTGCATCATTGCATCTACATCATAAGAAAAA-AATTG
*
18824001 CATTTGCATCA-TGACATTTACATCATAA-AAAAAGAATTTG
1 CATTTGCATCATTG-CATCTACATCATAAGAAAAA-AA-TTG
* *
18824041 CATTTGCATCATTGCATCTACATAATAAGAAAAACATGTG
1 CATTTGCATCATTGCATCTACATCATAAGAAAAAAAT-TG
* ***
18824081 CA-TT-CA-CATTTGTATCACTACATCATAAGAAAGTCATTCG
1 CATTTGCATCA-TTGCAT--CTACATCATAAGAAAAAAATT-G
18824121 CATTTGCATCATTGCATCTA
1 CATTTGCATCATTGCATCTA
18824141 TGTCACAAAA
Statistics
Matches: 146, Mismatches: 21, Indels: 30
0.74 0.11 0.15
Matches are distributed among these distances:
37 2 0.01
38 7 0.05
39 12 0.08
40 83 0.57
41 10 0.07
42 7 0.05
43 2 0.01
44 23 0.16
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (39 bp):
CATTTGCATCATTGCATCTACATCATAAGAAAAAAATTG
Found at i:18824103 original size:80 final size:80
Alignment explanation
Indices: 18823947--18824140 Score: 207
Period size: 80 Copynumber: 2.4 Consensus size: 80
18823937 CATCATAAAA
* * * * * **
18823947 AAAAAAAAAATTTGTATTTGCATCATTGCATCTACATCATGAGAAAAATACTTACATTTGCATCA
1 AAAAAAAGAATTTGCATTTGCATCATTGCATCTACATAATAAGAAAAACACTTACATTCACATCA
*
18824012 TGACATTTACATCAT
66 TGACATCTACATCAT
*
18824027 AAAAAAAGAATTTGCATTTGCATCATTGCATCTACATAATAAGAAAAACA-TGTGCATTCACAT-
1 AAAAAAAGAATTTGCATTTGCATCATTGCATCTACATAATAAGAAAAACACT-TACATTCACATC
*
18824090 TTGTATCA-CTACATCAT
65 ATG-A-CATCTACATCAT
* * *
18824107 -AAGAAAGTCATTCGCATTTGCATCATTGCATCTA
1 AAAAAAAG-AATTTGCATTTGCATCATTGCATCTA
18824141 TGTCACAAAA
Statistics
Matches: 97, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
79 9 0.09
80 86 0.89
81 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (80 bp):
AAAAAAAGAATTTGCATTTGCATCATTGCATCTACATAATAAGAAAAACACTTACATTCACATCA
TGACATCTACATCAT
Found at i:18824253 original size:40 final size:40
Alignment explanation
Indices: 18824209--18824380 Score: 193
Period size: 40 Copynumber: 4.3 Consensus size: 40
18824199 TGCATTACAC
18824209 GAAAGACATTTACATTTGCATCATTGCATTTAG-ATCATGA
1 GAAAGACATTTACATTTGCATCATTGCATTT-GCATCATGA
* * ** * *
18824249 GAAAGACATTCACATTTGCATTATTGCATTCACATTATAA
1 GAAAGACATTTACATTTGCATCATTGCATTTGCATCATGA
* * * *
18824289 CAAAGACATTTGCATTTACATCATTGCATTTGCATGATGA
1 GAAAGACATTTACATTTGCATCATTGCATTTGCATCATGA
* * *
18824329 GAAAAGACATTTACATGTGCATCATTACATCTGCATCATGA
1 G-AAAGACATTTACATTTGCATCATTGCATTTGCATCATGA
*
18824370 GAAAGATATTT
1 GAAAGACATTT
18824381 GCATATGTGT
Statistics
Matches: 107, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
40 73 0.68
41 34 0.32
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (40 bp):
GAAAGACATTTACATTTGCATCATTGCATTTGCATCATGA
Found at i:18825113 original size:39 final size:41
Alignment explanation
Indices: 18825044--18825138 Score: 124
Period size: 39 Copynumber: 2.4 Consensus size: 41
18825034 CAGAACAATC
* * *
18825044 ATGAG-AAAGACATTCGCATTTGCATTATTGCATTCGCATT
1 ATGAGAAAAGACATTTGCATTTACATCATTGCATTCGCATT
* *
18825084 AT-A-ACAAGACATTTGCATTTACATCATTGCATTTGCATT
1 ATGAGAAAAGACATTTGCATTTACATCATTGCATTCGCATT
18825123 ATGAGAAAAGACATTT
1 ATGAGAAAAGACATTT
18825139 ACGTGTGCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
39 33 0.72
40 3 0.07
41 10 0.22
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Consensus pattern (41 bp):
ATGAGAAAAGACATTTGCATTTACATCATTGCATTCGCATT
Found at i:18825257 original size:40 final size:40
Alignment explanation
Indices: 18825041--18825257 Score: 159
Period size: 40 Copynumber: 5.4 Consensus size: 40
18825031 AGCCAGAACA
* * * * *
18825041 ATCATGAGAAAGACATTCGCATTTGCATTATTGCAT-TCGC
1 ATCATGAAAAAGACATTTGCATATGCATCATTACATCT-GC
* * * * * *
18825081 ATTAT-AACAAGACATTTGCATTTACATCATTGCATTTGC
1 ATCATGAAAAAGACATTTGCATATGCATCATTACATCTGC
* * * * *
18825120 ATTATGAGAAAAGACATTTACGTGTGCATTATTACATCTGC
1 ATCATGA-AAAAGACATTTGCATATGCATCATTACATCTGC
* ** * *
18825161 ATCATGAACAAGATTTTTGCATATGCGTCATTACATTTGC
1 ATCATGAAAAAGACATTTGCATATGCATCATTACATCTGC
* * * *
18825201 ATCTTGAGAAAGACATTTGTATATGCATCATTACATCTGT
1 ATCATGAAAAAGACATTTGCATATGCATCATTACATCTGC
* *
18825241 ATCATAAAAAAAACATT
1 ATCATGAAAAAGACATT
18825258 CACACTTGTA
Statistics
Matches: 137, Mismatches: 37, Indels: 6
0.76 0.21 0.03
Matches are distributed among these distances:
39 32 0.23
40 74 0.54
41 31 0.23
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (40 bp):
ATCATGAAAAAGACATTTGCATATGCATCATTACATCTGC
Found at i:18825289 original size:32 final size:34
Alignment explanation
Indices: 18825241--18825324 Score: 91
Period size: 32 Copynumber: 2.5 Consensus size: 34
18825231 TTACATCTGT
* *
18825241 ATCATAAAAAAAACATTCACACTTGTA-T-TTGA
1 ATCATAAGAAAGACATTCACACTTGTATTATTGA
** * *
18825273 ATCATAAGAAAGACATTTGCATTTGTATTATTGC
1 ATCATAAGAAAGACATTCACACTTGTATTATTGA
*
18825307 ATCACAAGAAAGACATTC
1 ATCATAAGAAAGACATTC
18825325 GCATAAGCAT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
32 22 0.52
33 1 0.02
34 19 0.45
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (34 bp):
ATCATAAGAAAGACATTCACACTTGTATTATTGA
Found at i:18825340 original size:34 final size:34
Alignment explanation
Indices: 18825273--18825342 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 34
18825263 TTGTATTTGA
* * ** * *
18825273 ATCATAAGAAAGACATTTGCATTTGTATTATTGC
1 ATCACAAGAAAGACATTCGCATAAGCATCATTGC
18825307 ATCACAAGAAAGACATTCGCATAAGCATCATTGC
1 ATCACAAGAAAGACATTCGCATAAGCATCATTGC
18825341 AT
1 AT
18825343 TTACATCATG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (34 bp):
ATCACAAGAAAGACATTCGCATAAGCATCATTGC
Found at i:18825729 original size:17 final size:17
Alignment explanation
Indices: 18825706--18825740 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
18825696 ATATAAACAA
*
18825706 AAAAAAAAAGGTAAAAAG
1 AAAAAAGAAGG-AAAAAG
18825724 AAAAAAGAAGGAAAAAG
1 AAAAAAGAAGGAAAAAG
18825741 TGTCAGTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (17 bp):
AAAAAAGAAGGAAAAAG
Found at i:18828410 original size:17 final size:17
Alignment explanation
Indices: 18828388--18828428 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
18828378 AAGATTTATT
*
18828388 TAAATAACCAAAATAAA
1 TAAATAACAAAAATAAA
* *
18828405 TAAATAATAAAAATAAG
1 TAAATAACAAAAATAAA
18828422 TAAATAA
1 TAAATAA
18828429 AAATGTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (17 bp):
TAAATAACAAAAATAAA
Found at i:18828618 original size:19 final size:18
Alignment explanation
Indices: 18828594--18828641 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
18828584 TAGATAATCA
*
18828594 CATAATAATAAATAATTAT
1 CATAATAATAAA-AAGTAT
*
18828613 CATAAT-TTAAAAAGTAT
1 CATAATAATAAAAAGTAT
18828630 -ATAATAATAAAA
1 CATAATAATAAAA
18828642 TAGTTGTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 5 0.20
17 10 0.40
18 4 0.16
19 6 0.24
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (18 bp):
CATAATAATAAAAAGTAT
Found at i:18829376 original size:89 final size:89
Alignment explanation
Indices: 18829223--18829398 Score: 228
Period size: 89 Copynumber: 2.0 Consensus size: 89
18829213 TGAAAAATTA
* * * * *
18829223 CAAAATATTATTAAACCCTACTTTTTCTAAAACATCTATACTCTTAAATGAACATTACTGGTAAA
1 CAAAATATTATTAAACCCTAATTTTTCTAAAAAATCCACACTCTTAAATGAACATTACTAGTAAA
* **
18829288 AATGTGTTTGAGGGAAATCAACTG
66 AATATGTTTGAGAAAAATCAACTG
* * * *
18829312 CAAAATATTATTAGACCTTAATTTTT-TAAAAAACTCCACACTCTTAAATGGATATTACTAGTAA
1 CAAAATATTATTAAACCCTAATTTTTCTAAAAAA-TCCACACTCTTAAATGAACATTACTAGTAA
18829376 AAATATGTTTGAGAAAAATCAAC
65 AAATATGTTTGAGAAAAATCAAC
18829399 ATTTTTTCTT
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
88 6 0.08
89 68 0.92
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.34
Consensus pattern (89 bp):
CAAAATATTATTAAACCCTAATTTTTCTAAAAAATCCACACTCTTAAATGAACATTACTAGTAAA
AATATGTTTGAGAAAAATCAACTG
Found at i:18833541 original size:2 final size:2
Alignment explanation
Indices: 18833534--18833561 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18833524 CATGTGCTGT
18833534 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18833562 GCTCATGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18835702 original size:2 final size:2
Alignment explanation
Indices: 18835697--18835724 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18835687 AGTTTGATAC
18835697 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
18835725 TGCTTTTGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18842871 original size:10 final size:10
Alignment explanation
Indices: 18842858--18843079 Score: 61
Period size: 10 Copynumber: 22.5 Consensus size: 10
18842848 GAAAATTTCA
18842858 AAAAAATTTT
1 AAAAAATTTT
*
18842868 AAAAAATTCTC
1 AAAAAATT-TT
*
18842879 AAAAAATATT
1 AAAAAATTTT
*
18842889 AAAAATTTTT
1 AAAAAATTTT
*
18842899 ATAAAATTTT
1 AAAAAATTTT
**
18842909 CTAAAATTTT
1 AAAAAATTTT
* * **
18842919 -TAAAACTCC
1 AAAAAATTTT
18842928 AACAAAATTTT
1 AA-AAAATTTT
*
18842939 -AAAAA-CTT
1 AAAAAATTTT
* *
18842947 -AACAATTCT
1 AAAAAATTTT
18842956 AAACAAATTTT
1 AAA-AAATTTT
*
18842967 --AAATTTTCT
1 AAAAAATTT-T
*
18842976 AAAAAAAAATTCT
1 ---AAAAAATTTT
18842989 -AAAAATTTT
1 AAAAAATTTT
*
18842998 AAAAAATTAT
1 AAAAAATTTT
*
18843008 AAAATATTTT
1 AAAAAATTTT
** *
18843018 -TTAATTTTT
1 AAAAAATTTT
* *
18843027 AAGAACTTATT
1 AAAAAATT-TT
*
18843038 -AAAAATTCT
1 AAAAAATTTT
*
18843047 -AAAAGTTTT
1 AAAAAATTTT
*
18843056 -AAAATTTTT
1 AAAAAATTTT
*
18843065 TAAAAATTTT
1 AAAAAATTTT
18843075 AAAAA
1 AAAAA
18843080 CTTAAATAAG
Statistics
Matches: 153, Mismatches: 43, Indels: 32
0.67 0.19 0.14
Matches are distributed among these distances:
8 11 0.07
9 42 0.27
10 74 0.48
11 20 0.13
13 1 0.01
14 5 0.03
ACGTcount: A:0.53, C:0.07, G:0.01, T:0.40
Consensus pattern (10 bp):
AAAAAATTTT
Found at i:18842874 original size:21 final size:21
Alignment explanation
Indices: 18842849--18842893 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
18842839 CATATAAAAG
*
18842849 AAAATT-TCAAAAAAATTTTAA
1 AAAATTCTC-AAAAAATATTAA
18842870 AAAATTCTCAAAAAATATTAA
1 AAAATTCTCAAAAAATATTAA
18842891 AAA
1 AAA
18842894 TTTTTATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAATTCTCAAAAAATATTAA
Found at i:18843171 original size:10 final size:9
Alignment explanation
Indices: 18843156--18843504 Score: 116
Period size: 9 Copynumber: 36.3 Consensus size: 9
18843146 CATAAAAAAG
18843156 AAAATTTCTA
1 AAAATTT-TA
18843166 AAAATTTCTAA
1 AAAATTT-T-A
18843177 AAAATTTTTTA
1 AAAA--TTTTA
18843188 AAAATTTT-
1 AAAATTTTA
*
18843196 AAAATTTTT
1 AAAATTTTA
* **
18843205 AAAAGTCCA
1 AAAATTTTA
* *
18843214 AAATTTTTTTT
1 AAA--ATTTTA
*
18843225 AAAA-CTTA
1 AAAATTTTA
*
18843233 AAAATTCTA
1 AAAATTTTA
*
18843242 AACAAATTTA
1 AA-AATTTTA
*
18843252 AAAAGTTTGAA
1 AAAA-TTT-TA
*
18843263 AAAATTGTA
1 AAAATTTTA
18843272 AAATATTTTAA
1 AAA-ATTTT-A
18843283 AAAATTTTA
1 AAAATTTTA
* *
18843292 AAAACTCTA
1 AAAATTTTA
*
18843301 AAAATTTTTT
1 AAAA-TTTTA
* *
18843311 ATAATTCTA
1 AAAATTTTA
18843320 AAATATTTTTA
1 AAA-A-TTTTA
*
18843331 AAAACTTTTT
1 AAAA-TTTTA
*
18843341 AAAATTCTA
1 AAAATTTTA
*
18843350 AAATTTTTGA
1 AAAATTTT-A
*
18843360 AAAATTCT-
1 AAAATTTTA
18843368 AAAATTTTA
1 AAAATTTTA
*
18843377 AAAA-CTTA
1 AAAATTTTA
*
18843385 AATAATTCTAA
1 AA-AATT-TTA
18843396 AAAATTTTA
1 AAAATTTTA
* *
18843405 AAAATGATGA
1 AAAAT-TTTA
*
18843415 CAAATTTTAA
1 AAAATTTT-A
18843425 AAAATTTT-
1 AAAATTTTA
* *
18843433 -TAATTTAA
1 AAAATTTTA
18843441 AAAATTTATAAA
1 AAAATTT-T--A
*
18843453 AAAATACTTAA
1 AAAAT--TTTA
*
18843464 AAAATTTTT
1 AAAATTTTA
*
18843473 AAAATTCTA
1 AAAATTTTA
18843482 AAATTATTTTA
1 AAA--ATTTTA
* *
18843493 GAAATTTCA
1 AAAATTTTA
18843502 AAA
1 AAA
18843505 CTTTCTTTAG
Statistics
Matches: 245, Mismatches: 63, Indels: 63
0.66 0.17 0.17
Matches are distributed among these distances:
7 5 0.02
8 26 0.11
9 86 0.35
10 69 0.28
11 47 0.19
12 7 0.03
13 3 0.01
14 2 0.01
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.40
Consensus pattern (9 bp):
AAAATTTTA
Found at i:18843178 original size:9 final size:10
Alignment explanation
Indices: 18843156--18843409 Score: 59
Period size: 10 Copynumber: 26.5 Consensus size: 10
18843146 CATAAAAAAG
18843156 AAAATTTCTA
1 AAAATTTCTA
18843166 AAAATTTCTAA
1 AAAATTTCT-A
*
18843177 AAAATTTTTTA
1 AAAA-TTTCTA
18843188 AAAATTT-T-
1 AAAATTTCTA
*
18843196 AAAATTT-TT
1 AAAATTTCTA
* *
18843205 AAAA-GTCCA
1 AAAATTTCTA
* * *
18843214 AAATTTTTTTT
1 AAA-ATTTCTA
*
18843225 AAAA-CT-TA
1 AAAATTTCTA
18843233 AAAA-TTCTA
1 AAAATTTCTA
*
18843242 AACAAATT-TA
1 AA-AATTTCTA
*
18843252 AAAAGTTT-GA
1 AAAA-TTTCTA
* *
18843262 AAAAATTGTA
1 AAAATTTCTA
18843272 AAATATTT-TAA
1 AAA-ATTTCT-A
18843283 AAAATTT-TA
1 AAAATTTCTA
*
18843292 AAAA-CTCTA
1 AAAATTTCTA
* *
18843301 AAAATTTTTT
1 AAAATTTCTA
*
18843311 ATAA-TTCTA
1 AAAATTTCTA
*
18843320 AAATATTTTTA
1 AAA-ATTTCTA
*
18843331 AAAACTTT-TT
1 AAAA-TTTCTA
18843341 AAAA-TTCT-
1 AAAATTTCTA
*
18843349 AAAATTTTTGA
1 AAAATTTCT-A
18843360 AAAA-TTCT-
1 AAAATTTCTA
18843368 AAAATTT-TA
1 AAAATTTCTA
*
18843377 AAAA-CT-TA
1 AAAATTTCTA
18843385 AATAA-TTCTAA
1 AA-AATTTCT-A
18843396 AAAATTT-TA
1 AAAATTTCTA
18843405 AAAAT
1 AAAAT
18843410 GATGACAAAT
Statistics
Matches: 184, Mismatches: 32, Indels: 57
0.67 0.12 0.21
Matches are distributed among these distances:
8 32 0.17
9 52 0.28
10 54 0.29
11 42 0.23
12 4 0.02
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (10 bp):
AAAATTTCTA
Found at i:18843181 original size:11 final size:11
Alignment explanation
Indices: 18843156--18843199 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
18843146 CATAAAAAAG
18843156 AAAATTTCT-A
1 AAAATTTCTAA
18843166 AAAATTTCTAA
1 AAAATTTCTAA
* *
18843177 AAAATTTTTTA
1 AAAATTTCTAA
18843188 AAAATTT-TAA
1 AAAATTTCTAA
18843198 AA
1 AA
18843200 TTTTTAAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
10 13 0.43
11 17 0.57
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (11 bp):
AAAATTTCTAA
Found at i:18843201 original size:19 final size:19
Alignment explanation
Indices: 18843177--18843375 Score: 70
Period size: 19 Copynumber: 10.4 Consensus size: 19
18843167 AAATTTCTAA
18843177 AAAATTTTTTAAAAATTTT
1 AAAATTTTTTAAAAATTTT
* **
18843196 AAAA-TTTTT-AAAAGTCC
1 AAAATTTTTTAAAAATTTT
* *
18843213 AAAATTTTTTTTAAAA-CTT
1 AAAA-TTTTTTAAAAATTTT
* * * *
18843232 AAAAATTCTAAACAAATTTA
1 AAAATTTTTTAA-AAATTTT
* ** *
18843252 AAAAGTTTGAAAAAATTGT
1 AAAATTTTTTAAAAATTTT
*
18843271 AAAATATTTTAAAAAATTTT
1 AAAAT-TTTTTAAAAATTTT
** *
18843291 AAAA-ACTCTAAAAATTTTTT
1 AAAATTTTTTAAAAA--TTTT
* *
18843311 ATAA--TTCTAAAATATTTTT
1 AAAATTTTTTAAAA-A-TTTT
* *
18843330 AAAAACTTTTT-AAAATTCT
1 -AAAATTTTTTAAAAATTTT
* *
18843349 AAAATTTTTGAAAAATTCT
1 AAAATTTTTTAAAAATTTT
18843368 AAAATTTT
1 AAAATTTT
18843376 AAAAACTTAA
Statistics
Matches: 136, Mismatches: 31, Indels: 26
0.70 0.16 0.13
Matches are distributed among these distances:
17 9 0.07
18 23 0.17
19 56 0.41
20 42 0.31
21 3 0.02
22 3 0.02
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (19 bp):
AAAATTTTTTAAAAATTTT
Found at i:18843255 original size:20 final size:19
Alignment explanation
Indices: 18843232--18843409 Score: 71
Period size: 19 Copynumber: 9.3 Consensus size: 19
18843222 TTTAAAACTT
18843232 AAAAATTCTAAACAAATTTA
1 AAAAATTCTAAA-AAATTTA
*
18843252 AAAAGTT-TGAAAAAATTGTA
1 AAAAATTCT-AAAAAATT-TA
* * *
18843272 AAATATTTTAAAAAATTTT
1 AAAAATTCTAAAAAATTTA
* * *
18843291 AAAAACTCTAAAAATTTTT
1 AAAAATTCTAAAAAATTTA
* * *
18843310 TATAATTCTAAAATATTTTTA
1 AAAAATTCTAAAA-A-ATTTA
* **
18843331 AAAACTT-TTTAAAATTCT-
1 AAAAATTCTAAAAAATT-TA
* * *
18843349 AAAATTTTTGAAAAATTCT-
1 AAAAATTCTAAAAAATT-TA
* *
18843368 -AAAATT-TTAAAAACTTA
1 AAAAATTCTAAAAAATTTA
* *
18843385 AATAATTCTAAAAAATTTT
1 AAAAATTCTAAAAAATTTA
18843404 AAAAAT
1 AAAAAT
18843410 GATGACAAAT
Statistics
Matches: 119, Mismatches: 29, Indels: 21
0.70 0.17 0.12
Matches are distributed among these distances:
16 1 0.01
17 7 0.06
18 18 0.15
19 56 0.47
20 28 0.24
21 9 0.08
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (19 bp):
AAAAATTCTAAAAAATTTA
Found at i:18843285 original size:11 final size:10
Alignment explanation
Indices: 18843232--18843476 Score: 95
Period size: 10 Copynumber: 25.3 Consensus size: 10
18843222 TTTAAAACTT
*
18843232 AAAAATTCTA
1 AAAAATTTTA
18843242 AACAAA-TTTA
1 AA-AAATTTTA
* *
18843252 AAAAGTTTGA
1 AAAAATTTTA
*
18843262 AAAAATTGTA
1 AAAAATTTTA
*
18843272 AAATATTTTA
1 AAAAATTTTA
18843282 AAAAATTTT-
1 AAAAATTTTA
* *
18843291 AAAAACTCT-
1 AAAAATTTTA
*
18843300 AAAAATTTTT
1 AAAAATTTTA
* * *
18843310 TATAATTCTA
1 AAAAATTTTA
*
18843320 AAATATTTTTA
1 AAA-AATTTTA
*
18843331 AAAACTTTT-
1 AAAAATTTTA
* *
18843340 TAAAATTCT-
1 AAAAATTTTA
* *
18843349 AAAATTTTTG
1 AAAAATTTTA
*
18843359 AAAAATTCT-
1 AAAAATTTTA
18843368 -AAAATTTT-
1 AAAAATTTTA
*
18843376 AAAAA-CTTA
1 AAAAATTTTA
* *
18843385 AATAATTCTA
1 AAAAATTTTA
18843395 AAAAATTTT-
1 AAAAATTTTA
** *
18843404 AAAAATGATG
1 AAAAATTTTA
*
18843414 ACAAATTTTA
1 AAAAATTTTA
18843424 AAAAATTTT-
1 AAAAATTTTA
*
18843433 --TAA-TTTA
1 AAAAATTTTA
18843440 AAAAATTTATAA
1 AAAAATTT-T-A
*
18843452 AAAAATACTTA
1 AAAAAT-TTTA
18843463 AAAAATTTTTA
1 AAAAA-TTTTA
18843474 AAA
1 AAA
18843477 TTCTAAAATT
Statistics
Matches: 170, Mismatches: 48, Indels: 33
0.68 0.19 0.13
Matches are distributed among these distances:
6 3 0.02
7 2 0.01
8 9 0.05
9 45 0.26
10 77 0.45
11 24 0.14
12 9 0.05
13 1 0.01
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (10 bp):
AAAAATTTTA
Found at i:18843497 original size:20 final size:20
Alignment explanation
Indices: 18843468--18843520 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
18843458 ACTTAAAAAA
18843468 TTTTTA-AAA-TTCTAAAA-T
1 TTTTTAGAAATTTC-AAAACT
18843486 TATTTTAGAAATTTCAAAACT
1 T-TTTTAGAAATTTCAAAACT
18843507 TTCTTTAGAAATTT
1 TT-TTTAGAAATTT
18843521 TTAGAAATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
18 1 0.03
19 5 0.17
20 8 0.27
21 16 0.53
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.49
Consensus pattern (20 bp):
TTTTTAGAAATTTCAAAACT
Found at i:18843827 original size:28 final size:28
Alignment explanation
Indices: 18843771--18843827 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
18843761 GAATGTTCAT
***
18843771 GTACCAATGTGATAAAAAATTTCTTTAG
1 GTACCAATGTGATAAAAAATTTAAATAG
* *
18843799 GTACCATTGTGATAAAAATTTTAAATAG
1 GTACCAATGTGATAAAAAATTTAAATAG
18843827 G
1 G
18843828 AGCAAAATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (28 bp):
GTACCAATGTGATAAAAAATTTAAATAG
Found at i:18844384 original size:23 final size:24
Alignment explanation
Indices: 18844340--18844385 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
18844330 ACATTAATTT
*
18844340 AATAAAAATAATAAATGCAACACA
1 AATAAAAATAATAAATACAACACA
* *
18844364 AATAAAAATGA-AAATATAACAC
1 AATAAAAATAATAAATACAACAC
18844386 TAATGATAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.67, C:0.11, G:0.04, T:0.17
Consensus pattern (24 bp):
AATAAAAATAATAAATACAACACA
Found at i:18846708 original size:18 final size:18
Alignment explanation
Indices: 18846685--18846719 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
18846675 AAAAGAAAAT
*
18846685 TTCTAAAATTTTTTAAAC
1 TTCTAAAAATTTTTAAAC
18846703 TTCTAAAAATTTTTAAA
1 TTCTAAAAATTTTTAAA
18846720 ACTTAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (18 bp):
TTCTAAAAATTTTTAAAC
Found at i:18846713 original size:19 final size:18
Alignment explanation
Indices: 18846680--18846723 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
18846670 CATAAAAAAG
*
18846680 AAAATTTCTAAAATTTTT
1 AAAACTTCTAAAATTTTT
*
18846698 TAAACTTCTAAAAATTTTT
1 AAAACTTCT-AAAATTTTT
18846717 AAAACTT
1 AAAACTT
18846724 AAAAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (18 bp):
AAAACTTCTAAAATTTTT
Found at i:18846729 original size:19 final size:19
Alignment explanation
Indices: 18846689--18846730 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
18846679 GAAAATTTCT
* **
18846689 AAAATTTTTTAAACTTCTA
1 AAAATTTTTAAAACTTAAA
18846708 AAAATTTTTAAAACTTAAA
1 AAAATTTTTAAAACTTAAA
18846727 AAAA
1 AAAA
18846731 AAAAATTAAA
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:0.07, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATTTTTAAAACTTAAA
Found at i:18846774 original size:9 final size:9
Alignment explanation
Indices: 18846756--18847011 Score: 81
Period size: 9 Copynumber: 26.6 Consensus size: 9
18846746 TACAATTCTA
18846756 AAAAATTTTT
1 AAAAA-TTTT
18846766 AAAAATTTT
1 AAAAATTTT
*
18846775 GAAAAAAATTCT
1 ---AAAAATTTT
*
18846787 AAAATATTTA
1 AAAA-ATTTT
18846797 AAATAATTTT
1 AAA-AATTTT
** * *
18846807 AAATGTATA
1 AAAAATTTT
18846816 AAAAATTAATTT
1 AAAAA-T--TTT
*
18846828 GAAAAAATTAT
1 -AAA-AATTTT
*
18846839 AAAAAATTCT
1 AA-AAATTTT
*
18846849 AAACATTTT
1 AAAAATTTT
*
18846858 ACAAAATTAT
1 A-AAAATTTT
**
18846868 AAATGTTTT
1 AAAAATTTT
18846877 AAAAATTTGT
1 AAAAATTT-T
18846887 AAAAATTTT
1 AAAAATTTT
*
18846896 -AAAA-CTT
1 AAAAATTTT
***
18846903 AAAAAAAAT
1 AAAAATTTT
**
18846912 -AAAACCTT
1 AAAAATTTT
18846920 AAATAATTTT
1 AAA-AATTTT
*
18846930 AAATAATTCTAA
1 AAA-AATT-T-T
18846942 AAAAATTTT
1 AAAAATTTT
18846951 AAAAATTTT
1 AAAAATTTT
18846960 AAAAATTTT
1 AAAAATTTT
*
18846969 GAAAAAAATTTC
1 ---AAAAATTTT
18846981 AAAAATTTT
1 AAAAATTTT
*
18846990 --TAATTTT
1 AAAAATTTT
*
18846997 AGAAAATTAT
1 A-AAAATTTT
18847007 AAAAA
1 AAAAA
18847012 AATATTAAAG
Statistics
Matches: 183, Mismatches: 38, Indels: 51
0.67 0.14 0.19
Matches are distributed among these distances:
7 8 0.04
8 13 0.07
9 64 0.35
10 63 0.34
11 9 0.05
12 20 0.11
13 4 0.02
14 2 0.01
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.38
Consensus pattern (9 bp):
AAAAATTTT
Found at i:18846790 original size:10 final size:10
Alignment explanation
Indices: 18846749--18846989 Score: 75
Period size: 10 Copynumber: 24.6 Consensus size: 10
18846739 AAAACTTTAC
*
18846749 AATTCTAAAA
1 AATTTTAAAA
*
18846759 AATTTTTAAA
1 AATTTTAAAA
18846769 AATTTTGAAAAA
1 AATTTT--AAAA
*
18846781 AATTCTAAAA
1 AATTTTAAAA
*
18846791 TA-TTTAAAA
1 AATTTTAAAA
18846800 TAATTTT---A
1 -AATTTTAAAA
*
18846808 AATGTATAAAA
1 AAT-TTTAAAA
18846819 AATTAATTTGAAAA
1 AA-T--TTT-AAAA
*
18846833 AATTATAAAA
1 AATTTTAAAA
*
18846843 AATTCT-AAA
1 AATTTTAAAA
* *
18846852 CATTTTACAA
1 AATTTTAAAA
*
18846862 AATTAT-AAA
1 AATTTTAAAA
**
18846871 TGTTTT-AAA
1 AATTTTAAAA
18846880 AATTTGT-AAA
1 AATTT-TAAAA
18846890 AATTTT--AA
1 AATTTTAAAA
*
18846898 AA-CTTAAAA
1 AATTTTAAAA
18846907 AA----AATAA
1 AATTTTAA-AA
** *
18846914 AACCTTAAAT
1 AATTTTAAAA
*
18846924 AATTTTAAAT
1 AATTTTAAAA
*
18846934 AATTCTAAAAA
1 AATT-TTAAAA
18846945 AATTTT-AAA
1 AATTTTAAAA
18846954 AATTTT-AAA
1 AATTTTAAAA
18846963 AATTTTGAAAA
1 AATTTT-AAAA
* *
18846974 AAATTTCAAA
1 AATTTTAAAA
18846984 AATTTT
1 AATTTT
18846990 TAATTTTAGA
Statistics
Matches: 175, Mismatches: 33, Indels: 46
0.69 0.13 0.18
Matches are distributed among these distances:
6 2 0.01
7 9 0.05
8 7 0.04
9 47 0.27
10 66 0.38
11 26 0.15
12 9 0.05
13 3 0.02
14 6 0.03
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (10 bp):
AATTTTAAAA
Found at i:18846865 original size:19 final size:18
Alignment explanation
Indices: 18846840--18846899 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
18846830 AAAAATTATA
*
18846840 AAAAATTCTAAACATTTT
1 AAAAATTATAAACATTTT
**
18846858 ACAAAATTATAAATGTTTT
1 A-AAAATTATAAACATTTT
* *
18846877 AAAAATTTGTAAAAATTTT
1 AAAAA-TTATAAACATTTT
18846896 AAAA
1 AAAA
18846900 CTTAAAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 5 0.15
19 29 0.85
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.38
Consensus pattern (18 bp):
AAAAATTATAAACATTTT
Found at i:18846907 original size:16 final size:17
Alignment explanation
Indices: 18846886--18846932 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
18846876 TAAAAATTTG
18846886 TAAAAATTTTAAAA-CT
1 TAAAAATTTTAAAACCT
***
18846902 TAAAAAAAATAAAACCT
1 TAAAAATTTTAAAACCT
18846919 TAAATAATTTTAAA
1 TAAA-AATTTTAAA
18846933 TAATTCTAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
16 11 0.48
17 6 0.26
18 6 0.26
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAAATTTTAAAACCT
Found at i:18846958 original size:30 final size:30
Alignment explanation
Indices: 18846918--18846989 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
18846908 AAATAAAACC
18846918 TTAAATAATTTTAAATAATTCT-AAAAAAATT
1 TTAAA-AATTTTAAA-AATTCTGAAAAAAATT
*
18846949 TTAAAAATTTTAAAAATTTTGAAAAAAATT
1 TTAAAAATTTTAAAAATTCTGAAAAAAATT
*
18846979 TCAAAAATTTT
1 TTAAAAATTTT
18846990 TAATTTTAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
29 5 0.13
30 28 0.74
31 5 0.13
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (30 bp):
TTAAAAATTTTAAAAATTCTGAAAAAAATT
Found at i:18847077 original size:22 final size:19
Alignment explanation
Indices: 18847009--18847087 Score: 68
Period size: 20 Copynumber: 3.8 Consensus size: 19
18846999 AAAATTATAA
*
18847009 AAAAATATTAAAGTTTTTTT
1 AAAAAT-TTAAAATTTTTTT
* *
18847029 AAAAATTCTAAAATTATGTT
1 AAAAATT-TAAAATTTTTTT
18847049 ATAAAATTTAAAACTTTTTTTT
1 A-AAAATTTAAAA--TTTTTTT
18847071 AGAAAATTTTAAAATTT
1 A-AAAA-TTTAAAATTT
18847088 CTTAAAATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
19 1 0.02
20 21 0.44
21 9 0.19
22 10 0.21
23 7 0.15
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (19 bp):
AAAAATTTAAAATTTTTTT
Found at i:18847106 original size:10 final size:10
Alignment explanation
Indices: 18847093--18847159 Score: 63
Period size: 10 Copynumber: 7.1 Consensus size: 10
18847083 AATTTCTTAA
18847093 AATTTTTTTG
1 AATTTTTTTG
*
18847103 AATTTTTTAG
1 AATTTTTTTG
*
18847113 -ATTTTTTAG
1 AATTTTTTTG
18847122 -ATTTTTTT-
1 AATTTTTTTG
*
18847130 AA-CTTTTTG
1 AATTTTTTTG
18847139 AATTTTTTAT-
1 AATTTTTT-TG
18847149 AATTTTTTTG
1 AATTTTTTTG
18847159 A
1 A
18847160 TTATTTTGGA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
8 5 0.10
9 20 0.42
10 22 0.46
11 1 0.02
ACGTcount: A:0.24, C:0.01, G:0.07, T:0.67
Consensus pattern (10 bp):
AATTTTTTTG
Found at i:18847110 original size:9 final size:8
Alignment explanation
Indices: 18847096--18847147 Score: 50
Period size: 9 Copynumber: 5.9 Consensus size: 8
18847086 TTCTTAAAAT
18847096 TTTTTTGAA
1 TTTTTT-AA
18847105 TTTTTTAGA
1 TTTTTTA-A
18847114 TTTTTTAGA
1 TTTTTTA-A
18847123 TTTTTTTAA
1 -TTTTTTAA
*
18847132 CTTTTTGAA
1 -TTTTTTAA
18847141 TTTTTTA
1 TTTTTTA
18847148 TAATTTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
8 7 0.18
9 24 0.63
10 7 0.18
ACGTcount: A:0.21, C:0.02, G:0.08, T:0.69
Consensus pattern (8 bp):
TTTTTTAA
Found at i:18847116 original size:19 final size:18
Alignment explanation
Indices: 18847093--18847159 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 18
18847083 AATTTCTTAA
18847093 AATTTTTTTGAATTTTTT
1 AATTTTTTTGAATTTTTT
* *
18847111 AGATTTTTTAGATTTTTTT
1 A-ATTTTTTTGAATTTTTT
*
18847130 AA-CTTTTTGAATTTTTTAT
1 AATTTTTTTGAA-TTTTT-T
18847149 AATTTTTTTGA
1 AATTTTTTTGA
18847160 TTATTTTGGA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 6 0.15
18 7 0.18
19 19 0.49
20 7 0.18
ACGTcount: A:0.24, C:0.01, G:0.07, T:0.67
Consensus pattern (18 bp):
AATTTTTTTGAATTTTTT
Found at i:18847117 original size:8 final size:9
Alignment explanation
Indices: 18847094--18847128 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
18847084 ATTTCTTAAA
*
18847094 ATTTTTTTG
1 ATTTTTTAG
18847103 AATTTTTTAG
1 -ATTTTTTAG
18847113 ATTTTTTAG
1 ATTTTTTAG
18847122 ATTTTTT
1 ATTTTTT
18847129 TAACTTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.71
Consensus pattern (9 bp):
ATTTTTTAG
Found at i:18847154 original size:18 final size:18
Alignment explanation
Indices: 18847097--18847155 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
18847087 TCTTAAAATT
*
18847097 TTTTTGAATTTTTTA-GA
1 TTTTTGAATTTTTTATAA
*
18847114 TTTTTTAGATTTTTT-TAA
1 TTTTTGA-ATTTTTTATAA
18847132 CTTTTTGAATTTTTTATAA
1 -TTTTTGAATTTTTTATAA
18847151 TTTTT
1 TTTTT
18847156 TTGATTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
17 6 0.17
18 20 0.57
19 9 0.26
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.69
Consensus pattern (18 bp):
TTTTTGAATTTTTTATAA
Found at i:18858420 original size:56 final size:55
Alignment explanation
Indices: 18858275--18858446 Score: 195
Period size: 56 Copynumber: 3.0 Consensus size: 55
18858265 AATTGATACT
* * * * *
18858275 TTCAATTTTTCCTTAAAATGTTTTTTTT-AACAATTTTATTTTCAAAGAAATTTGATA
1 TTCAACTTTTCCTCAAAATATTTTTTTTGAA-AATTTTATTTTCAAGGAAAATTG--A
*
18858332 CTTTCAACTTTTTACTCAAAA-ATATTTTTTTGAAAATTTTATTTTCAAGGAAAATTGA
1 --TTCAAC-TTTTCCTCAAAATAT-TTTTTTTGAAAATTTTATTTTCAAGGAAAATTGA
*
18858390 TTCAACTTTTCCTCAAAAGTATTTTTTTTGAAAATTTTATTTTTAAGGAAAATTGA
1 TTCAACTTTTCCTCAAAA-TATTTTTTTTGAAAATTTTATTTTCAAGGAAAATTGA
18858446 T
1 T
18858447 ACTTTCAACT
Statistics
Matches: 100, Mismatches: 8, Indels: 13
0.83 0.07 0.11
Matches are distributed among these distances:
55 11 0.11
56 40 0.40
57 2 0.02
58 1 0.01
59 6 0.06
60 38 0.38
61 2 0.02
ACGTcount: A:0.34, C:0.09, G:0.07, T:0.49
Consensus pattern (55 bp):
TTCAACTTTTCCTCAAAATATTTTTTTTGAAAATTTTATTTTCAAGGAAAATTGA
Found at i:18858553 original size:68 final size:68
Alignment explanation
Indices: 18858414--18858553 Score: 178
Period size: 66 Copynumber: 2.1 Consensus size: 68
18858404 AAAAGTATTT
* * * *
18858414 TTTTTGAAAATTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTAAAAAATGTTCTTTTT
1 TTTTTGAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTAAAAAATATTCTTTTA
**
18858479 CTA
66 AGA
18858482 TTTTTGAAAA-TTT-TTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAAATATAT-TT
1 TTTTTGAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCT--AAAAAATAT-TCTT
18858544 TTAAGA
63 TTAAGA
18858550 TTTT
1 TTTT
18858554 GTTTTAGGAA
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
66 32 0.51
67 3 0.05
68 27 0.43
69 1 0.02
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.49
Consensus pattern (68 bp):
TTTTTGAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTAAAAAATATTCTTTTA
AGA
Found at i:18859802 original size:42 final size:41
Alignment explanation
Indices: 18859646--18859935 Score: 289
Period size: 42 Copynumber: 7.0 Consensus size: 41
18859636 AAATAAATGT
* * * * *
18859646 TCCTTTAAATAGAGGCACCAAAACTTTGAAAAATAAATTAC
1 TCCTCTAAACAGAGGCACCACAACTTTGAAAAAAAAATTGC
*
18859687 TCCTCTAAACAGAGGCATCACAACTTTGAAAAAAATAAATTGC
1 TCCTCTAAACAGAGGCACCACAACTTTG-AAAAAA-AAATTGC
* * * *
18859730 TCATCTAAACAAAGGCATCATAAC-TT-AAAAAAAAATTTGC
1 TCCTCTAAACAGAGGCACCACAACTTTGAAAAAAAAA-TTGC
* *
18859770 TCCTCTAAACAGAGGCACCACCACTTTGAAAAATAAAAATGC
1 TCCTCTAAACAGAGGCACCACAACTTTGAAAAA-AAAATTGC
* ** *
18859812 TCCTTTAAACAGAGGCACCATTACTTTTAAAAAATAAATTGC
1 TCCTCTAAACAGAGGCACCACAACTTTGAAAAAA-AAATTGC
* * *
18859854 ACCTCTAAACAAAGGCACCGCAACTTTGAAAAATAAAA-TGC
1 TCCTCTAAACAGAGGCACCACAACTTTGAAAAA-AAAATTGC
* * *
18859895 TCCTCTAAACAGAGACACCATAGCTTTTGAAAAAACAAATT
1 TCCTCTAAACAGAGGCACCACAAC-TTTGAAAAAA-AAATT
18859936 ACTCATTGAC
Statistics
Matches: 205, Mismatches: 33, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
39 3 0.01
40 29 0.14
41 49 0.24
42 91 0.44
43 33 0.16
ACGTcount: A:0.45, C:0.21, G:0.10, T:0.24
Consensus pattern (41 bp):
TCCTCTAAACAGAGGCACCACAACTTTGAAAAAAAAATTGC
Found at i:18859879 original size:124 final size:125
Alignment explanation
Indices: 18859636--18859928 Score: 335
Period size: 124 Copynumber: 2.4 Consensus size: 125
18859626 GCTCAATAAT
* * * *
18859636 AAAT-AAATGTTCCTTTAAATAGAGGCACCAAAACTTTGAAAAATAAATTACTCCTCTAAACAGA
1 AAATAAAATGCTCCTCTAAACAGAGGCACCAAAACTTTGAAAAATAAAATACTCCTCTAAACAGA
* * * *
18859700 GGCATCACAACTTTGAAAAAAATAAATTGCTCATCTAAACAAAGGCATCATAAC-TT-AA
66 GGCACCACAACTTTGAAAAAAATAAATTGCACATCTAAACAAAGGCACCACAACTTTGAA
** * *
18859758 AAA-AAAATTTGCTCCTCTAAACAGAGGCACCACCACTTTGAAAAATAAAAATGCTCCTTTAAAC
1 AAATAAAA--TGCTCCTCTAAACAGAGGCACCAAAACTTTGAAAAAT-AAAATACTCCTCTAAAC
** * * *
18859822 AGAGGCACCATTACTTT-TAAAAAATAAATTGCACCTCTAAACAAAGGCACCGCAACTTTGAA
63 AGAGGCACCACAACTTTGAAAAAAATAAATTGCACATCTAAACAAAGGCACCACAACTTTGAA
* * *
18859884 AAATAAAATGCTCCTCTAAACAGAGACACCATAGCTTTTGAAAAA
1 AAATAAAATGCTCCTCTAAACAGAGGCACCAAAAC-TTTGAAAAA
18859929 ACAAATTACT
Statistics
Matches: 142, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
122 6 0.04
124 65 0.46
125 53 0.37
126 14 0.10
127 4 0.03
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.24
Consensus pattern (125 bp):
AAATAAAATGCTCCTCTAAACAGAGGCACCAAAACTTTGAAAAATAAAATACTCCTCTAAACAGA
GGCACCACAACTTTGAAAAAAATAAATTGCACATCTAAACAAAGGCACCACAACTTTGAA
Found at i:18859880 original size:84 final size:83
Alignment explanation
Indices: 18859640--18859935 Score: 339
Period size: 83 Copynumber: 3.5 Consensus size: 83
18859630 AATAATAAAT
* * * * * * *
18859640 AAATGTTCCTTTAAATAGAGGCACCAAAACTTTGAAAAATAAATTACTCCTCTAAACAGAGGCAT
1 AAATGCTCCTCTAAACAGAGGCACCATAACTTTAAAAAATAAATTGCTCCTCTAAACAGAGGCAC
18859705 CACAACTTTGAAAAA-AA
66 CACAACTTTGAAAAATAA
* * *
18859722 TAAATTGCTCATCTAAACAAAGGCATCATAAC-TTAAAAAA-AAATTTGCTCCTCTAAACAGAGG
1 -AAA-TGCTCCTCTAAACAGAGGCACCATAACTTTAAAAAATAAA-TTGCTCCTCTAAACAGAGG
*
18859785 CACCACCACTTTGAAAAATAA
63 CACCACAACTTTGAAAAATAA
* * * *
18859806 AAATGCTCCTTTAAACAGAGGCACCATTACTTTTAAAAAATAAATTGCACCTCTAAACAAAGGCA
1 AAATGCTCCTCTAAACAGAGGCACCATAAC-TTTAAAAAATAAATTGCTCCTCTAAACAGAGGCA
*
18859871 CCGCAACTTTGAAAAAT-A
65 CCACAACTTTGAAAAATAA
* * *
18859889 AAATGCTCCTCTAAACAGAGACACCATAGCTTTTGAAAAAACAAATT
1 AAATGCTCCTCTAAACAGAGGCACCATAAC-TTT-AAAAAATAAATT
18859936 ACTCATTGAC
Statistics
Matches: 181, Mismatches: 25, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
82 25 0.14
83 78 0.43
84 75 0.41
85 3 0.02
ACGTcount: A:0.45, C:0.21, G:0.10, T:0.24
Consensus pattern (83 bp):
AAATGCTCCTCTAAACAGAGGCACCATAACTTTAAAAAATAAATTGCTCCTCTAAACAGAGGCAC
CACAACTTTGAAAAATAA
Found at i:18860951 original size:10 final size:9
Alignment explanation
Indices: 18860935--18861027 Score: 91
Period size: 9 Copynumber: 10.0 Consensus size: 9
18860925 TTGAGTCTTC
18860935 CTTTTTTTT
1 CTTTTTTTT
18860944 C-TTTTTTT
1 CTTTTTTTT
*
18860952 CATTTTTTT
1 CTTTTTTTT
*
18860961 CATTTTTTT
1 CTTTTTTTT
18860970 CATTTTTTTT
1 C-TTTTTTTT
*
18860980 CATTTTTTT
1 CTTTTTTTT
18860989 CTATTTTTTT
1 CT-TTTTTTT
18860999 CTCTTTTGTTT
1 CT-TTTT-TTT
18861010 -TTTTTCTTT
1 CTTTTT-TTT
*
18861019 GTTTTTTTT
1 CTTTTTTTT
18861028 TTCAAGCATA
Statistics
Matches: 74, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
8 8 0.11
9 36 0.49
10 27 0.36
11 3 0.04
ACGTcount: A:0.05, C:0.11, G:0.02, T:0.82
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:18860998 original size:13 final size:13
Alignment explanation
Indices: 18860982--18861027 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
18860972 TTTTTTTTCA
*
18860982 TTTTTTTCTAT-T
1 TTTTTTTCTTTGT
*
18860994 TTTTTCTCTTTTGT
1 TTTTTTTC-TTTGT
18861008 TTTTTTTCTTTGT
1 TTTTTTTCTTTGT
18861021 TTTTTTT
1 TTTTTTT
18861028 TTCAAGCATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
12 7 0.24
13 14 0.48
14 8 0.28
ACGTcount: A:0.02, C:0.09, G:0.04, T:0.85
Consensus pattern (13 bp):
TTTTTTTCTTTGT
Found at i:18861026 original size:14 final size:13
Alignment explanation
Indices: 18860936--18861028 Score: 64
Period size: 14 Copynumber: 6.6 Consensus size: 13
18860926 TGAGTCTTCC
18860936 TTTTTTTTCTTTT
1 TTTTTTTTCTTTT
* *
18860949 TTTCATTTT-TTTC
1 TTT-TTTTTCTTTT
*
18860962 ATTTTTTTCATTTT
1 TTTTTTTTC-TTTT
18860976 TTTTCATTTT-TTTCT
1 TTTT--TTTTCTTT-T
18860991 ATTTTTTTCTCTTTT
1 -TTTTTTT-TCTTTT
18861006 GTTTTTTTTCTTTGT
1 -TTTTTTTTCTTT-T
18861021 TTTTTTTT
1 TTTTTTTT
18861029 TCAAGCATAA
Statistics
Matches: 63, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
12 4 0.06
13 8 0.13
14 29 0.46
15 11 0.17
16 11 0.17
ACGTcount: A:0.05, C:0.10, G:0.02, T:0.83
Consensus pattern (13 bp):
TTTTTTTTCTTTT
Found at i:18861029 original size:19 final size:18
Alignment explanation
Indices: 18860936--18861029 Score: 73
Period size: 19 Copynumber: 5.1 Consensus size: 18
18860926 TGAGTCTTCC
*
18860936 TTTTTTTTC-TTTTTTTC
1 TTTTTTTTCTTTTTTTTT
* **
18860953 ATTTTTTTCATTTTTTTCA
1 TTTTTTTTC-TTTTTTTTT
18860972 TTTTTTTTCATTTTTTTCTAT
1 TTTTTTTTC-TTTTTTT-T-T
* *
18860993 TTTTTTCTCTTTTGTTTT
1 TTTTTTTTCTTTTTTTTT
* *
18861011 TTTTCTTTGTTTTTTTTT
1 TTTTTTTTCTTTTTTTTT
18861029 T
1 T
18861030 CAAGCATAAT
Statistics
Matches: 61, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
17 8 0.13
18 16 0.26
19 23 0.38
20 6 0.10
21 8 0.13
ACGTcount: A:0.05, C:0.10, G:0.02, T:0.83
Consensus pattern (18 bp):
TTTTTTTTCTTTTTTTTT
Found at i:18867046 original size:558 final size:560
Alignment explanation
Indices: 18865987--18867084 Score: 1781
Period size: 558 Copynumber: 2.0 Consensus size: 560
18865977 GCAGCATCAA
* *
18865987 GCTTAGAGACATTCTCTTCTTGCTCTTAGACTATTATGTCATTGCCATATTTCCATGGCATAGCC
1 GCTTAGAGACATTCTCTTCTTGCTCTTAGACTATTATGTCATAGCCATATTTCCATGGCACAGCC
* * * *
18866052 CTATTGCTCTTGTAAGGGAATGGAATAGGGACTTTAAAGGTTACTGGCTTGGGAGCAAACTTGTC
66 ATATTGCTCTTGTAAAGGAATGGAATAGGGACTTTAAAGGTTACAGGCGTGGGAGCAAACTTGTC
* *
18866117 TATGGTTGACTTTGGCCTATCCCTACAATAAATTATTAATGGCCTTAAAAATAATTTGGGTGGTT
131 TATGGTCGACTTTGGCCTATCCCCACAATAAATTATTAA--G-CTTAAAAATAATTTGGGTGGTT
* * * * *
18866182 GATTGGTTATAAACACCTCAGCATTCTTTGAATCTTCTATTTTTTCATAGAATTCAATCTGATAT
193 GATTGGTCATAAACACCTCAGCATTCTTTGAACCCTCCATTTCTTCATAGAATTCAATCTGATAT
* * * *
18866247 GAATCCATGAGCTTTTGTTCCTCCTGGTAAAATTTTTCACAATTTTCAATAGAGTGGCCAATTGC
258 GAATCCATGAGCTTTTGTACCTCATAGCAAAATTTTTCACAATTTTCAATAGAGTGGCCAATTGC
* * *
18866312 CCCACTATGATATTTATAGCTTGTACCTGCCACATATGCTTCATGATAACTATGTAGAACTACTG
323 CCCACTATGATATTTATAGCTTGTACCTACCACATATGCTCCATGATAACTATGAAGAACTACTG
* *
18866377 GTTGTATCATGTCAACTTTCCATAAAGCATCAAATAGCTGATTGAGAGGTATCTTAATATCTGCC
388 GTTGTATCATGTCAACTTTCCATAAAGCATCAAATAGCTGACTGAGAGGTATCTTAATATCTACC
*
18866442 ACTTTTCTCTTCAAATAACACTCATGTTCCTTACTAAGAGCATTCACGTTATGATTAGGCAAAAG
453 ACTTTTCTCTTCAAATAACACTCATGTTCCTTACTAAGAGCATTCACATTATGATTAGGCAAAAG
18866507 ATTGCCACTAACATTTGGTGCAGTTACCCCTTTTATATCAAAG
518 ATTGCCACTAACATTTGGTGCAGTTACCCCTTTTATATCAAAG
18866550 GCTTAGAGACATTCTCTTCTTGCTCTTAGACTATTATGTCATAGCCATATTTCCATGGCACAGCC
1 GCTTAGAGACATTCTCTTCTTGCTCTTAGACTATTATGTCATAGCCATATTTCCATGGCACAGCC
18866615 ATATTGCTCTTGTAAAGGAATGGAATAGGGACTTTAAAGGTTACAGGCGTGGGAGCAAACTTGTC
66 ATATTGCTCTTGTAAAGGAATGGAATAGGGACTTTAAAGGTTACAGGCGTGGGAGCAAACTTGTC
* *
18866680 TATGGTCGACTTTGGCCTATCCCCATAATAAATTGTT-A-CTTAAAAATAATTTGGGTGGTTGAT
131 TATGGTCGACTTTGGCCTATCCCCACAATAAATTATTAAGCTTAAAAATAATTTGGGTGGTTGAT
* * *
18866743 TGGTCATAGACACCTCAGCATTCTTTGAACCCTCCCTTTCTTCATAGAATTCAATCTTATATGAA
196 TGGTCATAAACACCTCAGCATTCTTTGAACCCTCCATTTCTTCATAGAATTCAATCTGATATGAA
*
18866808 TCCATGAGCTTTTGTACCTCATAGCAAAATTGTTT-GCAATTTTCAATAGAGTGGCCAATTGCCC
261 TCCATGAGCTTTTGTACCTCATAGCAAAATT-TTTCACAATTTTCAATAGAGTGGCCAATTGCCC
* * * *
18866872 TACTATGA-ATTTATAGCTTGTACCTATCACATATGCTCCATGATATCTATGAAGACCTACTGGT
325 CACTATGATATTTATAGCTTGTACCTACCACATATGCTCCATGATAACTATGAAGAACTACTGGT
* *
18866936 TGTATCATGTCAACTTTCCATAAAAGCATCAAATAGCTGACTGATAGGTATCTTAATATCTATCA
390 TGTATCATGTCAACTTTCCAT-AAAGCATCAAATAGCTGACTGAGAGGTATCTTAATATCTACCA
* * *
18867001 CTTTTCTCTTCAAATAACACTCATGTTCTTTACTCAGAGCATTCACATTATGATTAGGCAAATGA
454 CTTTTCTCTTCAAATAACACTCATGTTCCTTACTAAGAGCATTCACATTATGATTAGGCAAAAGA
18867066 TTGCCACTAACATTTGGTG
519 TTGCCACTAACATTTGGTG
18867085 TACTTATCCC
Statistics
Matches: 495, Mismatches: 38, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
557 71 0.14
558 263 0.53
559 3 0.01
562 1 0.00
563 157 0.32
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.35
Consensus pattern (560 bp):
GCTTAGAGACATTCTCTTCTTGCTCTTAGACTATTATGTCATAGCCATATTTCCATGGCACAGCC
ATATTGCTCTTGTAAAGGAATGGAATAGGGACTTTAAAGGTTACAGGCGTGGGAGCAAACTTGTC
TATGGTCGACTTTGGCCTATCCCCACAATAAATTATTAAGCTTAAAAATAATTTGGGTGGTTGAT
TGGTCATAAACACCTCAGCATTCTTTGAACCCTCCATTTCTTCATAGAATTCAATCTGATATGAA
TCCATGAGCTTTTGTACCTCATAGCAAAATTTTTCACAATTTTCAATAGAGTGGCCAATTGCCCC
ACTATGATATTTATAGCTTGTACCTACCACATATGCTCCATGATAACTATGAAGAACTACTGGTT
GTATCATGTCAACTTTCCATAAAGCATCAAATAGCTGACTGAGAGGTATCTTAATATCTACCACT
TTTCTCTTCAAATAACACTCATGTTCCTTACTAAGAGCATTCACATTATGATTAGGCAAAAGATT
GCCACTAACATTTGGTGCAGTTACCCCTTTTATATCAAAG
Found at i:18868819 original size:15 final size:15
Alignment explanation
Indices: 18868793--18868829 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
18868783 TTATGTTGTT
*
18868793 AAATGTAATGAATGA
1 AAATGCAATGAATGA
*
18868808 AAGTGCAATGAATGA
1 AAATGCAATGAATGA
18868823 AAATGCA
1 AAATGCA
18868830 TACATGCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.22, T:0.22
Consensus pattern (15 bp):
AAATGCAATGAATGA
Found at i:18872220 original size:60 final size:58
Alignment explanation
Indices: 18872031--18872385 Score: 384
Period size: 59 Copynumber: 6.2 Consensus size: 58
18872021 TGTTTTTATA
* * *
18872031 CAAGGAAAATTGATACTTTCAACTTTACCTTAAAATGTTCTTTTT-AACAATTTTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAATATT-TTTTTGAA-AATTTTATTTT
* * * *
18872090 TAAGGAAAATTGATACTTTCAACTTTTCCTTAAAATGTTTTTTTTAATAA-TTTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAATATTTTTTTGAA-AATTTTATTTT
* *
18872148 CAAGAAAAATTGATACTTTCAACTTTTTGCTCAATAATATTTTTTTGAAAATTTTATTTT
1 CAAGGAAAATTGATACTTTCAAC-TTTTCCTCAA-AATATTTTTTTGAAAATTTTATTTT
18872208 CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAGTATTTTTTTTTGAAAATTTTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAA-TA--TTTTTTTGAAAATTTTATTTT
18872269 C-----------ATACTTTCAACTTTTCCTCAAAAATATTTCTTTTTGAAAATTTTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTCCTC-AAAATA-TT-TTTTTGAAAATTTTATTTT
18872319 CAA-GAAAATTGATACTTTCAACTTTTCCTCAAAAATATATTTTTT-AAAGATTTTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTCCTC-AAAATAT-TTTTTTGAAA-ATTTTATTTT
18872378 --AGGAAAAT
1 CAAGGAAAAT
18872386 CATTGAAAAA
Statistics
Matches: 263, Mismatches: 11, Indels: 45
0.82 0.03 0.14
Matches are distributed among these distances:
49 3 0.01
50 41 0.16
51 4 0.02
57 1 0.00
58 45 0.17
59 78 0.30
60 69 0.26
61 22 0.08
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.48
Consensus pattern (58 bp):
CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAATATTTTTTTGAAAATTTTATTTT
Found at i:18872279 original size:50 final size:50
Alignment explanation
Indices: 18872220--18872320 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 50
18872210 AGGAAAATTG
* *
18872220 ATACTTTCAACTTTTCCTCAAAAGTATTTTTTTTTGAAAATTTTATTTTC
1 ATACTTTCAACTTTTCCTCAAAAATATTTCTTTTTGAAAATTTTATTTTC
18872270 ATACTTTCAACTTTTCCTCAAAAATATTTCTTTTTGAAAATTTTATTTTC
1 ATACTTTCAACTTTTCCTCAAAAATATTTCTTTTTGAAAATTTTATTTTC
18872320 A
1 A
18872321 AGAAAATTGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.30, C:0.15, G:0.03, T:0.52
Consensus pattern (50 bp):
ATACTTTCAACTTTTCCTCAAAAATATTTCTTTTTGAAAATTTTATTTTC
Found at i:18872334 original size:110 final size:109
Alignment explanation
Indices: 18872160--18872377 Score: 343
Period size: 110 Copynumber: 2.0 Consensus size: 109
18872150 AGAAAAATTG
* *
18872160 ATACTTTCAACTTTTTGCTCAATAATATTTTTTTGAAAATTTTATTTTCAAGGAAAATTGATACT
1 ATACTTTCAACTTTTTCCTCAAAAATATTTTTTTGAAAATTTTATTTTCAAGGAAAATTGATACT
* *
18872225 TTCAACTTTTCCTCAAAAGTATTTTTTTTTGAAA-ATTTTATTTTC
66 TTCAACTTTTCCTCAAAAATA-TATTTTTT-AAAGATTTTATTTTC
18872270 ATACTTTCAAC-TTTTCCTCAAAAATATTTCTTTTTGAAAATTTTATTTTCAA-GAAAATTGATA
1 ATACTTTCAACTTTTTCCTCAAAAATA-TT-TTTTTGAAAATTTTATTTTCAAGGAAAATTGATA
18872333 CTTTCAACTTTTCCTCAAAAATATATTTTTTAAAGATTTTATTTT
64 CTTTCAACTTTTCCTCAAAAATATATTTTTTAAAGATTTTATTTT
18872378 AGGAAAATCA
Statistics
Matches: 101, Mismatches: 4, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
108 3 0.03
109 30 0.30
110 46 0.46
111 22 0.22
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50
Consensus pattern (109 bp):
ATACTTTCAACTTTTTCCTCAAAAATATTTTTTTGAAAATTTTATTTTCAAGGAAAATTGATACT
TTCAACTTTTCCTCAAAAATATATTTTTTAAAGATTTTATTTTC
Found at i:18872439 original size:4 final size:4
Alignment explanation
Indices: 18872432--18872484 Score: 63
Period size: 4 Copynumber: 13.2 Consensus size: 4
18872422 ATTCCAATTT
* * *
18872432 AATA AATA AATA AATA AGTA AAAA AAT- AATA ATATA AATA AATT AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA A-ATA AATA AATA AATA
18872480 AATA A
1 AATA A
18872485 TGAAAAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 3 0.07
4 34 0.83
5 4 0.10
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:18873277 original size:9 final size:9
Alignment explanation
Indices: 18873271--18873321 Score: 66
Period size: 9 Copynumber: 5.6 Consensus size: 9
18873261 TCTTTTTTTT
18873271 TTTTTTTCA
1 TTTTTTTCA
18873280 TTTTTTTCA
1 TTTTTTTCA
18873289 TTTTTTTTCA
1 -TTTTTTTCA
**
18873299 GATTTTTCA
1 TTTTTTTCA
*
18873308 TTCTTTTCA
1 TTTTTTTCA
18873317 TTTTT
1 TTTTT
18873322 ATTAATAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
9 26 0.74
10 9 0.26
ACGTcount: A:0.12, C:0.12, G:0.02, T:0.75
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:18873292 original size:19 final size:19
Alignment explanation
Indices: 18873270--18873321 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
18873260 TTCTTTTTTT
18873270 TTTTTTTTCATTTTTTTCA
1 TTTTTTTTCATTTTTTTCA
**
18873289 TTTTTTTTCAGATTTTTCA
1 TTTTTTTTCATTTTTTTCA
*
18873308 -TTCTTTTCATTTTT
1 TTTTTTTTCATTTTT
18873322 ATTAATAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 11 0.39
19 17 0.61
ACGTcount: A:0.12, C:0.12, G:0.02, T:0.75
Consensus pattern (19 bp):
TTTTTTTTCATTTTTTTCA
Found at i:18875326 original size:16 final size:16
Alignment explanation
Indices: 18875278--18875326 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
18875268 TACTTGGTAT
* *
18875278 GATAGAAAAATGGAAA
1 GATAGAAAAGTAGAAA
* *
18875294 GAT-GAAAAGTTGGAA
1 GATAGAAAAGTAGAAA
18875309 GATAGAAAAGTAGAAA
1 GATAGAAAAGTAGAAA
18875325 GA
1 GA
18875327 AGGAAAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 12 0.44
16 15 0.56
ACGTcount: A:0.57, C:0.00, G:0.29, T:0.14
Consensus pattern (16 bp):
GATAGAAAAGTAGAAA
Found at i:18877628 original size:3 final size:3
Alignment explanation
Indices: 18877622--18877650 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
18877612 TTTTTTTCCA
18877622 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
18877651 ATTTTCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:18890928 original size:19 final size:19
Alignment explanation
Indices: 18890904--18890969 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 19
18890894 ATTGCAAATA
18890904 TTTAAAAAATAATGTATAT
1 TTTAAAAAATAATGTATAT
*
18890923 TTT-AAAAATAAAAGTATAAAT
1 TTTAAAAAAT-AATGTAT--AT
* * *
18890944 TTTATAAAATAATTTTTA-
1 TTTAAAAAATAATGTATAT
18890962 TTTAAAAA
1 TTTAAAAA
18890970 TAAAAAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
18 13 0.35
19 10 0.27
21 9 0.24
22 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TTTAAAAAATAATGTATAT
Found at i:18890964 original size:40 final size:40
Alignment explanation
Indices: 18890899--18890974 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
18890889 CTAAAATTGC
18890899 AAATATTTAAAAAATAATGTATATTTTAAAAATAAAAGTAT
1 AAATATTTAAAAAATAATGTATA-TTTAAAAATAAAAGTAT
* * *
18890940 AAAT-TTTATAAAATAATTTTTATTTAAAAATAAAA
1 AAATATTTAAAAAATAATGTATATTTAAAAATAAAA
18890975 AATTTTCAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 13 0.41
40 15 0.47
41 4 0.12
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (40 bp):
AAATATTTAAAAAATAATGTATATTTAAAAATAAAAGTAT
Found at i:18891917 original size:145 final size:145
Alignment explanation
Indices: 18891766--18892082 Score: 460
Period size: 145 Copynumber: 2.2 Consensus size: 145
18891756 TTATTACATT
* **
18891766 TTAGTTTCATTATATTTCATGATTTTTGGTACACTTGAAATCATAGCAATAGCCC-AGGATGTGC
1 TTAGTTTCATTATATTTCATGATTTTTGGTACACTTGAAATCATAGCAATA-CCCTAGAAAATGC
** *
18891830 AAAATTACCAAAATACCTTTATAAGGGTATTTTCGTAATTTGGCCTTCTCAAGCTTGA-AATTTC
65 AAAATTACCAAAATACCCCTATAAGGGTATTTTCGTAATTTGGCCTTCTCAAG-TTCAGAATTTC
18891894 ATGAAACTTTCCAGATC
129 ATGAAACTTTCCAGATC
* * *
18891911 TTAGTTTCATAATATTTCATAATTTTTGGTGCACTTGAAATCATAGCAATACCCTAGAAAATGCA
1 TTAGTTTCATTATATTTCATGATTTTTGGTACACTTGAAATCATAGCAATACCCTAGAAAATGCA
*
18891976 AAATTACCAAAATACCCCTATAAGGGTATTTTCGTAATTTGGCCTTCTCGAGTTCAGAATTTCAT
66 AAATTACCAAAATACCCCTATAAGGGTATTTTCGTAATTTGGCCTTCTCAAGTTCAGAATTTCAT
*
18892041 GAAACTTTTCAGATC
131 GAAACTTTCCAGATC
* * *
18892056 ATATTTTTA-TAGTATTTCATGATTTTT
1 TTAGTTTCATTA-TATTTCATGATTTTT
18892083 TTTTTTAAAT
Statistics
Matches: 153, Mismatches: 16, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
144 7 0.05
145 146 0.95
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (145 bp):
TTAGTTTCATTATATTTCATGATTTTTGGTACACTTGAAATCATAGCAATACCCTAGAAAATGCA
AAATTACCAAAATACCCCTATAAGGGTATTTTCGTAATTTGGCCTTCTCAAGTTCAGAATTTCAT
GAAACTTTCCAGATC
Found at i:18892471 original size:28 final size:29
Alignment explanation
Indices: 18892439--18892498 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
18892429 AACCAATGTA
18892439 AAAGAAAAAAAAAAAGAAAGA-AGCTA-CC
1 AAAGAAAAAAAAAAA-AAAGAGAGCTAGCC
* *
18892467 AAAGAAAAAACAACAAAAGAGAGCTAGCC
1 AAAGAAAAAAAAAAAAAAGAGAGCTAGCC
18892496 AAA
1 AAA
18892499 TAGAGAAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 5 0.18
28 18 0.64
29 5 0.18
ACGTcount: A:0.68, C:0.13, G:0.15, T:0.03
Consensus pattern (29 bp):
AAAGAAAAAAAAAAAAAAGAGAGCTAGCC
Found at i:18892778 original size:19 final size:20
Alignment explanation
Indices: 18892737--18892778 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
18892727 ATTAGTTTTC
*
18892737 ATGTTGTGTTCTTACTGCAT
1 ATGTTGTGTTCTCACTGCAT
18892757 ATGTT-TGTTCTCA-TGCAGT
1 ATGTTGTGTTCTCACTGCA-T
18892776 ATG
1 ATG
18892779 GTTTCTTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 4 0.20
19 11 0.55
20 5 0.25
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (20 bp):
ATGTTGTGTTCTCACTGCAT
Found at i:18895479 original size:3 final size:3
Alignment explanation
Indices: 18895466--18895513 Score: 78
Period size: 3 Copynumber: 15.7 Consensus size: 3
18895456 TAATTTTTTC
*
18895466 TAA TAAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
18895512 TA
1 TA
18895514 GGGAAAAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:18897014 original size:20 final size:20
Alignment explanation
Indices: 18896970--18897016 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
18896960 CATTTCATTT
*
18896970 TTTTTTCTTTTCCTTTGTTC
1 TTTTTTCTTTTCATTTGTTC
*
18896990 TTTTTTC-TTTCATTTTTTC
1 TTTTTTCTTTTCATTTGTTC
18897009 TCTTTTTC
1 T-TTTTTC
18897017 CTCACCTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (20 bp):
TTTTTTCTTTTCATTTGTTC
Found at i:18897409 original size:86 final size:86
Alignment explanation
Indices: 18897262--18897434 Score: 292
Period size: 86 Copynumber: 2.0 Consensus size: 86
18897252 TGGCCATTTA
* *
18897262 TCATTTCAAGCACAATCACTTAAACTGAAAAGCACTTCCTTTTGGGAAAATGAACTTGAAGAAAG
1 TCATTTCAAGCACAATCACTTAAACTGAAAAGCACTTCCCTTTGGGAAAATGAACTCGAAGAAAG
18897327 GTTTTTCAATTCAAAAGTTTT
66 GTTTTTCAATTCAAAAGTTTT
** *
18897348 TCATTTCAAGCATGATCATTTAAACTGAAAAGCACTTCCCTTTGGGAAAATGAACTCGAAGAAAG
1 TCATTTCAAGCACAATCACTTAAACTGAAAAGCACTTCCCTTTGGGAAAATGAACTCGAAGAAAG
*
18897413 GTTTTTCATTTCAAAAGTTTT
66 GTTTTTCAATTCAAAAGTTTT
18897434 T
1 T
18897435 TTCTTTTTTC
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
86 81 1.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (86 bp):
TCATTTCAAGCACAATCACTTAAACTGAAAAGCACTTCCCTTTGGGAAAATGAACTCGAAGAAAG
GTTTTTCAATTCAAAAGTTTT
Found at i:18903962 original size:13 final size:13
Alignment explanation
Indices: 18903946--18903995 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
18903936 TTAGGGTTTC
18903946 ATTTAAGGTTTTA
1 ATTTAAGGTTTTA
*
18903959 ATTTTAAGG-TTTC
1 A-TTTAAGGTTTTA
18903972 ATTT-AGGATTTTA
1 ATTTAAGG-TTTTA
*
18903985 ATTTAGGGTTT
1 ATTTAAGGTTT
18903996 CGTTTTAGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
11 3 0.10
12 3 0.10
13 15 0.50
14 9 0.30
ACGTcount: A:0.26, C:0.02, G:0.18, T:0.54
Consensus pattern (13 bp):
ATTTAAGGTTTTA
Found at i:18903995 original size:25 final size:26
Alignment explanation
Indices: 18903933--18903996 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
18903923 AATATCTAAG
18903933 ATTTTAGGGTTTCATTTAAGGTTTTA
1 ATTTTAGGGTTTCATTTAAGGTTTTA
*
18903959 ATTTTAAGGTTTCATTT-AGGATTTTA
1 ATTTTAGGGTTTCATTTAAGG-TTTTA
18903985 A-TTTAGGGTTTC
1 ATTTTAGGGTTTC
18903997 GTTTTAGGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
25 13 0.37
26 22 0.63
ACGTcount: A:0.23, C:0.05, G:0.19, T:0.53
Consensus pattern (26 bp):
ATTTTAGGGTTTCATTTAAGGTTTTA
Found at i:18904002 original size:26 final size:25
Alignment explanation
Indices: 18903933--18904004 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 25
18903923 AATATCTAAG
*
18903933 ATTTTAGGGTTTCATTTAAGGTTTTA
1 ATTTTAGGGTTTC-TTTTAGGTTTTA
* *
18903959 ATTTTAAGGTTTCATTTAGGATTTTA
1 ATTTTAGGGTTTCTTTTAGG-TTTTA
18903985 A-TTTAGGGTTTCGTTTTAGG
1 ATTTTAGGGTTTC-TTTTAGG
18904005 GTGTAGATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
25 15 0.38
26 24 0.62
ACGTcount: A:0.22, C:0.04, G:0.21, T:0.53
Consensus pattern (25 bp):
ATTTTAGGGTTTCTTTTAGGTTTTA
Found at i:18904137 original size:19 final size:21
Alignment explanation
Indices: 18904095--18904139 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
18904085 GTATTATTGC
*
18904095 TATTATTATTGTTATTATAATT
1 TATTAATATTGTTATTAT-ATT
18904117 TATTAATATT-TTATTAT-TT
1 TATTAATATTGTTATTATATT
18904136 TATT
1 TATT
18904140 TTTAATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 6 0.27
21 7 0.32
22 9 0.41
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TATTAATATTGTTATTATATT
Found at i:18907979 original size:8 final size:8
Alignment explanation
Indices: 18907966--18908041 Score: 50
Period size: 8 Copynumber: 9.6 Consensus size: 8
18907956 GGGCCAAACG
18907966 TTTTATTT
1 TTTTATTT
18907974 TTTTATTAT
1 TTTTATT-T
18907983 TTATTA-TT
1 TT-TTATTT
*
18907991 TATTATTT
1 TTTTATTT
* *
18907999 ATTGA-TT
1 TTTTATTT
**
18908006 TTTT-GGT
1 TTTTATTT
18908013 TTTTATTT
1 TTTTATTT
18908021 TTTTATTT
1 TTTTATTT
* *
18908029 TTATATAT
1 TTTTATTT
18908037 TTTTA
1 TTTTA
18908042 ATATTTTATA
Statistics
Matches: 51, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
7 12 0.24
8 32 0.63
9 4 0.08
10 3 0.06
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (8 bp):
TTTTATTT
Found at i:18907985 original size:7 final size:7
Alignment explanation
Indices: 18907975--18908006 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
18907965 GTTTTATTTT
18907975 TTTATTA
1 TTTATTA
18907982 TTTATTA
1 TTTATTA
18907989 TTTATTA
1 TTTATTA
18907996 TTTATTGA
1 TTTATT-A
18908004 TTT
1 TTT
18908007 TTTGGTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.83
8 4 0.17
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (7 bp):
TTTATTA
Found at i:18908029 original size:14 final size:14
Alignment explanation
Indices: 18907966--18908032 Score: 71
Period size: 14 Copynumber: 4.4 Consensus size: 14
18907956 GGGCCAAACG
18907966 TTTTATTTTTTTAT
1 TTTTATTTTTTTAT
18907980 TATTTATTATTTATTAT
1 T-TTTATT-TTT-TTAT
**
18907997 TTATTGATTTTTTGGT
1 TT-TT-ATTTTTTTAT
18908013 TTTTATTTTTTTAT
1 TTTTATTTTTTTAT
18908027 TTTTAT
1 TTTTAT
18908033 ATATTTTTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
14 15 0.34
15 8 0.18
16 8 0.18
17 10 0.23
18 3 0.07
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (14 bp):
TTTTATTTTTTTAT
Found at i:18908037 original size:18 final size:19
Alignment explanation
Indices: 18908016--18908054 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
18908006 TTTTGGTTTT
*
18908016 TATTTTTTTAT-TTTTATA
1 TATTTTTTAATATTTTATA
18908034 TA-TTTTTAATATTTTATA
1 TATTTTTTAATATTTTATA
18908052 TAT
1 TAT
18908055 ACTTTATCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TATTTTTTAATATTTTATA
Found at i:18908045 original size:11 final size:10
Alignment explanation
Indices: 18908016--18908054 Score: 50
Period size: 8 Copynumber: 4.3 Consensus size: 10
18908006 TTTTGGTTTT
18908016 TATTTTT-T-
1 TATTTTTATA
18908024 TATTTTTATA
1 TATTTTTATA
18908034 TATTTTTA-A
1 TATTTTTATA
18908043 TA-TTTTATA
1 TATTTTTATA
18908052 TAT
1 TAT
18908055 ACTTTATCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 12 0.44
9 7 0.26
10 8 0.30
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TATTTTTATA
Found at i:18912004 original size:23 final size:23
Alignment explanation
Indices: 18911967--18912014 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
18911957 TTATTTTTAG
18911967 TTCCTTGCAAAGCTTTCACATTTT
1 TTCCTTGCAAAGCTTTCAC-TTTT
* *
18911991 TTCCTT-CCAAGCTTTCTCTTTT
1 TTCCTTGCAAAGCTTTCACTTTT
18912013 TT
1 TT
18912015 AGTGTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.27
23 10 0.45
24 6 0.27
ACGTcount: A:0.15, C:0.27, G:0.06, T:0.52
Consensus pattern (23 bp):
TTCCTTGCAAAGCTTTCACTTTT
Found at i:18913374 original size:69 final size:68
Alignment explanation
Indices: 18913237--18913633 Score: 476
Period size: 68 Copynumber: 5.9 Consensus size: 68
18913227 TTAAATCTCA
* * * *
18913237 AAAAATTTTGAATG-TCCCTCTAATCAGAGG-CTTGAAACTTT--AAATTTAAAATGTTTTACAA
1 AAAACTTTTGAATGCT-CCTCCAATCAGAGGCCATGAAACTTTAAAAATTTAAAATGTTTTGCAA
18913298 ATTTC
65 A-TTC
*
18913303 AAAACTTTTGAATGCTCCTCCAATCAGAGGCCATGAAACTTTAAAAATTTAAAATGTTTTGGAAA
1 AAAACTTTTGAATGCTCCTCCAATCAGAGGCCATGAAACTTTAAAAATTTAAAATGTTTTGCAAA
18913368 TGTC
66 T-TC
** * *
18913372 AAAACTTTTGAATGCTTGTCCAATC-GAAGGCCATGAAACTTT--AAATATAAAATATTTTGCAA
1 AAAACTTTTGAATGCTCCTCCAATCAG-AGGCCATGAAACTTTAAAAATTTAAAATGTTTTGCAA
18913434 A-TC
65 ATTC
* * *
18913437 AAAACTTTTGAATGCTCCACCAATCAAAGGCCATGAAACTTTAAAAATTTAGAATGTTTTGCAAA
1 AAAACTTTTGAATGCTCCTCCAATCAGAGGCCATGAAACTTTAAAAATTTAAAATGTTTTGCAAA
18913502 CTTC
66 -TTC
* * * *
18913506 -AAACTTTTGAATGATCTTTCAATAAGAGGCCATGAAACTTTAAAAATTT-AAATGTTTTGCAAA
1 AAAACTTTTGAATGCTCCTCCAATCAGAGGCCATGAAACTTTAAAAATTTAAAATGTTTTGCAAA
18913569 TATC
66 T-TC
* *
18913573 AAAACTTTTGAATG-TTCTCCCAATCAGAGGCTATGAAACTTTAAAAATTTTAAAA-GTTTTG
1 AAAACTTTTGAATGCTCCT-CCAATCAGAGGCCATGAAACTTTAAAAA-TTTAAAATGTTTTG
18913634 AGATTAAAAT
Statistics
Matches: 286, Mismatches: 29, Indels: 29
0.83 0.08 0.08
Matches are distributed among these distances:
65 39 0.14
66 27 0.09
67 64 0.22
68 83 0.29
69 70 0.24
70 3 0.01
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (68 bp):
AAAACTTTTGAATGCTCCTCCAATCAGAGGCCATGAAACTTTAAAAATTTAAAATGTTTTGCAAA
TTC
Found at i:18913471 original size:134 final size:131
Alignment explanation
Indices: 18913269--18913633 Score: 468
Period size: 134 Copynumber: 2.7 Consensus size: 131
18913259 ATCAGAGGCT
* *
18913269 TGAAACTTTAAATTTAAAATGTTTTACAAATTTCAAAACTTTTGAATGCTCCTCCAATCAGAGGC
1 TGAAACTTTAAATATAAAATGTTTTGCAAA--TCAAAACTTTTGAATGCTCC-CCAATCAGAGGC
*
18913334 CATGAAACTTTAAAAATTTAAAATGTTTTGGAAA-TGTCAAAACTTTTGAATG-CTTGTCCAAT-
63 CATGAAACTTTAAAAATTTAAAATGTTTTGCAAACT-TC-AAACTTTTGAATGACTT-T-CAATA
*
18913396 CGAAGGCCA
124 AG-AGGCCA
* *
18913405 TGAAACTTTAAATATAAAATATTTTGCAAATCAAAACTTTTGAATGCTCCACCAATCAAAGGCCA
1 TGAAACTTTAAATATAAAATGTTTTGCAAATCAAAACTTTTGAATGCTCC-CCAATCAGAGGCCA
*
18913470 TGAAACTTTAAAAATTTAGAATGTTTTGCAAACTTCAAACTTTTGAATGATCTTTCAATAAGAGG
65 TGAAACTTTAAAAATTTAAAATGTTTTGCAAACTTCAAACTTTTGAATGA-CTTTCAATAAGAGG
18913535 CCA
129 CCA
* * *
18913538 TGAAACTTTAAAAATTTAAATGTTTTGCAAATATCAAAACTTTTGAATGTTCTCCCAATCAGAGG
1 TGAAACTTTAAATA-TAAAATGTTTTGC-AA-ATCAAAACTTTTGAATGCTC-CCCAATCAGAGG
*
18913603 CTATGAAACTTTAAAAATTTTAAAA-GTTTTG
62 CCATGAAACTTTAAAAA-TTTAAAATGTTTTG
18913634 AGATTAAAAT
Statistics
Matches: 205, Mismatches: 15, Indels: 18
0.86 0.06 0.08
Matches are distributed among these distances:
133 36 0.18
134 78 0.38
135 6 0.03
136 78 0.38
137 7 0.03
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (131 bp):
TGAAACTTTAAATATAAAATGTTTTGCAAATCAAAACTTTTGAATGCTCCCCAATCAGAGGCCAT
GAAACTTTAAAAATTTAAAATGTTTTGCAAACTTCAAACTTTTGAATGACTTTCAATAAGAGGCC
A
Found at i:18914853 original size:22 final size:21
Alignment explanation
Indices: 18914817--18914866 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
18914807 GTCCTCTTTC
18914817 ATTTTTTATTCTTTTATTCTCT
1 ATTTTTTATTCTTTTATTC-CT
* * * *
18914839 TTTTTTTGTTTTTTTTTTCCT
1 ATTTTTTATTCTTTTATTCCT
18914860 ATTTTTT
1 ATTTTTT
18914867 CTCCTTCTCA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.08, C:0.10, G:0.02, T:0.80
Consensus pattern (21 bp):
ATTTTTTATTCTTTTATTCCT
Found at i:18923356 original size:20 final size:21
Alignment explanation
Indices: 18923323--18923361 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
18923313 GAGTCTCAAA
* *
18923323 TTTTCTTTTCTCAATTTCTCT
1 TTTTCTATTCTCAAGTTCTCT
18923344 TTTTCTATT-TCAAGTTCT
1 TTTTCTATTCTCAAGTTCT
18923362 TGCTTAACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.13, C:0.21, G:0.03, T:0.64
Consensus pattern (21 bp):
TTTTCTATTCTCAAGTTCTCT
Found at i:18923644 original size:15 final size:16
Alignment explanation
Indices: 18923624--18923656 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18923614 GTGGCAGGGA
*
18923624 CAAATT-ACTTCGCAC
1 CAAATTGACTTAGCAC
18923639 CAAATTGACTTAGCAC
1 CAAATTGACTTAGCAC
18923655 CA
1 CA
18923657 TTAGTGGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.36, C:0.30, G:0.09, T:0.24
Consensus pattern (16 bp):
CAAATTGACTTAGCAC
Found at i:18925068 original size:19 final size:20
Alignment explanation
Indices: 18925046--18925098 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
18925036 TAATTTTGGG
*
18925046 TTTAAAGTTTGGTTTA-AGA
1 TTTAAAGTTTGGTTTACAAA
* *
18925065 TTTAAGGTTTAGTTTACAAA
1 TTTAAAGTTTGGTTTACAAA
18925085 TTT--AGTTTGGTTTA
1 TTTAAAGTTTGGTTTA
18925099 GGGTTTAAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 9 0.32
19 14 0.50
20 5 0.18
ACGTcount: A:0.28, C:0.02, G:0.19, T:0.51
Consensus pattern (20 bp):
TTTAAAGTTTGGTTTACAAA
Found at i:18925162 original size:26 final size:26
Alignment explanation
Indices: 18925123--18925250 Score: 100
Period size: 26 Copynumber: 4.9 Consensus size: 26
18925113 AGGTTTTGAC
18925123 TTGCATGGTGGTTTAGGGTTTAGGGT
1 TTGCATGGTGGTTTAGGGTTTAGGGT
* * *
18925149 TTTCATGGTGGTTTAGGATTTGGGGT
1 TTGCATGGTGGTTTAGGGTTTAGGGT
* ** *
18925175 TTAGCAT--TTGCATGGTGGTTTAGGGT
1 TT-GCATGGTGGTTTAG-GGTTTAGGGT
* *
18925201 TTGCATGATGGTTTAAGGTTTAGGGT
1 TTGCATGGTGGTTTAGGGTTTAGGGT
* * *
18925227 TTTCATAGTGATTT-GGGATTTAGG
1 TTGCATGGTGGTTTAGGG-TTTAGG
18925251 TTCTTTGCTT
Statistics
Matches: 77, Mismatches: 20, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
25 10 0.13
26 61 0.79
27 6 0.08
ACGTcount: A:0.16, C:0.05, G:0.36, T:0.44
Consensus pattern (26 bp):
TTGCATGGTGGTTTAGGGTTTAGGGT
Found at i:18925163 original size:19 final size:19
Alignment explanation
Indices: 18925139--18925221 Score: 77
Period size: 19 Copynumber: 4.6 Consensus size: 19
18925129 GGTGGTTTAG
*
18925139 GGTTTAGGGTTTTCATGGT
1 GGTTTAGGGTTTGCATGGT
*
18925158 GGTTTA-GGATT---TGG-
1 GGTTTAGGGTTTGCATGGT
**
18925172 GGTTTAGCATTTGCATGGT
1 GGTTTAGGGTTTGCATGGT
*
18925191 GGTTTAGGGTTTGCATGAT
1 GGTTTAGGGTTTGCATGGT
*
18925210 GGTTTAAGGTTT
1 GGTTTAGGGTTT
18925222 AGGGTTTTCA
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
14 6 0.12
15 5 0.10
18 7 0.14
19 33 0.65
ACGTcount: A:0.14, C:0.05, G:0.36, T:0.45
Consensus pattern (19 bp):
GGTTTAGGGTTTGCATGGT
Found at i:18925176 original size:33 final size:33
Alignment explanation
Indices: 18925138--18925203 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
18925128 TGGTGGTTTA
** *
18925138 GGGTTTAGGGTTTTCATGGTGGTTTAGGATTTG
1 GGGTTTAGCATTTGCATGGTGGTTTAGGATTTG
*
18925171 GGGTTTAGCATTTGCATGGTGGTTTAGGGTTTG
1 GGGTTTAGCATTTGCATGGTGGTTTAGGATTTG
18925204 CATGATGGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.12, C:0.05, G:0.39, T:0.44
Consensus pattern (33 bp):
GGGTTTAGCATTTGCATGGTGGTTTAGGATTTG
Found at i:18929051 original size:18 final size:19
Alignment explanation
Indices: 18929016--18929057 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
18929006 ATTTTTTGGC
18929016 TTTTATTTTTACAACTTCA
1 TTTTATTTTTACAACTTCA
*
18929035 TTTT-TTTTT-CAATCTTCC
1 TTTTATTTTTACAA-CTTCA
18929053 TTTTA
1 TTTTA
18929058 CCTCTCTACC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 3 0.15
18 13 0.65
19 4 0.20
ACGTcount: A:0.19, C:0.17, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTATTTTTACAACTTCA
Found at i:18929438 original size:10 final size:10
Alignment explanation
Indices: 18929423--18929454 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
18929413 TTATTTATTT
18929423 TATAATAAAA
1 TATAATAAAA
18929433 TATAATAAAA
1 TATAATAAAA
18929443 T-TAAT-AAA
1 TATAATAAAA
18929451 TATA
1 TATA
18929455 TTTATTGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 4 0.19
9 6 0.29
10 11 0.52
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
TATAATAAAA
Found at i:18938842 original size:21 final size:18
Alignment explanation
Indices: 18938818--18938862 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 18
18938808 AAAAATTAGG
18938818 GAAAAAGGAGAAATAAACAAA
1 GAAAAAGGA-AAA-AAA-AAA
*
18938839 GAAAGAGGAAAAAAAAAA
1 GAAAAAGGAAAAAAAAAA
18938857 GAAAAA
1 GAAAAA
18938863 AAAAAGAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 8 0.36
19 3 0.14
20 3 0.14
21 8 0.36
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (18 bp):
GAAAAAGGAAAAAAAAAA
Found at i:18939100 original size:13 final size:13
Alignment explanation
Indices: 18939097--18939121 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18939087 AAGAAAAAGT
18939097 AAAAGTAAATAAA
1 AAAAGTAAATAAA
18939110 AAAAGTAAATAA
1 AAAAGTAAATAA
18939122 CTTAACACTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (13 bp):
AAAAGTAAATAAA
Found at i:18939227 original size:18 final size:17
Alignment explanation
Indices: 18939193--18939230 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
18939183 AATATTTATT
18939193 AAATATATAAAAAAAGA
1 AAATATATAAAAAAAGA
18939210 AAATA-ATAGAAAATAAGA
1 AAATATATA-AAAA-AAGA
18939228 AAA
1 AAA
18939231 AAAAAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.16
17 9 0.47
18 7 0.37
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (17 bp):
AAATATATAAAAAAAGA
Found at i:18940064 original size:25 final size:24
Alignment explanation
Indices: 18940010--18940066 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 24
18940000 GAAATAATAT
*
18940010 AAAAAATAAAGAAAATAAAATGGGT
1 AAAAAATAAAGAAAATAAAAT-GGA
* *
18940035 TAAAAATAAAGTAAAAATAAAATGAA
1 AAAAAATAAAG--AAAATAAAATGGA
18940061 AAAAAA
1 AAAAAA
18940067 AAACCTGCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 10 0.38
26 6 0.23
27 10 0.38
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.16
Consensus pattern (24 bp):
AAAAAATAAAGAAAATAAAATGGA
Found at i:18940066 original size:27 final size:25
Alignment explanation
Indices: 18940010--18940067 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
18940000 GAAATAATAT
***
18940010 AAAAAATAAAGAAAATAAAATGGGT
1 AAAAAATAAAGAAAATAAAATGAAA
*
18940035 TAAAAATAAAGTAAAAATAAAATGAAA
1 AAAAAATAAAG--AAAATAAAATGAAA
18940062 AAAAAA
1 AAAAAA
18940068 AACCTGCAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 10 0.38
27 16 0.62
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (25 bp):
AAAAAATAAAGAAAATAAAATGAAA
Found at i:18940919 original size:15 final size:15
Alignment explanation
Indices: 18940896--18940932 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
18940886 AACAAAAAAG
18940896 GAAAGAAGAAAAGAAA
1 GAAA-AAGAAAAGAAA
*
18940912 GAAAAAGAAAAGAAC
1 GAAAAAGAAAAGAAA
18940927 GAAAAA
1 GAAAAA
18940933 AAATATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.76, C:0.03, G:0.22, T:0.00
Consensus pattern (15 bp):
GAAAAAGAAAAGAAA
Found at i:18940948 original size:12 final size:12
Alignment explanation
Indices: 18940933--18940981 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
18940923 GAACGAAAAA
*
18940933 AAATATAAATAT
1 AAATAAAAATAT
18940945 AAATAAAAATAT
1 AAATAAAAATAT
*
18940957 AAATAATAATAAT
1 AAATAAAAAT-AT
*
18940970 AATATAATAATA
1 AA-ATAAAAATA
18940982 ACAATAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
12 20 0.61
13 5 0.15
14 8 0.24
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAATAAAAATAT
Done.