Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold175
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: 1052864
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.33
Warning! 31646 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:378973 original size:31 final size:29
Alignment explanation
Indices: 378938--378996 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
378928 AATAGTAATT
*
378938 TATTAATTTAATATTAAAGTGATTATCTTAG
1 TATTAAATTAA-ATTAAA-TGATTATCTTAG
* *
378969 TATTAAATTAAATTTAATGTTTATCTTA
1 TATTAAATTAAATTAAATGATTATCTTA
378997 TAGATAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 10 0.40
30 5 0.20
31 10 0.40
ACGTcount: A:0.39, C:0.03, G:0.07, T:0.51
Consensus pattern (29 bp):
TATTAAATTAAATTAAATGATTATCTTAG
Found at i:381676 original size:35 final size:35
Alignment explanation
Indices: 381626--381871 Score: 264
Period size: 35 Copynumber: 7.0 Consensus size: 35
381616 CATTCCACAC
*
381626 ACCTCATTCAATTAACATCTCGCCACAACACCAAT
1 ACCTCATTCATTTAACATCTCGCCACAACACCAAT
**
381661 ACCTCATTCATTTAACAT-TCCGCCACAAGGCCAAT
1 ACCTCATTCATTTAACATCT-CGCCACAACACCAAT
* * * *
381696 ACCTCGTACATTTAACATCTCGACACAATACCAAT
1 ACCTCATTCATTTAACATCTCGCCACAACACCAAT
* * *
381731 ACCTCATTAATTTAACATCCCGCGACAACACCAAT
1 ACCTCATTCATTTAACATCTCGCCACAACACCAAT
* * * ** *
381766 ACCTTATTCATTTAACATCCCACCACAATGCCAAC
1 ACCTCATTCATTTAACATCTCGCCACAACACCAAT
* **
381801 ACTTCATTCATTTAACAT-TCTGTTACAACACCAAT
1 ACCTCATTCATTTAACATCTC-GCCACAACACCAAT
*
381836 ACCTCGTTCATTTAACATC-CTGCCACAACACCAAT
1 ACCTCATTCATTTAACATCTC-GCCACAACACCAAT
381871 A
1 A
381872 TTTCATAACA
Statistics
Matches: 172, Mismatches: 35, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
34 2 0.01
35 169 0.98
36 1 0.01
ACGTcount: A:0.35, C:0.34, G:0.05, T:0.26
Consensus pattern (35 bp):
ACCTCATTCATTTAACATCTCGCCACAACACCAAT
Found at i:381813 original size:105 final size:105
Alignment explanation
Indices: 381626--381871 Score: 316
Period size: 105 Copynumber: 2.3 Consensus size: 105
381616 CATTCCACAC
* * *
381626 ACCTCATTCAA-TTAACATCTCGCCACAACACCAATACCTCATTCATTTAACATTCCGCCACAAG
1 ACCTCATT-AATTTAACATCCCGCCACAACACCAATACCTCATTCATTTAACATCCCACCACAAG
* * *
381690 GCCAATACCTCGTACATTTAACA-TCTCGACACAATACCAAT
65 GCCAACACCTCATACATTTAACATTCT-GACACAACACCAAT
* * *
381731 ACCTCATTAATTTAACATCCCGCGACAACACCAATACCTTATTCATTTAACATCCCACCACAATG
1 ACCTCATTAATTTAACATCCCGCCACAACACCAATACCTCATTCATTTAACATCCCACCACAAGG
* * **
381796 CCAACACTTCATTCATTTAACATTCTGTTACAACACCAAT
66 CCAACACCTCATACATTTAACATTCTGACACAACACCAAT
* * *
381836 ACCTCGTTCATTTAACATCCTGCCACAACACCAATA
1 ACCTCATTAATTTAACATCCCGCCACAACACCAATA
381872 TTTCATAACA
Statistics
Matches: 122, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
104 2 0.02
105 117 0.96
106 3 0.02
ACGTcount: A:0.35, C:0.34, G:0.05, T:0.26
Consensus pattern (105 bp):
ACCTCATTAATTTAACATCCCGCCACAACACCAATACCTCATTCATTTAACATCCCACCACAAGG
CCAACACCTCATACATTTAACATTCTGACACAACACCAAT
Found at i:392159 original size:4 final size:4
Alignment explanation
Indices: 392150--392179 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
392140 ACTTTCCCTC
392150 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT
392180 TTCTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:394101 original size:19 final size:19
Alignment explanation
Indices: 394062--394101 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
394052 TACTTACCTA
**
394062 ATCTTTCTATTTGTTTTGT
1 ATCTTTCTATTTGTTAGGT
394081 ATCTTTCTATTTGTTAGGT
1 ATCTTTCTATTTGTTAGGT
394100 AT
1 AT
394102 GGCCGCCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (19 bp):
ATCTTTCTATTTGTTAGGT
Found at i:395949 original size:17 final size:18
Alignment explanation
Indices: 395905--395949 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
395895 CAAACCCATT
395905 TTTAATATTTATATTATA
1 TTTAATATTTATATTATA
*
395923 TTT-ATCTTTATA-TATTA
1 TTTAATATTTATATTA-TA
395940 TTTAAT-TTTA
1 TTTAATATTTA
395950 GATCACATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 2 0.08
17 17 0.71
18 5 0.21
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTAATATTTATATTATA
Found at i:396127 original size:152 final size:153
Alignment explanation
Indices: 395945--396253 Score: 611
Period size: 152 Copynumber: 2.0 Consensus size: 153
395935 TATTATTTAA
395945 TTTTAGATCACATAAAATTAAATTTATAATAGTTTTAATTTTCGTTATATAATTATGAAGTGAAA
1 TTTTAGATCACATAAAATTAAATTTATAATAGTTTTAATTTTCGTTATATAATTATGAAGTGAAA
396010 ATGTTATATTAATTCAACAGCAAATTTAATAGTAAATGTTAAATAAATTCTTGAAACACAAGTTT
66 ATGTTATATTAATTCAACAGCAAATTTAATAGTAAATGTTAAATAAATTCTTGAAACACAAGTTT
396075 AAATTTATAAAGAATCCATGGGG
131 AAATTTATAAAGAATCCATGGGG
396098 TTTTAGATCAC-TAAAATTAAATTTATAATAGTTTTAATTTTCGTTATATAATTATGAAGTGAAA
1 TTTTAGATCACATAAAATTAAATTTATAATAGTTTTAATTTTCGTTATATAATTATGAAGTGAAA
396162 ATGTTATATTAATTCAACAGCAAATTTAATAGTAAATGTTAAATAAATTCTTGAAACACAAGTTT
66 ATGTTATATTAATTCAACAGCAAATTTAATAGTAAATGTTAAATAAATTCTTGAAACACAAGTTT
396227 AAATTTATAAAGAATCCATGGGG
131 AAATTTATAAAGAATCCATGGGG
396250 TTTT
1 TTTT
396254 GTATTATAGG
Statistics
Matches: 156, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
152 145 0.93
153 11 0.07
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.39
Consensus pattern (153 bp):
TTTTAGATCACATAAAATTAAATTTATAATAGTTTTAATTTTCGTTATATAATTATGAAGTGAAA
ATGTTATATTAATTCAACAGCAAATTTAATAGTAAATGTTAAATAAATTCTTGAAACACAAGTTT
AAATTTATAAAGAATCCATGGGG
Found at i:397655 original size:25 final size:27
Alignment explanation
Indices: 397603--397670 Score: 104
Period size: 25 Copynumber: 2.6 Consensus size: 27
397593 AAAAATAAAA
397603 ATTTACCAAAATATTATAACTTTTTTTT
1 ATTTACCAAAATA-TATAACTTTTTTTT
397631 ATTTACCAAAATAT-T-ACTTTTTTTT
1 ATTTACCAAAATATATAACTTTTTTTT
*
397656 ATTTACGAAAATATA
1 ATTTACCAAAATATA
397671 ACAAAAAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
25 23 0.61
26 1 0.03
27 1 0.03
28 13 0.34
ACGTcount: A:0.38, C:0.10, G:0.01, T:0.50
Consensus pattern (27 bp):
ATTTACCAAAATATATAACTTTTTTTT
Found at i:400829 original size:6 final size:6
Alignment explanation
Indices: 400818--400846 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
400808 TCATTATTTG
400818 GCTTAT GCTTAT GCTTAT GCTTAT GCTTA
1 GCTTAT GCTTAT GCTTAT GCTTAT GCTTA
400847 AATTGTATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.48
Consensus pattern (6 bp):
GCTTAT
Found at i:400862 original size:11 final size:11
Alignment explanation
Indices: 400846--400872 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
400836 GCTTATGCTT
400846 AAATTGTATCC
1 AAATTGTATCC
400857 AAATTGTATCC
1 AAATTGTATCC
400868 AAATT
1 AAATT
400873 AAGTTATAAA
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:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (11 bp):
AAATTGTATCC
Found at i:401195 original size:35 final size:35
Alignment explanation
Indices: 401156--401226 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
401146 TCGGCGCAGG
*
401156 TGGGGGTGTGACAAATATAGAGGAAAAATCATCAT
1 TGGGGGTGTGACAAACATAGAGGAAAAATCATCAT
*
401191 TGGGGGTGTGGCAAACATAGAGGAAAAATCATCAT
1 TGGGGGTGTGACAAACATAGAGGAAAAATCATCAT
401226 T
1 T
401227 CGCCGCCGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.38, C:0.10, G:0.30, T:0.23
Consensus pattern (35 bp):
TGGGGGTGTGACAAACATAGAGGAAAAATCATCAT
Found at i:404013 original size:26 final size:26
Alignment explanation
Indices: 403983--404058 Score: 68
Period size: 26 Copynumber: 2.9 Consensus size: 26
403973 TAATCAACAT
403983 AAATACGTATAATGTACATAACATCA
1 AAATACGTATAATGTACATAACATCA
* * *
404009 AAATA--TAT-ATGCTAAATAAAATATTA
1 AAATACGTATAATG-TACAT--AACATCA
*
404035 AAATACGTATAATTTACATAACAT
1 AAATACGTATAATGTACATAACAT
404059 AAATTTTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
23 3 0.08
24 7 0.18
26 19 0.50
28 7 0.18
29 2 0.05
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.32
Consensus pattern (26 bp):
AAATACGTATAATGTACATAACATCA
Found at i:404103 original size:17 final size:18
Alignment explanation
Indices: 404073--404106 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
404063 TTTTAACAAA
404073 TAAATATTACAAAAAAAT
1 TAAATATTACAAAAAAAT
*
404091 TAAAT-TTATAAAAAAA
1 TAAATATTACAAAAAAA
404107 AATTACATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAATATTACAAAAAAAT
Found at i:404129 original size:10 final size:10
Alignment explanation
Indices: 404114--404161 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
404104 AAAAATTACA
404114 TTTTTTTCCT
1 TTTTTTTCCT
404124 TTTTTTTCCT
1 TTTTTTTCCT
** *
404134 TCCTTCTCTCT
1 TTTTTTTC-CT
*
404145 TTTTCTTCCT
1 TTTTTTTCCT
404155 TTTTTTT
1 TTTTTTT
404162 TTTCTCTTCT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
10 23 0.79
11 6 0.21
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTTTTCCT
Found at i:404171 original size:31 final size:29
Alignment explanation
Indices: 404114--404176 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
404104 AAAAATTACA
404114 TTTTTTTCCTTTTTTTTCCTTCCTTCTCTC
1 TTTTTTTCCTTTTTTTTCCTTCCTTCTC-C
*
404144 TTTTTCTTCCTTTTTTTT-TTTCTCTTCTCC
1 TTTTT-TTCCTTTTTTTTCCTTC-CTTCTCC
404174 TTT
1 TTT
404177 CCTTTTCTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 12 0.40
31 18 0.60
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (29 bp):
TTTTTTTCCTTTTTTTTCCTTCCTTCTCC
Found at i:404175 original size:41 final size:41
Alignment explanation
Indices: 404133--404279 Score: 124
Period size: 41 Copynumber: 3.6 Consensus size: 41
404123 TTTTTTTTCC
404133 TTCCTTCTCTCTTTTTCTTCCTTTTTTTTTTTCTCTTCTCCT
1 TTCCTTCT-TCTTTTTCTTCCTTTTTTTTTTTCTCTTCTCCT
* * *
404175 TTCCTT-TTC-TTTCCTTCTTTTTCTTTCTTTTTTCTTCTCCT
1 TTCCTTCTTCTTTTTCTTCCTTTT-TTT-TTTTCTCTTCTCCT
* * * *
404216 TTCC-TCTTCTTCTTCTTTC-TTTCTTTTTCCTCCTT-TCCTT
1 TTCCTTCTTCTTTTTCTTCCTTTTTTTTTTTCT-CTTCTCC-T
* *
404256 TTCTTTCCTTCTTTTTCTTTCTTT
1 TTCCTT-CTTCTTTTTCTTCCTTT
404280 CCTCTCCTTC
Statistics
Matches: 84, Mismatches: 12, Indels: 17
0.74 0.11 0.15
Matches are distributed among these distances:
39 18 0.21
40 15 0.18
41 25 0.30
42 24 0.29
43 2 0.02
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (41 bp):
TTCCTTCTTCTTTTTCTTCCTTTTTTTTTTTCTCTTCTCCT
Found at i:404188 original size:10 final size:10
Alignment explanation
Indices: 404173--404306 Score: 50
Period size: 10 Copynumber: 14.5 Consensus size: 10
404163 TTCTCTTCTC
404173 CTTTCCTTTT
1 CTTTCCTTTT
404183 CTTTCCTTCTT
1 CTTTCCTT-TT
404194 -TTT-C-TTT
1 CTTTCCTTTT
404201 C-TT--TTTT
1 CTTTCCTTTT
*
404208 CTTCTCCTTTC
1 CTT-TCCTTTT
404219 CTCTT-CTTCTT
1 CT-TTCCTT-TT
404230 CTTT-CTTTCT
1 CTTTCCTTT-T
* *
404240 TTTTCC--TC
1 CTTTCCTTTT
404248 CTTTCCTTTT
1 CTTTCCTTTT
404258 CTTTCCTTCTT
1 CTTTCCTT-TT
404269 -TTT-C-TTT
1 CTTTCCTTTT
*
404276 CTTTCC-TCT
1 CTTTCCTTTT
*
404285 CCTTCC-TTT
1 CTTTCCTTTT
404294 CTTT-C-TTT
1 CTTTCCTTTT
404302 CTTTC
1 CTTTC
404307 TTTCCCTCTC
Statistics
Matches: 97, Mismatches: 10, Indels: 35
0.68 0.07 0.25
Matches are distributed among these distances:
7 10 0.10
8 19 0.20
9 18 0.19
10 35 0.36
11 14 0.14
12 1 0.01
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (10 bp):
CTTTCCTTTT
Found at i:404196 original size:36 final size:36
Alignment explanation
Indices: 404122--404305 Score: 166
Period size: 36 Copynumber: 5.1 Consensus size: 36
404112 CATTTTTTTC
* * * *
404122 CTTTTT-TTTCCTTCCTTCTCTCTTTTTC-TTCCTT
1 CTTTTTCTTTCTTTCCTCCTTTCCTTTTCTTTCCTT
*
404156 -TTTTTTTTTCTCTT-CTCCTTTCCTTTTCTTTCCTT
1 CTTTTTCTTTCT-TTCCTCCTTTCCTTTTCTTTCCTT
* * *
404191 CTTTTTCTTTCTTT-TTTCTTCTCCTTTCCTCTT-CTT
1 CTTTTTCTTTCTTTCCTCCTT-TCCTTTTCT-TTCCTT
404227 CTTCTTTCTTTCTTTTTCCTCCTTTCCTTTTCTTTCCTT
1 CTT-TTTCTTTC--TTTCCTCCTTTCCTTTTCTTTCCTT
* *
404266 CTTTTTCTTTCTTTCCTCTCCTTCC-TTTCTTTCTTT
1 CTTTTTCTTTCTTTCCTC-CTTTCCTTTTCTTTCCTT
404302 CTTT
1 CTTT
404306 CTTTCCCTCT
Statistics
Matches: 125, Mismatches: 13, Indels: 22
0.78 0.08 0.14
Matches are distributed among these distances:
33 5 0.04
34 15 0.12
35 14 0.11
36 45 0.36
37 15 0.12
38 10 0.08
39 17 0.14
40 4 0.03
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (36 bp):
CTTTTTCTTTCTTTCCTCCTTTCCTTTTCTTTCCTT
Found at i:404198 original size:14 final size:14
Alignment explanation
Indices: 404179--404276 Score: 81
Period size: 14 Copynumber: 6.6 Consensus size: 14
404169 TCTCCTTTCC
404179 TTTTCTTTCCTTCT
1 TTTTCTTTCCTTCT
* *
404193 TTTTCTTTCTTTTT
1 TTTTCTTTCCTTCT
404207 TCTTCTCCTTTCCTCTTCT
1 T-TT-T-CTTT-C-CTTCT
* *
404226 TCTTCTTTCTTTCT
1 TTTTCTTTCCTTCT
* *
404240 TTTTC-CTCCTTTCC
1 TTTTCTTTCC-TTCT
404254 TTTTCTTTCCTTCT
1 TTTTCTTTCCTTCT
404268 TTTTCTTTC
1 TTTTCTTTC
404277 TTTCCTCTCC
Statistics
Matches: 65, Mismatches: 12, Indels: 14
0.71 0.13 0.15
Matches are distributed among these distances:
13 2 0.03
14 41 0.63
15 6 0.09
16 5 0.08
17 5 0.08
18 2 0.03
19 4 0.06
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTCTTTCCTTCT
Found at i:404201 original size:4 final size:4
Alignment explanation
Indices: 404180--404310 Score: 73
Period size: 4 Copynumber: 33.0 Consensus size: 4
404170 CTCCTTTCCT
*
404180 TTTC TTTC CTTC -TT- TTTC TTTC TTT- TTTC TTCTCC TTTCC TCTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-T-C TTT-C T-TTC
* * *
404225 -TTC -TTC TTTC TTTC -TT- TTTC CTCC TTTCC TTTTC TTTC CTTC -TT-
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT-C -TTTC TTTC TTTC TTTC
* *
404269 TTTC TTTC TTTCC TCTCC TTCC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTT-C T-TTC TTTC TTTC TTTC TTTC TTTC TTTC
404311 CCTCTCCTTC
Statistics
Matches: 104, Mismatches: 8, Indels: 30
0.73 0.06 0.21
Matches are distributed among these distances:
3 21 0.20
4 62 0.60
5 12 0.12
6 9 0.09
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (4 bp):
TTTC
Found at i:404262 original size:18 final size:18
Alignment explanation
Indices: 404161--404298 Score: 72
Period size: 18 Copynumber: 7.5 Consensus size: 18
404151 TCCTTTTTTT
404161 TTTTCTCTT-CTCCTTTCC
1 TTTTCT-TTCCTCCTTTCC
* *
404179 TTTTCTTTCCTTCTTTTTCT
1 TTTTCTTTCC-TC-CTTTCC
*
404199 TTCTTTTTTCTTCTCCTTTCC
1 TT-TTCTTTC--CTCCTTTCC
* *
404220 TCTTC-TT-CTTCTTT-C
1 TTTTCTTTCCTCCTTTCC
*
404235 TTTCTTTTTCCTCCTTTCC
1 TTT-TCTTTCCTCCTTTCC
* *
404254 TTTTCTTTCCTTCTTT-T
1 TTTTCTTTCCTCCTTTCC
*
404271 TCTTTCTTTCCTCTCCTTCC
1 T-TTTCTTTCCTC-CTTTCC
404291 -TTTCTTTC
1 TTTTCTTTC
404299 TTTCTTTCTT
Statistics
Matches: 90, Mismatches: 17, Indels: 26
0.68 0.13 0.20
Matches are distributed among these distances:
15 3 0.03
16 7 0.08
17 5 0.06
18 42 0.47
19 11 0.12
20 8 0.09
21 11 0.12
22 2 0.02
23 1 0.01
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTCTTTCCTCCTTTCC
Found at i:404265 original size:75 final size:68
Alignment explanation
Indices: 404170--404309 Score: 208
Period size: 75 Copynumber: 2.0 Consensus size: 68
404160 TTTTTCTCTT
*
404170 CTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTCTTCTTCTTCTTTC
1 CTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTC---TTTCCTCTCC-TTCCT-TTC-T-TTCTTTC
404235 TTTCTTTTTC
59 TTTCTTTTTC
404245 CTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCCTTCCTTTCTTTCTTTCTTTCTTT
1 CTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCCTTCCTTTCTTTCTTTCTTTCTTT
404310 CCCTCTCCTT
Statistics
Matches: 64, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
68 14 0.22
69 1 0.02
70 3 0.05
71 5 0.08
72 9 0.14
75 32 0.50
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (68 bp):
CTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCCTTCCTTTCTTTCTTTCTTTCTTT
TTC
Found at i:404496 original size:24 final size:23
Alignment explanation
Indices: 404469--404514 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
404459 TTTTTTTGGT
*
404469 ATATTTTGGTAATTTAAAAAAAAA
1 ATATTTTGGTAA-ATAAAAAAAAA
404493 ATATTTTGGTAAATAAAAAAAA
1 ATATTTTGGTAAATAAAAAAAA
404515 GGGATAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.35
Consensus pattern (23 bp):
ATATTTTGGTAAATAAAAAAAAA
Found at i:405716 original size:177 final size:177
Alignment explanation
Indices: 405420--405770 Score: 702
Period size: 177 Copynumber: 2.0 Consensus size: 177
405410 GCATCATTTG
405420 TTTAAACATTTCGATTCGGATGTGCAACTAATATTGACATAGGTTGCTAGGTATGGTAGAATGAC
1 TTTAAACATTTCGATTCGGATGTGCAACTAATATTGACATAGGTTGCTAGGTATGGTAGAATGAC
405485 TTGGAAATTCTTAAGCGTCTTTTTCTCAGCTGCCCCTTTGCAAAAGCAGTATGATGGGAGTGGGA
66 TTGGAAATTCTTAAGCGTCTTTTTCTCAGCTGCCCCTTTGCAAAAGCAGTATGATGGGAGTGGGA
405550 TCTGGAGGTGAGAGCCCTTGTGCTAATGTAGCGAGATAATCCTTTTA
131 TCTGGAGGTGAGAGCCCTTGTGCTAATGTAGCGAGATAATCCTTTTA
405597 TTTAAACATTTCGATTCGGATGTGCAACTAATATTGACATAGGTTGCTAGGTATGGTAGAATGAC
1 TTTAAACATTTCGATTCGGATGTGCAACTAATATTGACATAGGTTGCTAGGTATGGTAGAATGAC
405662 TTGGAAATTCTTAAGCGTCTTTTTCTCAGCTGCCCCTTTGCAAAAGCAGTATGATGGGAGTGGGA
66 TTGGAAATTCTTAAGCGTCTTTTTCTCAGCTGCCCCTTTGCAAAAGCAGTATGATGGGAGTGGGA
405727 TCTGGAGGTGAGAGCCCTTGTGCTAATGTAGCGAGATAATCCTT
131 TCTGGAGGTGAGAGCCCTTGTGCTAATGTAGCGAGATAATCCTT
405771 GGATGGGTTA
Statistics
Matches: 174, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
177 174 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (177 bp):
TTTAAACATTTCGATTCGGATGTGCAACTAATATTGACATAGGTTGCTAGGTATGGTAGAATGAC
TTGGAAATTCTTAAGCGTCTTTTTCTCAGCTGCCCCTTTGCAAAAGCAGTATGATGGGAGTGGGA
TCTGGAGGTGAGAGCCCTTGTGCTAATGTAGCGAGATAATCCTTTTA
Found at i:409343 original size:44 final size:44
Alignment explanation
Indices: 409280--409373 Score: 188
Period size: 44 Copynumber: 2.1 Consensus size: 44
409270 GTCTCGACTT
409280 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAA
1 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAA
409324 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAA
1 TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAA
409368 TCATTT
1 TCATTT
409374 ATTGAATATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (44 bp):
TCATTTTCATATGCTTATCAAATATAAGTATTGTATTAACCAAA
Found at i:409367 original size:22 final size:22
Alignment explanation
Indices: 409298--409368 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
409288 ATATGCTTAT
409298 CAAATATAAGTATTGTATTAAC
1 CAAATATAAGTATTGTATTAAC
** * *
409320 CAAATCAT-TTTCATATG-CTT-AT
1 CAAAT-ATAAGT-AT-TGTATTAAC
409342 CAAATATAAGTATTGTATTAAC
1 CAAATATAAGTATTGTATTAAC
409364 CAAAT
1 CAAAT
409369 CATTTATTGA
Statistics
Matches: 35, Mismatches: 8, Indels: 12
0.64 0.15 0.22
Matches are distributed among these distances:
20 2 0.06
21 6 0.17
22 19 0.54
23 6 0.17
24 2 0.06
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (22 bp):
CAAATATAAGTATTGTATTAAC
Found at i:409377 original size:21 final size:22
Alignment explanation
Indices: 409352--409395 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
409342 CAAATATAAG
* *
409352 TATTGTAT-TAACCAAATCATT
1 TATTGAATATAACCAAATAATT
409373 TATTGAATATAACCAAATAATT
1 TATTGAATATAACCAAATAATT
409395 T
1 T
409396 TCATATGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (22 bp):
TATTGAATATAACCAAATAATT
Found at i:409981 original size:13 final size:13
Alignment explanation
Indices: 409963--409987 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
409953 ACACTCAAAT
409963 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
409976 TTCTCAAAAGCA
1 TTCTCAAAAGCA
409988 ATAAAGAACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.28, G:0.08, T:0.24
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:410229 original size:7 final size:7
Alignment explanation
Indices: 410219--410244 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
410209 TTGATAGTTG
410219 ATTGCTA
1 ATTGCTA
410226 ATTGCTA
1 ATTGCTA
410233 ATTGCTA
1 ATTGCTA
410240 ATTGC
1 ATTGC
410245 AGTGGCTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (7 bp):
ATTGCTA
Found at i:412787 original size:23 final size:25
Alignment explanation
Indices: 412730--412787 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
412720 CGTTGTCATG
* *
412730 ATTTAAAAATAAAATGAATTATTAC
1 ATTTAAAATTAAAATGAATTATAAC
* *
412755 ATTCAAAATTAAAAT-ATTTATAAC
1 ATTTAAAATTAAAATGAATTATAAC
412779 -TTTAAAATT
1 ATTTAAAATT
412788 TCAAAATTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 8 0.29
24 7 0.25
25 13 0.46
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (25 bp):
ATTTAAAATTAAAATGAATTATAAC
Found at i:415823 original size:48 final size:48
Alignment explanation
Indices: 415752--415847 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 48
415742 TCTTTAAGGT
415752 GCAATTTTTACACGGGAAGAAAAAGAAAAATGTTCATAGGTTTGCTTA
1 GCAATTTTTACACGGGAAGAAAAAGAAAAATGTTCATAGGTTTGCTTA
* * *
415800 GCAATTTTTATACGGGAAGAAAAAGAAAAGTGTTTATAGGTTTGCTTA
1 GCAATTTTTACACGGGAAGAAAAAGAAAAATGTTCATAGGTTTGCTTA
415848 ATAAAATATT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (48 bp):
GCAATTTTTACACGGGAAGAAAAAGAAAAATGTTCATAGGTTTGCTTA
Found at i:419606 original size:21 final size:21
Alignment explanation
Indices: 419581--419620 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
419571 CATTCTTGAT
* *
419581 AATAATTAATAATATTGATTA
1 AATAATAAATAATAGTGATTA
419602 AATAATAAATAATAGTGAT
1 AATAATAAATAATAGTGAT
419621 ATTTTAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (21 bp):
AATAATAAATAATAGTGATTA
Found at i:420791 original size:21 final size:22
Alignment explanation
Indices: 420765--420822 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
420755 CCCAACAAGG
*
420765 TTGTTTTCAAAATTCAATAC-T
1 TTGTTTTCAAAATTCAACACAT
*
420786 TTGTTTTCAAAACTCAACACTAT
1 TTGTTTTCAAAATTCAACAC-AT
*
420809 TTGTTTACAAAATT
1 TTGTTTTCAAAATT
420823 GATATTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 18 0.58
23 13 0.42
ACGTcount: A:0.34, C:0.16, G:0.05, T:0.45
Consensus pattern (22 bp):
TTGTTTTCAAAATTCAACACAT
Found at i:424745 original size:13 final size:13
Alignment explanation
Indices: 424727--424753 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
424717 AACATAGGAT
424727 TTTATTTTTCTAG
1 TTTATTTTTCTAG
424740 TTTATTTTTCTAG
1 TTTATTTTTCTAG
424753 T
1 T
424754 GTTTCTTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.70
Consensus pattern (13 bp):
TTTATTTTTCTAG
Found at i:429792 original size:26 final size:26
Alignment explanation
Indices: 429756--429807 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
429746 GATGAGGTGA
*
429756 TGATACCTGACTTTTTTTTATACACT
1 TGATACCTGACTTTTGTTTATACACT
429782 TGATACCTGACTTTTGTTTATACACT
1 TGATACCTGACTTTTGTTTATACACT
429808 GAGTATACTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.23, C:0.19, G:0.10, T:0.48
Consensus pattern (26 bp):
TGATACCTGACTTTTGTTTATACACT
Found at i:430162 original size:23 final size:26
Alignment explanation
Indices: 430136--430184 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
430126 TTGTGACTTG
*
430136 ATATT-AAATG-ATTTCGTA-TAATT
1 ATATTCAAATGTATCTCGTACTAATT
430159 ATATTCAAATGTATCTCGTACTAATT
1 ATATTCAAATGTATCTCGTACTAATT
430185 TGTGTATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 5 0.23
24 5 0.23
25 7 0.32
26 5 0.23
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (26 bp):
ATATTCAAATGTATCTCGTACTAATT
Found at i:436552 original size:64 final size:64
Alignment explanation
Indices: 436424--436553 Score: 170
Period size: 64 Copynumber: 2.0 Consensus size: 64
436414 GCGAGCATCT
* * * * ** *
436424 TGATCGGTATTGATCATGCATATGTTGCAGACATACCGCAGCTCTTTGTGAGAGTCTTGTTATA
1 TGATCGATATGGATCATGCATATATTGCAGACATACCGCAGCTCTTTATGAGAGTCCCGATATA
* * *
436488 TGATCGATATGGATCCTGCATATATTGCGGACATACCGCAGCTCTTTATGAGTGTCCCGATATA
1 TGATCGATATGGATCATGCATATATTGCAGACATACCGCAGCTCTTTATGAGAGTCCCGATATA
436552 TG
1 TG
436554 GCTCTTAATG
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (64 bp):
TGATCGATATGGATCATGCATATATTGCAGACATACCGCAGCTCTTTATGAGAGTCCCGATATA
Found at i:436575 original size:26 final size:25
Alignment explanation
Indices: 436528--436605 Score: 65
Period size: 26 Copynumber: 3.1 Consensus size: 25
436518 ACATACCGCA
*
436528 GCTCTTTATGAG-TGTCCCGATATATG
1 GCTC-TTATGAGCT-TCCTGATATATG
436554 GCTCTTAATGAGCTTCCTG--ATATG
1 GCTCTT-ATGAGCTTCCTGATATATG
* *
436578 GCTCGGT-TGAACTTCCTGATATATG
1 GCTC-TTATGAGCTTCCTGATATATG
436603 GCT
1 GCT
436606 ATCTGGAGCT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
23 10 0.23
24 9 0.20
25 11 0.25
26 13 0.30
27 1 0.02
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (25 bp):
GCTCTTATGAGCTTCCTGATATATG
Found at i:444473 original size:22 final size:22
Alignment explanation
Indices: 444448--444491 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
444438 AAATATACAC
*
444448 ATACTTACA-TTTTTATTTTATA
1 ATACTTACAGATTTT-TTTTATA
444470 ATACTTACAGATTTTTTTTATA
1 ATACTTACAGATTTTTTTTATA
444492 TATGTATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.57
Consensus pattern (22 bp):
ATACTTACAGATTTTTTTTATA
Found at i:444483 original size:24 final size:22
Alignment explanation
Indices: 444448--444493 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
444438 AAATATACAC
444448 ATACTTACATTTTTATTT-TATA
1 ATACTTACATTTTT-TTTATATA
444470 ATACTTACAGATTTTTTTTATATA
1 ATACTTAC--ATTTTTTTTATATA
444494 TGTATATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 8 0.38
23 3 0.14
24 10 0.48
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.57
Consensus pattern (22 bp):
ATACTTACATTTTTTTTATATA
Found at i:444980 original size:107 final size:106
Alignment explanation
Indices: 444827--445144 Score: 447
Period size: 107 Copynumber: 3.0 Consensus size: 106
444817 TTTCTAATCT
* * * *
444827 AAATAAGGCAATATTTCGCATTTGGAAAATCAAGAAAACGTGCCCTAACATGCTGGGTTTCGATT
1 AAATAAGGCAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTGGGTTTCGATT
444892 TCTCGCTTGACCAAATAGCCAAATATCCTTTTTAAACTTTTA
66 TCTCG-TTGACCAAATAGCCAAATATCCTTTTTAAACTTTTA
* * * * *
444934 AAATAAGGCAATATTTCGCGTTCGAAAAATTGAGGAAACGTGCCCTAACGTGTTGGGTTTCGACT
1 AAATAAGGCAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTGGGTTTCGATT
* *
444999 TCTCGTTTGACCAAATAGCCAAATATTCTTTTTAAAATTTTA
66 TCTCG-TTGACCAAATAGCCAAATATCCTTTTTAAACTTTTA
* * * *
445041 AAATATGGCAATACTTCGCGTTTGGAAAATCGAGGAAACGTTCCCTAGCGTGCTGGGTTTCGATT
1 AAATAAGGCAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTGGGTTTCGATT
* * *
445106 TCTCGTTCGACTAAATAGCCAAATATCCTCTTAAAACTT
66 TCTCGTT-GACCAAATAGCCAAATATCCTTTTTAAACTT
445145 CAAAGTATGG
Statistics
Matches: 184, Mismatches: 26, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
106 2 0.01
107 182 0.99
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Consensus pattern (106 bp):
AAATAAGGCAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTGGGTTTCGATT
TCTCGTTGACCAAATAGCCAAATATCCTTTTTAAACTTTTA
Found at i:445455 original size:15 final size:16
Alignment explanation
Indices: 445427--445459 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
445417 TCTGAATTTC
445427 GTAGACCAAAATCGTT
1 GTAGACCAAAATCGTT
445443 GTAGACC-AAATCGTT
1 GTAGACCAAAATCGTT
445458 GT
1 GT
445460 TTTAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.27
Consensus pattern (16 bp):
GTAGACCAAAATCGTT
Found at i:453423 original size:44 final size:45
Alignment explanation
Indices: 453352--453482 Score: 140
Period size: 45 Copynumber: 2.9 Consensus size: 45
453342 AATGAAGCTA
* * * *
453352 CAGATCTTGCCTTCTTACACTGGCAGTGAAGCGGATCGAAGACAC
1 CAGATCTTGCCTTCCTATACTGACAGTGAAGCAGATCGAAGACAC
* * * * *
453397 CAG-TCTTGCCTTCCTGTACTGACAGTGGAGCAGA-CTAAAGATAG
1 CAGATCTTGCCTTCCTATACTGACAGTGAAGCAGATC-GAAGACAC
* *
453441 CAGATCTTGCCTTCCTATACTGACGGCGAAGCAGATCGAAGA
1 CAGATCTTGCCTTCCTATACTGACAGTGAAGCAGATCGAAGA
453483 TGGCAGATTT
Statistics
Matches: 69, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
43 1 0.01
44 33 0.48
45 34 0.49
46 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.23
Consensus pattern (45 bp):
CAGATCTTGCCTTCCTATACTGACAGTGAAGCAGATCGAAGACAC
Found at i:453453 original size:45 final size:45
Alignment explanation
Indices: 453352--453516 Score: 129
Period size: 45 Copynumber: 3.7 Consensus size: 45
453342 AATGAAGCTA
* ** * * * * * *
453352 CAGATCTTGCCTTCTTACACTGGCAGTGAAGCGGATCGAAGACAC
1 CAGATCTTGCCTTCCTGTACTGACAGTGGAGCAGATCAAAGATAG
453397 CAG-TCTTGCCTTCCTGTACTGACAGTGGAGCAGA-CTAAAGATAG
1 CAGATCTTGCCTTCCTGTACTGACAGTGGAGCAGATC-AAAGATAG
* * * * * *
453441 CAGATCTTGCCTTCCTATACTGACGGCGAAGCAGATCGAAGATGG
1 CAGATCTTGCCTTCCTGTACTGACAGTGGAGCAGATCAAAGATAG
* * *
453486 CAGATTTTACCTCCCTGTGACT-ACAGTGGAG
1 CAGATCTTGCCTTCCTGT-ACTGACAGTGGAG
453517 TACATTGAAG
Statistics
Matches: 94, Mismatches: 22, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
43 1 0.01
44 33 0.35
45 56 0.60
46 4 0.04
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.24
Consensus pattern (45 bp):
CAGATCTTGCCTTCCTGTACTGACAGTGGAGCAGATCAAAGATAG
Found at i:453641 original size:44 final size:44
Alignment explanation
Indices: 453496--453641 Score: 109
Period size: 44 Copynumber: 3.2 Consensus size: 44
453486 CAGATTTTAC
453496 CTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAATTCTAT
1 CTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAATTCTAT
* * * ** * * *
453540 CTCCCTGGTTG-GT--AGTGGAATAGATTGAATATTGAAGATGGCGGATTTTAC
1 CTCCCT-G-TGACTACAGTGGAGTACATTG-A-A--GCCGAT----AATTCTAT
453591 CTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAATTCTAT
1 CTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAATTCTAT
453635 CTCCCTG
1 CTCCCTG
453642 GTTGGCAGTG
Statistics
Matches: 73, Mismatches: 16, Indels: 26
0.63 0.14 0.23
Matches are distributed among these distances:
43 12 0.16
44 19 0.26
45 3 0.04
46 2 0.03
47 4 0.05
48 4 0.05
49 2 0.03
50 3 0.04
51 12 0.16
52 12 0.16
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (44 bp):
CTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAATTCTAT
Found at i:453737 original size:95 final size:95
Alignment explanation
Indices: 453478--453717 Score: 410
Period size: 95 Copynumber: 2.5 Consensus size: 95
453468 GAAGCAGATC
*
453478 GAAGATGGCAGATTTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAATTCTATCTC
1 GAAGATGGCGGATTTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAATTCTATCTC
*
453543 CCTGGTTGGTAGTGGAATAGATTGAATATT
66 CCTGGTTGGCAGTGGAATAGATTGAATATT
453573 GAAGATGGCGGATTTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAATTCTATCTC
1 GAAGATGGCGGATTTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAATTCTATCTC
453638 CCTGGTTGGCAGTGGAATAGATTGAATATT
66 CCTGGTTGGCAGTGGAATAGATTGAATATT
* * * *
453668 GAAGATGGCGGATTTTACCTCTCGGAGATTACAG-GAGAGTACATTGAAGC
1 GAAGATGGCGGATTTTACCTCCCTGTGACTACAGTG-GAGTACATTGAAGC
453718 TAGTAGTTCT
Statistics
Matches: 138, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
94 1 0.01
95 137 0.99
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (95 bp):
GAAGATGGCGGATTTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAATTCTATCTC
CCTGGTTGGCAGTGGAATAGATTGAATATT
Found at i:453746 original size:95 final size:95
Alignment explanation
Indices: 453478--453758 Score: 343
Period size: 95 Copynumber: 3.0 Consensus size: 95
453468 GAAGCAGATC
* * * *
453478 GAAGATGGCAGATTTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAATTCTATCTC
1 GAAGATGGCGGATTTTACCTCCCGGAGACTACAGTGGAGTACATTGAAGCAGATAATTCTATCTC
*****
453543 CCTGGTTGGTAGTGGAATAGATTGAATATT
66 CCTGGACAACAGTGGAATAGATTGAATATT
* * *
453573 GAAGATGGCGGATTTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAATTCTATCTC
1 GAAGATGGCGGATTTTACCTCCCGGAGACTACAGTGGAGTACATTGAAGCAGATAATTCTATCTC
****
453638 CCTGGTTGGCAGTGGAATAGATTGAATATT
66 CCTGGACAACAGTGGAATAGATTGAATATT
* * *
453668 GAAGATGGCGGATTTTACCTCTCGGAGATTACAG-GAGAGTACATTGAAGCTAG-TAGTTCTA-C
1 GAAGATGGCGGATTTTACCTCCCGGAGACTACAGTG-GAGTACATTGAAGC-AGATAATTCTATC
453730 TTCCCTGGACAACAGTGGAATAGATTGAA
64 -TCCCTGGACAACAGTGGAATAGATTGAA
453759 GATTATAGAT
Statistics
Matches: 171, Mismatches: 12, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
94 2 0.01
95 168 0.98
96 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (95 bp):
GAAGATGGCGGATTTTACCTCCCGGAGACTACAGTGGAGTACATTGAAGCAGATAATTCTATCTC
CCTGGACAACAGTGGAATAGATTGAATATT
Found at i:453812 original size:132 final size:132
Alignment explanation
Indices: 453668--454288 Score: 1134
Period size: 132 Copynumber: 4.7 Consensus size: 132
453658 ATTGAATATT
453668 GAAGATGGCGGATTTTACCTCTCGGAGATTACAGGAGAGTACATTGAAGCTAGTAGTTCTACTTC
1 GAAGATGGCGGATTTTACCTCTCGGAGATTACAGGAGAGTACATTGAAGCTAGTAGTTCTACTTC
453733 CCTGGACAACAGTGGAATAGATTGAAGATTATAGATATTATCTCCCTAAGCAATAGGGGAGCAGA
66 CCTGGACAACAGTGGAATAGATTGAAGATTATAGATATTATCTCCCTAAGCAATAGGGGAGCAGA
453798 TC
131 TC
453800 GAAGATGGCGGATTTTACCTCTCGGAGATTACAGGAGAGTACATTGAAGCTAGTAGTTCTACTTC
1 GAAGATGGCGGATTTTACCTCTCGGAGATTACAGGAGAGTACATTGAAGCTAGTAGTTCTACTTC
453865 CCTGGACAACAGTGGAATAGATTGAAGATTATAGATATTATCTCCCTAAGCAATAGGGGAGCAGA
66 CCTGGACAACAGTGGAATAGATTGAAGATTATAGATATTATCTCCCTAAGCAATAGGGGAGCAGA
453930 TC
131 TC
453932 GAAGATGGCGGATTTTACCTCTCGGAGATTACAGGAGAGTACATTGAAGCTAGTAGTTCTACTTC
1 GAAGATGGCGGATTTTACCTCTCGGAGATTACAGGAGAGTACATTGAAGCTAGTAGTTCTACTTC
*
453997 CCTGGACAACAGTGGAATAGATTGAAGATTATAGATATTATCTCCCTAAGCAATAGTGGAGCAGA
66 CCTGGACAACAGTGGAATAGATTGAAGATTATAGATATTATCTCCCTAAGCAATAGGGGAGCAGA
454062 TC
131 TC
** ** * * *
454064 GAAGATGGCGGATTTTACCTCTCTAAGATTACAATAGAGTACATTGAAGCCAGAAATTCTACTTC
1 GAAGATGGCGGATTTTACCTCTCGGAGATTACAGGAGAGTACATTGAAGCTAGTAGTTCTACTTC
* * *
454129 CCTGGGCAACAGTGGAATAGATTGAAGATTACAGATATTATCTCCCTAAGCAATAGTGGAGCAGA
66 CCTGGACAACAGTGGAATAGATTGAAGATTATAGATATTATCTCCCTAAGCAATAGGGGAGCAGA
454194 TC
131 TC
*
454196 GAAGATGGCGGATTTTACCTCTCGGAGATTACAGTAGAGTACATTGAAGCTAGTAGTTCTACTTC
1 GAAGATGGCGGATTTTACCTCTCGGAGATTACAGGAGAGTACATTGAAGCTAGTAGTTCTACTTC
454261 CCTGGACAACAGTGGAATAGATTGAAGA
66 CCTGGACAACAGTGGAATAGATTGAAGA
454289 GCAGACTAAA
Statistics
Matches: 472, Mismatches: 17, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
132 472 1.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (132 bp):
GAAGATGGCGGATTTTACCTCTCGGAGATTACAGGAGAGTACATTGAAGCTAGTAGTTCTACTTC
CCTGGACAACAGTGGAATAGATTGAAGATTATAGATATTATCTCCCTAAGCAATAGGGGAGCAGA
TC
Found at i:454187 original size:44 final size:44
Alignment explanation
Indices: 454003--454188 Score: 119
Period size: 44 Copynumber: 4.2 Consensus size: 44
453993 CTTCCCTGGA
*
454003 CAACAGTGGAATAGATTGAAGATTATAGATATTATCTCCCTAAG
1 CAACAGTGGAATAGATTGAAGATTACAGATATTATCTCCCTAAG
* ** * ** * * * *
454047 CAATAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCTCTAAG
1 CAACAGTGGAATAGATTGAAGATTACAGATATTATCTCCCTAAG
* * * * * * * **
454091 -ATTACAATAGAGTACATTGAAG---CCAGAAATTCTACTTCCCTGGG
1 CA--ACAGTGGAATAGATTGAAGATTACAGATATTAT-C-TCCCTAAG
454135 CAACAGTGGAATAGATTGAAGATTACAGATATTATCTCCCTAAG
1 CAACAGTGGAATAGATTGAAGATTACAGATATTATCTCCCTAAG
*
454179 CAATAGTGGA
1 CAACAGTGGA
454189 GCAGATCGAA
Statistics
Matches: 98, Mismatches: 36, Indels: 16
0.65 0.24 0.11
Matches are distributed among these distances:
42 5 0.05
43 17 0.17
44 53 0.54
45 15 0.15
46 8 0.08
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (44 bp):
CAACAGTGGAATAGATTGAAGATTACAGATATTATCTCCCTAAG
Found at i:455800 original size:12 final size:12
Alignment explanation
Indices: 455783--455815 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
455773 TATTTTAAGT
455783 TATATATATGTA
1 TATATATATGTA
455795 TATATATATGTA
1 TATATATATGTA
455807 TATATATAT
1 TATATATAT
455816 TATTTACCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (12 bp):
TATATATATGTA
Found at i:456250 original size:106 final size:106
Alignment explanation
Indices: 456010--456303 Score: 466
Period size: 106 Copynumber: 2.8 Consensus size: 106
456000 TTCTCTACAT
*
456010 GCATTTGGAAAATCGA--AAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCGCTTGACCAAATA
1 GCATTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCGTTTGACCAAATA
*
456073 GCCAAATATCCTTTTTAAACTTTTAAAATAAGGCAATATTTC
66 GCCAAATATCC-TTTTAAACTTTTAAAATAAGGCAATACTTC
* * *
456115 GCATTTGGAAAATCGAGGAAACGTGCCCTAACGTGTTGGGTTTCGACTTCTCATTTGACCAAATA
1 GCATTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCGTTTGACCAAATA
* *
456180 GCCAAATATTCTTTTAAACTTTTAAAATATGGCAATACTTC
66 GCCAAATATCCTTTTAAACTTTTAAAATAAGGCAATACTTC
* * *
456221 GCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCGTTCGACTAAATA
1 GCATTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCGTTTGACCAAATA
*
456286 GCCAAATATCCTCTTAAA
66 GCCAAATATCCTTTTAAA
456304 GCTTCAAAGT
Statistics
Matches: 172, Mismatches: 15, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
105 16 0.09
106 103 0.60
107 53 0.31
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (106 bp):
GCATTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCGTTTGACCAAATA
GCCAAATATCCTTTTAAACTTTTAAAATAAGGCAATACTTC
Found at i:457085 original size:31 final size:30
Alignment explanation
Indices: 457030--457098 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
457020 ATACATGAAC
457030 TTTGATTTTGTACAAATATATACAT-TAAAT
1 TTTGATTTTGTACAAATATATACATAT-AAT
*
457060 TTTGATTTTG-ACTCAAATATGTACATATAAT
1 TTTGATTTTGTA--CAAATATATACATATAAT
*
457091 TCTGATTT
1 TTTGATTT
457099 AATTCAACTG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 1 0.03
30 10 0.29
31 22 0.65
32 1 0.03
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.48
Consensus pattern (30 bp):
TTTGATTTTGTACAAATATATACATATAAT
Found at i:457316 original size:7 final size:7
Alignment explanation
Indices: 457304--457328 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
457294 CGTATATAAC
457304 ATTGCAT
1 ATTGCAT
457311 ATTGCAT
1 ATTGCAT
457318 ATTGCAT
1 ATTGCAT
457325 ATTG
1 ATTG
457329 AATCAAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (7 bp):
ATTGCAT
Found at i:461169 original size:126 final size:126
Alignment explanation
Indices: 460971--461198 Score: 429
Period size: 126 Copynumber: 1.8 Consensus size: 126
460961 TAATTTCGAG
* *
460971 TTGACGTTTCTGATCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
1 TTGAAGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
461036 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
*
461097 TTGAAGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTTTG
1 TTGAAGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
461162 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
461199 CATGTTTGGG
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
126 99 1.00
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (126 bp):
TTGAAGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
Found at i:464191 original size:116 final size:116
Alignment explanation
Indices: 463987--464226 Score: 426
Period size: 116 Copynumber: 2.1 Consensus size: 116
463977 TGATAAATTG
* *
463987 TATTAACTCAAAAAATTTTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
1 TATTAACTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTAT
*
464052 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
66 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTACGTGAATGTAAAAT
*
464103 TATTAACTCTAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTAT
1 TATTAACTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTAT
* *
464168 TAGTAGCAGTCAAAACATTTTTCCAAATCTAACATTACGTGAATGTACAAT
66 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTACGTGAATGTAAAAT
464219 TATTAACT
1 TATTAACT
464227 TAGTTTAGGG
Statistics
Matches: 118, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
116 118 1.00
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (116 bp):
TATTAACTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTAT
TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTACGTGAATGTAAAAT
Found at i:464278 original size:21 final size:21
Alignment explanation
Indices: 464252--464371 Score: 136
Period size: 21 Copynumber: 5.6 Consensus size: 21
464242 AATTAAATTA
464252 GGTTAGGGTTTTAAAGTTAAG
1 GGTTAGGGTTTTAAAGTTAAG
*
464273 GGTTAGGGTTTTTAAGTTAAGG
1 GGTTAGGGTTTTAAAGTTAA-G
* *
464295 GGTTAGGGTTTTTAA-TTAAATTA
1 GGTTAGGGTTTTAAAGTT-AA--G
464318 GGTTAGGGTTTTTAAAGTTAAG
1 GGTTAGGG-TTTTAAAGTTAAG
*
464340 GTTTAGGGTTTT-AAGTTAAG
1 GGTTAGGGTTTTAAAGTTAAG
*
464360 GTTTAGGGTTTT
1 GGTTAGGGTTTT
464372 TAATTAAATT
Statistics
Matches: 88, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
20 20 0.23
21 25 0.28
22 25 0.28
23 8 0.09
24 8 0.09
25 2 0.02
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (21 bp):
GGTTAGGGTTTTAAAGTTAAG
Found at i:464329 original size:45 final size:45
Alignment explanation
Indices: 464273--464594 Score: 139
Period size: 45 Copynumber: 6.7 Consensus size: 45
464263 TAAAGTTAAG
464273 GGTTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAATTAAATTA
*
464318 GGTTAGGGTTTTTAAAGTTAA-GGTTTAGGG-TTTTAAGTT--A--A
1 GGTTAGGGTTTTT-AAGTTAAGGGGTTAGGGTTTTTAA-TTAAATTA
*
464359 GGTTTAGGGTTTTTAA-TTAAATTAGGTTAGAGTTAGGGTTATTAATTAAATTA
1 GG-TTAGGGTTTTTAAGTT--A--AGG---G-GTTAGGGTTTTTAATTAAATTA
* * *
464412 GGTTAGGGTTAGGGTTTTAA-TTAA---ATTAGGGTTTTTAATTTAA-GA
1 GGTTAGGG-T----TTTTAAGTTAAGGGGTTAGGGTTTTTAATTAAATTA
*
464457 GGGTTAGGGTTTTTAAGTTTAGGGTTTTTAAGTTTAGGGTTTAGGGTTTTGAATTAAATTA
1 -GGTTAGGGTTTTTAAGTTAAGGG-------G-TTAGGG--T----TTTT-AATTAAATTA
* ** * *
464518 GGTTAGGG-TTTTAATTTAATTAGGTTATGGTTTTTAATTTAATTA
1 GGTTAGGGTTTTTAAGTTAA-GGGGTTAGGGTTTTTAATTAAATTA
* *
464563 GGTTAGGGTTTTTAAGTTTAGGGTTTAGGGTT
1 GGTTAGGGTTTTTAAGTTAAGGGGTTAGGGTT
464595 NNNNNNNNNN
Statistics
Matches: 209, Mismatches: 23, Indels: 90
0.65 0.07 0.28
Matches are distributed among these distances:
40 2 0.01
41 11 0.05
42 15 0.07
43 1 0.00
44 7 0.03
45 51 0.24
46 44 0.21
48 1 0.00
49 8 0.04
50 6 0.03
51 1 0.00
52 11 0.05
53 12 0.06
55 2 0.01
57 8 0.04
59 13 0.06
60 15 0.07
61 1 0.00
ACGTcount: A:0.26, C:0.00, G:0.27, T:0.47
Consensus pattern (45 bp):
GGTTAGGGTTTTTAAGTTAAGGGGTTAGGGTTTTTAATTAAATTA
Found at i:464352 original size:66 final size:65
Alignment explanation
Indices: 464231--464577 Score: 270
Period size: 66 Copynumber: 5.2 Consensus size: 65
464221 TTAACTTAGT
*
464231 TTAGGGGTTTTAATTAAATTAGGTTAGGGTTTTAAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTAAAGTTAAGGGTTAGGGTTTTTAAGTTAA-GG
464296 G
65 G
*
464297 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAAGTTAAGGTTTAGGG-TTTTAAGTTAAGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG-TTTTAAAGTTAAGGGTTAGGGTTTTTAAGTTAAGG
*
464361 T
65 G
*
464362 TTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTATTAATTAAATTAGGTTAGGGTTAGGG-
1 TTAGGGTTTTTAATT-AA--A--TTAG-GTTAGGGTT-TT-A--AAGTTA----AGGGTTAGGGT
*
464426 TTTTAA-TTAA--A
52 TTTTAAGTTAAGGG
* * * *
464437 TTAGGGTTTTTAATTTAA-GAGGGTTAGGG-TTT----TTAA-GTTTAGGGTTTTTAAGTTTAGG
1 TTAGGGTTTTTAATTAAATTA-GGTTAGGGTTTTAAAGTTAAGGGTTAGGGTTTTTAAGTTAAGG
464495 G
65 G
* * * * *
464496 TTTAGGGTTTTGAATTAAATTAGGTTAGGGTTTT-AATTTAATTAGGTTATGGTTTTTAATTTAA
1 -TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTAAAGTTAA--GGGTTAGGGTTTTTAAGTTAA
*
464560 TTAGG
63 --GGG
464565 TTAGGGTTTTTAA
1 TTAGGGTTTTTAA
464578 GTTTAGGGTT
Statistics
Matches: 230, Mismatches: 20, Indels: 60
0.74 0.06 0.19
Matches are distributed among these distances:
55 7 0.03
56 7 0.03
57 3 0.01
60 27 0.12
61 4 0.02
64 4 0.02
65 17 0.07
66 41 0.18
67 38 0.17
68 14 0.06
69 10 0.04
70 7 0.03
71 9 0.04
72 2 0.01
74 6 0.03
75 15 0.07
77 4 0.02
78 15 0.07
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (65 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTAAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGG
Found at i:464394 original size:29 final size:29
Alignment explanation
Indices: 464362--464441 Score: 135
Period size: 29 Copynumber: 2.8 Consensus size: 29
464352 AAGTTAAGGT
464362 TTAGGGTTTTTAATTAAATTAGGTTAGAG
1 TTAGGGTTTTTAATTAAATTAGGTTAGAG
* *
464391 TTAGGGTTATTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGAG
464420 TTAGGG-TTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
464442 GTTTTTAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
28 15 0.31
29 33 0.69
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (29 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGAG
Found at i:464480 original size:15 final size:15
Alignment explanation
Indices: 464460--464498 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
464450 TTTAAGAGGG
464460 TTAGGGTTTTTAAGT
1 TTAGGGTTTTTAAGT
464475 TTAGGGTTTTTAAGT
1 TTAGGGTTTTTAAGT
464490 TTAGGGTTT
1 TTAGGGTTT
464499 AGGGTTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.18, C:0.00, G:0.28, T:0.54
Consensus pattern (15 bp):
TTAGGGTTTTTAAGT
Found at i:464552 original size:82 final size:75
Alignment explanation
Indices: 464414--464558 Score: 184
Period size: 82 Copynumber: 1.8 Consensus size: 75
464404 TTAAATTAGG
*
464414 TTAGGGTTAGGGTTTTAATTAAATTAGGGTTTTTAATTTAAGAGGGTTAGGGTTTTTAAGTTTAG
1 TTAGGGTTAGGGTTTTAATTAAATTAGGGGTTTTAATTTAAGAGGGTTAGGGTTTTTAA-TTTAG
464479 GGTTTTTAAGT
65 GGTTTTTAAGT
* *
464490 TTAGGGTTTAGGGTTTTGAATTAAATTAGGTTAGGGTTTTAATTTAATTA-GGTTATGGTTTTTA
1 TTAGGG-TTAGGGTTTT-AATTAAATTA-G---GGGTTTTAATTTAA-GAGGGTTAGGGTTTTTA
464554 ATTTA
59 ATTTA
464559 ATTAGGTTAG
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
76 6 0.10
77 10 0.17
78 10 0.17
79 1 0.02
81 4 0.07
82 27 0.46
83 1 0.02
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (75 bp):
TTAGGGTTAGGGTTTTAATTAAATTAGGGGTTTTAATTTAAGAGGGTTAGGGTTTTTAATTTAGG
GTTTTTAAGT
Found at i:464568 original size:105 final size:106
Alignment explanation
Indices: 464391--464588 Score: 285
Period size: 105 Copynumber: 1.9 Consensus size: 106
464381 TAGGTTAGAG
**
464391 TTAGGGTTATTAATTAAATTAGGTTAGGGTTAGGGTTTTAATTAAATTAGGGTTTTTAATTTAAG
1 TTAGGGTTATTAATTAAATTAGGTTAGGGTTAGGAATTTAATTAAATTAGGGTTTTTAATTTAAG
464456 AGGGTTAGGGTTTTTAAGTTTAGGGTTTTTAAGTTTAGGGT
66 AGGGTTAGGGTTTTTAAGTTTAGGGTTTTTAAGTTTAGGGT
** ** *
464497 TTAGGGTT-TTGAATTAAATTAGGTTAGGGTT-TTAATTTAATTAGGTTATGGTTTTTAATTTAA
1 TTAGGGTTATT-AATTAAATTAGGTTAGGGTTAGGAATTTAATTAAATTAGGGTTTTTAATTTAA
*
464560 TTA-GGTTAGGGTTTTTAAGTTTAGGGTTT
65 -GAGGGTTAGGGTTTTTAAGTTTAGGGTTT
464589 AGGGTTNNNN
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
105 53 0.65
106 29 0.35
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (106 bp):
TTAGGGTTATTAATTAAATTAGGTTAGGGTTAGGAATTTAATTAAATTAGGGTTTTTAATTTAAG
AGGGTTAGGGTTTTTAAGTTTAGGGTTTTTAAGTTTAGGGT
Found at i:464575 original size:23 final size:23
Alignment explanation
Indices: 464221--464582 Score: 163
Period size: 23 Copynumber: 15.1 Consensus size: 23
464211 TGTACAATTA
* *
464221 TTAACTTAGTTTAGGGGTTTTAAT
1 TTAA-TTAGGTTAGGGTTTTTAAT
* * *
464245 TAAATTAGGTTAGGGTTTTAAAG
1 TTAATTAGGTTAGGGTTTTTAAT
* *
464268 TTAA--GGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
**
464289 TTAA-GGGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
*
464311 TAAATTAGGTTAGGGTTTTTAA-
1 TTAATTAGGTTAGGGTTTTTAAT
* *
464333 --AGTTAAGGTTTAGGG-TTTTAAG
1 TTAATT-AGG-TTAGGGTTTTTAAT
464355 TT-A--AGGTTTAGGGTTTTTAATT
1 TTAATTAGG-TTAGGGTTTTTAA-T
* *
464377 AAATTAGGTTAGAGTTAGGGTTATTAAT
1 ---TTA-ATTAG-GTTAGGGTTTTTAAT
* *****
464405 TAAATTAGGTTAGGGTTAGGGTT
1 TTAATTAGGTTAGGGTTTTTAAT
**
464428 TTAATTAAATTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
*
464451 TTAA-GAGGGTTAGGGTTTTTAAGT
1 TTAATTA-GGTTAGGGTTTTTAA-T
* *
464475 TTAGGGTTTTTAAGTTTAGGGTTTAGGGTTTTGAAT
1 TTA-----ATT-AGGTTAGGG--T----TTTT-AAT
*
464511 TAAATTAGGTTAGGG-TTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
*
464533 TTAATTAGGTTATGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
464556 TTAATTAGGTTAGGGTTTTTAAGT
1 TTAATTAGGTTAGGGTTTTTAA-T
464580 TTA
1 TTA
464583 GGGTTTAGGG
Statistics
Matches: 260, Mismatches: 43, Indels: 70
0.70 0.12 0.19
Matches are distributed among these distances:
20 13 0.05
21 34 0.13
22 42 0.16
23 108 0.42
24 15 0.06
25 4 0.02
28 1 0.00
29 14 0.05
30 16 0.06
31 3 0.01
32 1 0.00
36 7 0.03
37 2 0.01
ACGTcount: A:0.27, C:0.00, G:0.26, T:0.46
Consensus pattern (23 bp):
TTAATTAGGTTAGGGTTTTTAAT
Found at i:465143 original size:18 final size:18
Alignment explanation
Indices: 465120--465154 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
465110 CGGAAAAGGA
*
465120 TACATATAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
465138 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
465155 AAACGCACCT
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:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:465805 original size:7 final size:7
Alignment explanation
Indices: 465793--465824 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
465783 TTATACACAT
465793 AATACTA
1 AATACTA
465800 AATACTA
1 AATACTA
465807 AATACTA
1 AATACTA
465814 AATACTA
1 AATACTA
465821 AATA
1 AATA
465825 TCGATCCACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:466449 original size:11 final size:11
Alignment explanation
Indices: 466433--466476 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
466423 ATTTTTACGG
466433 TTTAAAAAAAT
1 TTTAAAAAAAT
466444 TTTAAAAAATATT
1 TTTAAAAAA-A-T
**
466457 TTTAAAATTAT
1 TTTAAAAAAAT
466468 TTTAAAAAA
1 TTTAAAAAA
466477 GGAACTTAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
11 17 0.63
12 2 0.07
13 8 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TTTAAAAAAAT
Found at i:466457 original size:12 final size:12
Alignment explanation
Indices: 466433--466476 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
466423 ATTTTTACGG
466433 TTTAAAAAA-AT
1 TTTAAAAAATAT
466444 TTTAAAAAATAT
1 TTTAAAAAATAT
* *
466456 TTTTAAAATTAT
1 TTTAAAAAATAT
466468 TTTAAAAAA
1 TTTAAAAAA
466477 GGAACTTAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 9 0.32
12 19 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TTTAAAAAATAT
Found at i:467133 original size:29 final size:28
Alignment explanation
Indices: 467085--467157 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 28
467075 TTAAATTTAT
**
467085 TAAAAAATATTAAAA-ATTATAAAAGTCA
1 TAAAAAATA-TAAAATATTATAAAAACCA
*
467113 TAAAAGAATATAAAATTTTATAAAAACCA
1 TAAAA-AATATAAAATATTATAAAAACCA
467142 TAAAAAATTATAAAAT
1 TAAAAAA-TATAAAAT
467158 GCATCAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
28 12 0.31
29 27 0.69
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29
Consensus pattern (28 bp):
TAAAAAATATAAAATATTATAAAAACCA
Found at i:468730 original size:3 final size:3
Alignment explanation
Indices: 468722--468769 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
468712 GTTGTGGTTT
468722 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
468770 GGGTTAAATG
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:470602 original size:9 final size:9
Alignment explanation
Indices: 470588--470612 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
470578 GATATAGAAA
470588 TAACATGTT
1 TAACATGTT
470597 TAACATGTT
1 TAACATGTT
470606 TAACATG
1 TAACATG
470613 CTTGTATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (9 bp):
TAACATGTT
Found at i:471555 original size:10 final size:11
Alignment explanation
Indices: 471530--471559 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
471520 ACTTTGAAAA
471530 AAAAATAAATT
1 AAAAATAAATT
471541 AAAAATAAATT
1 AAAAATAAATT
471552 AAAAATAA
1 AAAAATAA
471560 TATAATCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAAATAAATT
Found at i:471561 original size:25 final size:25
Alignment explanation
Indices: 471527--471574 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
471517 AGAACTTTGA
471527 AAAAAAAATA-AATTAAAAATAAATT
1 AAAAAAAATATAA-TAAAAATAAATT
* *
471552 AAAAATAATATAATCAAAATAAA
1 AAAAAAAATATAATAAAAATAAA
471575 CCCCTCCCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (25 bp):
AAAAAAAATATAATAAAAATAAATT
Found at i:477104 original size:20 final size:20
Alignment explanation
Indices: 477066--477104 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
477056 TTAAAAGTTT
* *
477066 ATAAAAGAAATTGTAAAAAG
1 ATAAAAAAAATTATAAAAAG
477086 ATAAAAAAAATTATTAAAA
1 ATAAAAAAAATTA-TAAAA
477105 TTTTACAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (20 bp):
ATAAAAAAAATTATAAAAAG
Found at i:477320 original size:20 final size:20
Alignment explanation
Indices: 477275--477311 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
477265 AAATCTCTCC
477275 AAAT-TACAAAATATAAAAT
1 AAATATACAAAATATAAAAT
*
477294 AAATATACAAATTATAAA
1 AAATATACAAAATATAAA
477312 TTTAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (20 bp):
AAATATACAAAATATAAAAT
Found at i:479972 original size:17 final size:17
Alignment explanation
Indices: 479940--479973 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
479930 AATAGAAAAA
479940 TAAGCATTTATTTTAAT
1 TAAGCATTTATTTTAAT
479957 TAAG-ATTTATTATTAAT
1 TAAGCATTTATT-TTAAT
479974 AAATAATAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (17 bp):
TAAGCATTTATTTTAAT
Found at i:506014 original size:2 final size:2
Alignment explanation
Indices: 506007--506050 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
505997 TTGCAATGGA
506007 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
506049 TC
1 TC
506051 AATGAATACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:509881 original size:21 final size:21
Alignment explanation
Indices: 509855--509898 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
509845 TATAAAGTGC
509855 GCTGCTCATTCAACATTCATA
1 GCTGCTCATTCAACATTCATA
509876 GCTGCTCATTCAACATTCATA
1 GCTGCTCATTCAACATTCATA
509897 GC
1 GC
509899 ATCTGTCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.30, G:0.11, T:0.32
Consensus pattern (21 bp):
GCTGCTCATTCAACATTCATA
Found at i:512033 original size:18 final size:18
Alignment explanation
Indices: 512010--512052 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
512000 TTAATTTCAG
*
512010 CATGCTGCCAGTCAAGAT
1 CATGCTGCCAATCAAGAT
**
512028 CATGCTGTTAATCAAGAT
1 CATGCTGCCAATCAAGAT
512046 CATGCTG
1 CATGCTG
512053 GTCTTGCTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (18 bp):
CATGCTGCCAATCAAGAT
Found at i:520219 original size:27 final size:27
Alignment explanation
Indices: 520189--520240 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
520179 TTTCCTTCCT
**
520189 TAGATCGCCACAAAGGCTTCCATTTCA
1 TAGATCGCCACAAAAACTTCCATTTCA
*
520216 TAGATTGCCACAAAAACTTCCATTT
1 TAGATCGCCACAAAAACTTCCATTT
520241 TCTAACGTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.29
Consensus pattern (27 bp):
TAGATCGCCACAAAAACTTCCATTTCA
Found at i:520966 original size:25 final size:25
Alignment explanation
Indices: 520933--520989 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 25
520923 AAATAAAGCC
*
520933 TTACCTTTTCATACATTCAAACAAT
1 TTACTTTTTCATACATTCAAACAAT
*
520958 TTACTTTTTCATACATTCAAGCAAT
1 TTACTTTTTCATACATTCAAACAAT
520983 TCTACTT
1 T-TACTT
520990 GTAAGGCCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 24 0.83
26 5 0.17
ACGTcount: A:0.32, C:0.23, G:0.02, T:0.44
Consensus pattern (25 bp):
TTACTTTTTCATACATTCAAACAAT
Found at i:525613 original size:7 final size:7
Alignment explanation
Indices: 525601--525641 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
525591 AGAGTATTGA
525601 ATGAAAT
1 ATGAAAT
525608 ATGAAAT
1 ATGAAAT
525615 ATGAAAT
1 ATGAAAT
525622 ATGAAAT
1 ATGAAAT
525629 ATGAAAT
1 ATGAAAT
525636 ATGAAA
1 ATGAAA
525642 AAGATTCTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.27
Consensus pattern (7 bp):
ATGAAAT
Found at i:526313 original size:22 final size:20
Alignment explanation
Indices: 526285--526327 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
526275 CCCCGAGCAA
526285 CTTTAAAATGATTTTAAATTAT
1 CTTTAAAAT-ATTTT-AATTAT
*
526307 CTTTAAAATCTTTTAATTAT
1 CTTTAAAATATTTTAATTAT
526327 C
1 C
526328 CAAAACTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 4 0.20
22 9 0.45
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.51
Consensus pattern (20 bp):
CTTTAAAATATTTTAATTAT
Found at i:526755 original size:41 final size:41
Alignment explanation
Indices: 526710--526794 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
526700 AATGAGATGT
*
526710 TTATGTTTGTTTTGGCTTGAACCTGTGTCAAACAATCTGGG
1 TTATGTTTGTTTTGGCTTGAACCCGTGTCAAACAATCTGGG
526751 TTATGTTTGTTTTGGCTTGAACCCGTGTCAAACAATCTGGG
1 TTATGTTTGTTTTGGCTTGAACCCGTGTCAAACAATCTGGG
526792 TTA
1 TTA
526795 GAGCCTAAGA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.41
Consensus pattern (41 bp):
TTATGTTTGTTTTGGCTTGAACCCGTGTCAAACAATCTGGG
Found at i:527491 original size:63 final size:63
Alignment explanation
Indices: 527414--527542 Score: 231
Period size: 63 Copynumber: 2.0 Consensus size: 63
527404 TCTTTTACTC
*
527414 CATTGATTATAGATAAGATAATAATCATTGTTTTTTATATACTAAAAAAGTTAATATATATTA
1 CATTGATTATAGATAAGATAATAATCATTGTTTTTTATATACTAAAAAAGTTAATATATATCA
* *
527477 CATTGATTATAGATAAGGTAATAATCATTGTTTTTTATATATTAAAAAAGTTAATATATATCA
1 CATTGATTATAGATAAGATAATAATCATTGTTTTTTATATACTAAAAAAGTTAATATATATCA
527540 CAT
1 CAT
527543 CATGTCATAC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (63 bp):
CATTGATTATAGATAAGATAATAATCATTGTTTTTTATATACTAAAAAAGTTAATATATATCA
Found at i:531056 original size:19 final size:19
Alignment explanation
Indices: 531029--531071 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
531019 TTTTATAATG
*
531029 TTTTTTATTGCAAT-TTTAA
1 TTTTATATTGC-ATGTTTAA
*
531048 TTTTATATTTCATGTTTAA
1 TTTTATATTGCATGTTTAA
531067 TTTTA
1 TTTTA
531072 GTTTTTATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.65
Consensus pattern (19 bp):
TTTTATATTGCATGTTTAA
Found at i:534412 original size:25 final size:25
Alignment explanation
Indices: 534384--534446 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
534374 TCCACCGCTC
*
534384 GTGAGAGCATACCAATTTATAGCTA
1 GTGAGAGCATACCAATCTATAGCTA
* *
534409 GTGAGAGCATACCGATCTATAGCTC
1 GTGAGAGCATACCAATCTATAGCTA
* *
534434 GAGTGAGCATACC
1 GTGAGAGCATACC
534447 GATTCACAGC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (25 bp):
GTGAGAGCATACCAATCTATAGCTA
Found at i:534447 original size:25 final size:24
Alignment explanation
Indices: 534388--534470 Score: 78
Period size: 25 Copynumber: 3.3 Consensus size: 24
534378 CCGCTCGTGA
* * * *
534388 GAGCATACCAATTTATAGCTAGTGA
1 GAGCATACCGA-TTATAGCTCGAGT
534413 GAGCATACCGATCTATAGCTCGAGT
1 GAGCATACCGAT-TATAGCTCGAGT
*
534438 GAGCATACCGATTCACAGCTCGTA-T
1 GAGCATACCGATT-ATAGCTCG-AGT
534463 GAGCATAC
1 GAGCATAC
534471 ATGTACATGA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
24 2 0.04
25 47 0.94
26 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (24 bp):
GAGCATACCGATTATAGCTCGAGT
Found at i:534659 original size:31 final size:32
Alignment explanation
Indices: 534624--534685 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
534614 TTTACATGAA
*
534624 ATACATGGAAAT-GATTTTACATG-ATATATAG
1 ATACAT-GAAATGGATGTTACATGTATATATAG
*
534655 ATACATGATATGGATGTTACATGTATATATA
1 ATACATGAAATGGATGTTACATGTATATATA
534686 AACTTGATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 4 0.15
31 16 0.59
32 7 0.26
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.37
Consensus pattern (32 bp):
ATACATGAAATGGATGTTACATGTATATATAG
Found at i:538972 original size:90 final size:92
Alignment explanation
Indices: 538834--539010 Score: 245
Period size: 90 Copynumber: 1.9 Consensus size: 92
538824 GCTTAATTGC
* * *
538834 TATTTTGAAAAATTTTGAGGCTCTTTTTGATGCACTTTGAAAGTTCAAGTACTCAATTGAGTG-A
1 TATTTTGAAAAAGTTTAAGGCTCTTTTTGATACACTTTGAAAGTTCAAGTACTCAATTGAGTGAA
*
538898 -AAAAAAATAGGGGCTTAATTGCTTTT
66 GAAAAAAAAAGGGGCTTAATTGCTTTT
* *
538924 TATTTTGAAGAAGTTTAAGGGC-CTTTTTGATACA-TGTTGAAAGTTCAAGTGCTCAATTGAGTG
1 TATTTTGAAAAAGTTTAA-GGCTCTTTTTGATACACT-TTGAAAGTTCAAGTACTCAATTGAGTG
538987 CAAGAAAAAAAAAGGGGCTTAATT
64 -AAGAAAAAAAAAGGGGCTTAATT
539011 ATTATTATTT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
89 1 0.01
90 52 0.68
91 3 0.04
92 1 0.01
93 19 0.25
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.36
Consensus pattern (92 bp):
TATTTTGAAAAAGTTTAAGGCTCTTTTTGATACACTTTGAAAGTTCAAGTACTCAATTGAGTGAA
GAAAAAAAAAGGGGCTTAATTGCTTTT
Found at i:555100 original size:17 final size:17
Alignment explanation
Indices: 555080--555177 Score: 53
Period size: 17 Copynumber: 5.8 Consensus size: 17
555070 TATTTTAATA
555080 AATTTAATATTTAATTT
1 AATTTAATATTTAATTT
*
555097 AATTTAATACTT-ATCTT
1 AATTTAATATTTAAT-TT
* * *
555114 GATTT--TTTTTTA-TT
1 AATTTAATATTTAATTT
*
555128 AATTTAATATTAAAATGATT
1 AATTTAATATT-TAAT--TT
* *
555148 -ATCTTATTATTAAATTT
1 AAT-TTAATATTTAATTT
555165 AATTTAATATTTA
1 AATTTAATATTTA
555178 TCTTTTAGAT
Statistics
Matches: 60, Mismatches: 11, Indels: 20
0.66 0.12 0.22
Matches are distributed among these distances:
14 6 0.10
15 3 0.05
16 6 0.10
17 28 0.47
18 2 0.03
19 6 0.10
20 9 0.15
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (17 bp):
AATTTAATATTTAATTT
Found at i:555262 original size:58 final size:60
Alignment explanation
Indices: 555155--555267 Score: 149
Period size: 58 Copynumber: 1.9 Consensus size: 60
555145 ATTATCTTAT
* * *
555155 TATTAAATTTAATTTAATATTTATCTTTTAGATAAATATTCTATTAATTTAATATATTTAA
1 TATTAAATTTAATCTAATACTTA-CTTTTAGATAAATATTATATTAATTTAATATATTTAA
* * *
555216 TATTGAATTTAATCTAATACTTA-TTTT-GATAAGTTTTATATTAATTTAATAT
1 TATTAAATTTAATCTAATACTTACTTTTAGATAAATATTATATTAATTTAATAT
555268 TGAAGTGATT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
58 22 0.48
59 4 0.09
61 20 0.43
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (60 bp):
TATTAAATTTAATCTAATACTTACTTTTAGATAAATATTATATTAATTTAATATATTTAA
Found at i:558072 original size:52 final size:49
Alignment explanation
Indices: 558007--558118 Score: 143
Period size: 52 Copynumber: 2.2 Consensus size: 49
557997 AGCGATTATC
* * * *
558007 TTAATATTAAATTTAATTTAATAATTATCTTGTATATAGATATTCTATTACT
1 TTAATATTAAATTTAATCTAATAATTATC-TGGATA-AG-TATTATATTAAT
* *
558059 TTGATATTAAATTTAATCTAATATTTATCTGGATAAGTATTATATTAAT
1 TTAATATTAAATTTAATCTAATAATTATCTGGATAAGTATTATATTAAT
558108 TTAATATTAAA
1 TTAATATTAAA
558119 GTGATTAAGT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
49 20 0.38
50 2 0.04
51 5 0.09
52 26 0.49
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.50
Consensus pattern (49 bp):
TTAATATTAAATTTAATCTAATAATTATCTGGATAAGTATTATATTAAT
Found at i:562816 original size:32 final size:32
Alignment explanation
Indices: 562780--562842 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
562770 TTTGTTATTT
562780 TTTATTAATTAAGTTTACTAATTACTTGTAGC
1 TTTATTAATTAAGTTTACTAATTACTTGTAGC
*
562812 TTTATTAATTAAGTTTACTAATTTCTTGTAG
1 TTTATTAATTAAGTTTACTAATTACTTGTAG
562843 ATTTCAATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.30, C:0.08, G:0.10, T:0.52
Consensus pattern (32 bp):
TTTATTAATTAAGTTTACTAATTACTTGTAGC
Found at i:563970 original size:5 final size:5
Alignment explanation
Indices: 563960--563985 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
563950 CTACTTTAGA
563960 TTTAT TTTAT TTTAT TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT T
563986 ATTTTTTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:566727 original size:34 final size:34
Alignment explanation
Indices: 566684--566750 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
566674 GTTAGGAGTA
*
566684 TTACATTTAGTGGTATCAGAGCTTCAATTTAGTG
1 TTACATTTAGTGGTATCAAAGCTTCAATTTAGTG
*
566718 TTACATTTAGTGGTATCAAAGCTTCGATTTAGT
1 TTACATTTAGTGGTATCAAAGCTTCAATTTAGT
566751 CGATTCTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (34 bp):
TTACATTTAGTGGTATCAAAGCTTCAATTTAGTG
Found at i:573009 original size:107 final size:107
Alignment explanation
Indices: 572813--573014 Score: 264
Period size: 107 Copynumber: 1.9 Consensus size: 107
572803 TAGTGTTTAA
* * * **
572813 ATGTAAGACCATAGCTGGGCTATGGCATTTTAATTAAAAGACCATAACTGGGTTATGGCACCTTG
1 ATGTAAGACCATAGCTGGGCTATGGCATTCTAATGAAAAGACCATAACTGGGTTATGGCAACTCA
**
572878 AACATAAGACCATGGTTGGACCATGGCAATATATATATATAT
66 AACATAAGACCATGGAAGGACCATGGCAATATATATATATAT
* * *
572920 ATGTAAGACCATAGCTGGGCTGTGGCATTCTGATGATAAGACCATAACTGGGTTATGG-AACTAC
1 ATGTAAGACCATAGCTGGGCTATGGCATTCTAATGAAAAGACCATAACTGGGTTATGGCAACT-C
* *
572984 AAACGTAAGACCATGGCAAGG-CCATGTCAAT
65 AAACATAAGACCATGG-AAGGACCATGGCAAT
573015 GCATGTGTAA
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
106 3 0.04
107 76 0.94
108 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (107 bp):
ATGTAAGACCATAGCTGGGCTATGGCATTCTAATGAAAAGACCATAACTGGGTTATGGCAACTCA
AACATAAGACCATGGAAGGACCATGGCAATATATATATATAT
Found at i:582206 original size:26 final size:26
Alignment explanation
Indices: 582174--582247 Score: 105
Period size: 26 Copynumber: 2.8 Consensus size: 26
582164 ACGCACCAAC
582174 ATCGCAGTAAAGCTGCCAGTAATAGT
1 ATCGCAGTAAAGCTGCCAGTAATAGT
* * *
582200 ATTGCAGCAAGGCTGCCAGTAATAGT
1 ATCGCAGTAAAGCTGCCAGTAATAGT
582226 ATCGCAGT-AAGTCTGCCAGTAA
1 ATCGCAGTAAAG-CTGCCAGTAA
582248 CAATATATGT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
25 2 0.05
26 39 0.95
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.23
Consensus pattern (26 bp):
ATCGCAGTAAAGCTGCCAGTAATAGT
Found at i:582447 original size:27 final size:27
Alignment explanation
Indices: 582417--582475 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
582407 AATCTTCTAG
*
582417 GGGTACAACAGTCATTTTACCCTATGA
1 GGGTACAACAGTCATTTTACCCTACGA
*** *
582444 GGGTATTTCGGTCATTTTACCCTACGA
1 GGGTACAACAGTCATTTTACCCTACGA
582471 GGGTA
1 GGGTA
582476 TTTCGGTTGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (27 bp):
GGGTACAACAGTCATTTTACCCTACGA
Found at i:582489 original size:27 final size:27
Alignment explanation
Indices: 582427--582482 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
582417 GGGTACAACA
*
582427 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTACGAGGGTATTTCG
582454 GTCATTTTACCCTACGAGGGTATTTCG
1 GTCATTTTACCCTACGAGGGTATTTCG
582481 GT
1 GT
582483 TGTTTTATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (27 bp):
GTCATTTTACCCTACGAGGGTATTTCG
Found at i:593671 original size:21 final size:21
Alignment explanation
Indices: 593637--593689 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
593627 GTTGTAAGAC
*
593637 ATTTCTAGATTTAGTTTAATGT
1 ATTTC-AGTTTTAGTTTAATGT
593659 ATTTCAGTTTTAGTTTAATGT
1 ATTTCAGTTTTAGTTTAATGT
593680 ATTTCAGTTT
1 ATTTCAGTTT
593690 CTTTTATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 25 0.83
22 5 0.17
ACGTcount: A:0.25, C:0.06, G:0.13, T:0.57
Consensus pattern (21 bp):
ATTTCAGTTTTAGTTTAATGT
Found at i:598300 original size:70 final size:70
Alignment explanation
Indices: 598135--598288 Score: 281
Period size: 70 Copynumber: 2.2 Consensus size: 70
598125 GGTATATGGC
* **
598135 ATGTATAGGCTAGTGTCAATAGGATACATTTTGAGATATGAAATTAGTTATGTGAGTTGGCTTGT
1 ATGTATAGGCTAGTGTCAATAGGATACGTTTTGAGATATGAAATTAGCCATGTGAGTTGGCTTGT
598200 AAATG
66 AAATG
598205 ATGTATAGGCTAGTGTCAATAGGATACGTTTTGAGATATGAAATTAGCCATGTGAGTTGGCTTGT
1 ATGTATAGGCTAGTGTCAATAGGATACGTTTTGAGATATGAAATTAGCCATGTGAGTTGGCTTGT
598270 AAATG
66 AAATG
598275 ATGTATAGGCTAGT
1 ATGTATAGGCTAGT
598289 TTATTATGGA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 81 1.00
ACGTcount: A:0.31, C:0.07, G:0.27, T:0.36
Consensus pattern (70 bp):
ATGTATAGGCTAGTGTCAATAGGATACGTTTTGAGATATGAAATTAGCCATGTGAGTTGGCTTGT
AAATG
Found at i:600452 original size:29 final size:29
Alignment explanation
Indices: 600410--600468 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
600400 TTATTGATAG
600410 TAAGGGTCGATTCTAGGTAATCCCGACCT
1 TAAGGGTCGATTCTAGGTAATCCCGACCT
*
600439 TAAGGGTCGATTCTGGGTAATCCCGACCT
1 TAAGGGTCGATTCTAGGTAATCCCGACCT
600468 T
1 T
600469 CCGAATCAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (29 bp):
TAAGGGTCGATTCTAGGTAATCCCGACCT
Found at i:605195 original size:20 final size:21
Alignment explanation
Indices: 605155--605200 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
605145 GTATAAATAC
605155 CCCCTTTTTATGTGTAATTTG
1 CCCCTTTTTATGTGTAATTTG
* *
605176 CCCCTTTTTTTG-GTATTTTG
1 CCCCTTTTTATGTGTAATTTG
605196 CCCCT
1 CCCCT
605201 AATAATACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.09, C:0.26, G:0.13, T:0.52
Consensus pattern (21 bp):
CCCCTTTTTATGTGTAATTTG
Found at i:614041 original size:26 final size:26
Alignment explanation
Indices: 614011--614063 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
614001 TATGATAGTA
614011 TGACTTTGGAAGATTATACACTTAAC
1 TGACTTTGGAAGATTATACACTTAAC
614037 TGACTTTGGAAGATTATACACTTAAC
1 TGACTTTGGAAGATTATACACTTAAC
614063 T
1 T
614064 AATCTTTGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (26 bp):
TGACTTTGGAAGATTATACACTTAAC
Found at i:616037 original size:3 final size:3
Alignment explanation
Indices: 616031--616063 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
616021 ATAAAATCTC
616031 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
616064 TTGGGAAGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (3 bp):
CTG
Found at i:628106 original size:3 final size:3
Alignment explanation
Indices: 628098--628135 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
628088 TAATATAGGG
628098 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
628136 TAATAATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:628232 original size:17 final size:17
Alignment explanation
Indices: 628206--628243 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
628196 GTAGTAAAAG
*
628206 TAAAATAAAA-AATACAA
1 TAAAAGAAAATAATA-AA
628223 TAAAAGAAAATAATAAA
1 TAAAAGAAAATAATAAA
628240 TAAA
1 TAAA
628244 TGTGAAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (17 bp):
TAAAAGAAAATAATAAA
Found at i:629190 original size:16 final size:17
Alignment explanation
Indices: 629171--629203 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
629161 TAAACAGAAT
*
629171 AAACAGA-AAACGAAAA
1 AAACAGAGAAAAGAAAA
629187 AAACAGAGAAAAGAAAA
1 AAACAGAGAAAAGAAAA
629204 GAGAGCAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.76, C:0.09, G:0.15, T:0.00
Consensus pattern (17 bp):
AAACAGAGAAAAGAAAA
Found at i:629983 original size:41 final size:41
Alignment explanation
Indices: 629880--630132 Score: 155
Period size: 41 Copynumber: 5.8 Consensus size: 41
629870 AGTAGCTTTA
* * * * *
629880 ATCTGCTCCACTGCAACTCCAGGGATATAAGATTGGTATATTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTG-ATA-T-G
* * *
629924 ACCTGCTCCATTACAACTTCAGGGAGATAAGGTTTGATATG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGATATG
** * * *
629965 ATCTGCTTTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAG----GT--TTGATA---T-G
* * * * * *
630016 ATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTC
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTG--AT-ATG
*
630060 AGTCTGCTCCACTGTAACTTCAGGGAGATAAGGTTTGATATG
1 A-TCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGATATG
* *
630102 ATCTGCTCTACTGCAACTTCAGAGAGATAAG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAG
630133 ATCTGCAATT
Statistics
Matches: 159, Mismatches: 36, Indels: 31
0.70 0.16 0.14
Matches are distributed among these distances:
41 52 0.33
42 3 0.02
43 5 0.03
44 30 0.19
45 34 0.21
47 8 0.05
50 1 0.01
51 26 0.16
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (41 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGATATG
Found at i:630079 original size:45 final size:45
Alignment explanation
Indices: 629879--630726 Score: 311
Period size: 44 Copynumber: 18.8 Consensus size: 45
629869 TAGTAGCTTT
* * * *
629879 AATCTGCTCCACTGCAACTCCAGGGATATAAGATT-GGTATATTC
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTC
* * * * * * *
629923 AACCTGCTCCATTACAACTTCAGGGAGATAAGGTTTG--AT-AT-
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTC
* ** * * *
629964 GATCTGCTTTACTGCAACTTCAGAGAGATAAGA-TCTGTAATTTATAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTC-G----CTAT--CTTC
*
630015 AATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTC
* * * * * *
630060 AGTCTGCTCCACTGTAACTTCAGGGAGATAAGGTTTG--AT-AT-
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTC
* * * *
630101 GATCTGCTCTACTGCAACTTCAGAGAGATAAGA-TCTGCAATTTATAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTC-GC----TAT--CTTC
* * * * *
630152 AATTTGTTTCACTGCAACTTCAGGGGAATAAGATTCACTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTC
* * * *
630197 AGTCTGTTCCACTGCAACTTCAGAGAAATAAGACTT-G-TAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGA-TTCGCTATCTTC
* * * * * * * *
630241 AACCCGCTCCACTACAAATTCAGGGAGATAAGGTTTG--AT-AT-
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTC
* * *
630282 GATCTGCTCTACTGCAACTTCA-GAAAGATAAGA-TCTGCAATTTATAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAA-ATAAGATTC-GC----TAT--CTTC
* * * * *
630333 AATTTGTTTCACTGCAATTTCAGGGAAATAAGATTCACTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTC
* * * *
630378 AGTCTCCTCCACTGCAACTTCAGGGAAATAAGACTT-G-TAACTAC
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGA-TTCGCTATCTTC
* * * * * *
630422 AA-CTGGCTCCACTACAACTTCAAGGAGATAAGGCTT-AC-AACTTC
1 AATCT-GCTCCACTGCAACTTCAGGGAAATAA-GATTCGCTATCTTC
* * * * *
630466 AACCTGCTCCACTGTAACTTCAAGGAGATAACG-TTTGCTA---T-
1 AATCTGCTCCACTGCAACTTCAGGGAAATAA-GATTCGCTATCTTC
* ** * * *
630507 GATCTGCTCCACTGCAACTTCAGATAGATAAGA-TCTGTTATTTAGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTC-GCTA--T--CTTC
* * * *
630556 AATCCGTTCCACTACAACTTCAGGGAAATAATATTCGCTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTC
* * ** * * *
630601 AGTCTGCTCCACTGCAACTTCGGGGAGCTAAGAGTAG-TAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTC
* * * * * * **
630645 AACCTGTTCCACTGCAACTTCAGGGAGATACGACTAG-TGGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTC
* * * *
630689 AATCTACTCCACTACAACTTCAAGGAGATAAGATTCGC
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGC
630727 CATGATGACT
Statistics
Matches: 592, Mismatches: 152, Indels: 119
0.69 0.18 0.14
Matches are distributed among these distances:
40 7 0.01
41 104 0.18
42 4 0.01
43 11 0.02
44 193 0.33
45 133 0.22
46 4 0.01
47 16 0.03
48 1 0.00
49 28 0.05
50 5 0.01
51 77 0.13
52 9 0.02
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (45 bp):
AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTC
Found at i:630117 original size:137 final size:137
Alignment explanation
Indices: 629872--630228 Score: 527
Period size: 137 Copynumber: 2.6 Consensus size: 137
629862 CTAGAATTAG
* * * * * * ** *
629872 TAGCTTTAATCTGCTCCACTGCAACTCCAGGGATATAAGATT-GGTATATTCAACCTGCTCCATT
1 TAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACT
* *
629936 ACAACTTCAGGGAGATAAGGTTTGATATGATCTGCTTTACTGCAACTTCAGAGAGATAAGATCTG
66 GCAACTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTG
*
630001 TAATTTA
131 CAATTTA
630008 TAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACT
1 TAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACT
*
630073 GTAACTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTG
66 GCAACTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTG
630138 CAATTTA
131 CAATTTA
* * * * *
630145 TAGCTTCAATTTGTTTCACTGCAACTTCAGGGGAATAAGATTCACTATCTTCAGTCTGTTCCACT
1 TAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACT
* *
630210 GCAACTTCAGAGAAATAAG
66 GCAACTTCAGGGAGATAAG
630229 ACTTGTAACT
Statistics
Matches: 199, Mismatches: 21, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
136 38 0.19
137 161 0.81
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (137 bp):
TAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACT
GCAACTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTG
CAATTTA
Found at i:630183 original size:92 final size:92
Alignment explanation
Indices: 630069--630364 Score: 313
Period size: 92 Copynumber: 3.2 Consensus size: 92
630059 CAGTCTGCTC
*
630069 CACTGTAACTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGA
1 CACTGCAACTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGA
630134 TCTGCAATTTATAGCTTCAATTTGTTT
66 TCTGCAATTTATAGCTTCAATTTGTTT
* * * * * *
630161 CACTGCAACTTCAGGG-GAATAAGATTCACT-ATCTTCAGTCTGTTCCACTGCAACTTCAGAGAA
1 CACTGCAACTTCAGGGAG-ATAAGGTT---TGAT-ATGA-TCTGCTCTACTGCAACTTCAGAGAG
* *** * *
630224 ATAAGA-CT----TGTA-A-CTTCAACCCGCTC
60 ATAAGATCTGCAATTTATAGCTTCAATTTGTTT
* * *
630250 CACTACAAATTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAAAGATAAGA
1 CACTGCAACTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGA
630315 TCTGCAATTTATAGCTTCAATTTGTTT
66 TCTGCAATTTATAGCTTCAATTTGTTT
* *
630342 CACTGCAATTTCAGGGAAATAAG
1 CACTGCAACTTCAGGGAGATAAG
630365 ATTCACTATC
Statistics
Matches: 158, Mismatches: 31, Indels: 30
0.72 0.14 0.14
Matches are distributed among these distances:
85 27 0.17
86 5 0.03
87 2 0.01
89 29 0.18
90 5 0.03
91 5 0.03
92 50 0.32
94 2 0.01
95 5 0.03
96 28 0.18
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (92 bp):
CACTGCAACTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGA
TCTGCAATTTATAGCTTCAATTTGTTT
Found at i:630280 original size:181 final size:181
Alignment explanation
Indices: 630011--630454 Score: 701
Period size: 181 Copynumber: 2.4 Consensus size: 181
630001 TAATTTATAG
* * ** * **
630011 CTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGA-TTCGCTATCTTCAGTCTGCTCCACTGT
1 CTTCAGTCTGTTCCACTGCAACTTCAGGGAAATAAGACTT-G-TAACTTCAACCCGCTCCACTAC
*
630075 AACTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCA
64 AACTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAAAGATAAGATCTGCA
*
630140 ATTTATAGCTTCAATTTGTTTCACTGCAACTTCAGGGGAATAAGATTCACTAT
129 ATTTATAGCTTCAATTTGTTTCACTGCAACTTCAGGGAAATAAGATTCACTAT
*
630193 CTTCAGTCTGTTCCACTGCAACTTCAGAGAAATAAGACTTGTAACTTCAACCCGCTCCACTACAA
1 CTTCAGTCTGTTCCACTGCAACTTCAGGGAAATAAGACTTGTAACTTCAACCCGCTCCACTACAA
*
630258 ATTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAAAGATAAGATCTGCAAT
66 CTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAAAGATAAGATCTGCAAT
*
630323 TTATAGCTTCAATTTGTTTCACTGCAATTTCAGGGAAATAAGATTCACTAT
131 TTATAGCTTCAATTTGTTTCACTGCAACTTCAGGGAAATAAGATTCACTAT
** * **
630374 CTTCAGTCTCCTCCACTGCAACTTCAGGGAAATAAGACTTGTAACTACAACTGGCTCCACTACAA
1 CTTCAGTCTGTTCCACTGCAACTTCAGGGAAATAAGACTTGTAACTTCAACCCGCTCCACTACAA
*
630439 CTTCAAGGAGATAAGG
66 CTTCAGGGAGATAAGG
630455 CTTACAACTT
Statistics
Matches: 241, Mismatches: 20, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
181 203 0.84
182 36 0.15
183 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (181 bp):
CTTCAGTCTGTTCCACTGCAACTTCAGGGAAATAAGACTTGTAACTTCAACCCGCTCCACTACAA
CTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAGAAAGATAAGATCTGCAAT
TTATAGCTTCAATTTGTTTCACTGCAACTTCAGGGAAATAAGATTCACTAT
Found at i:630410 original size:96 final size:96
Alignment explanation
Indices: 630103--630410 Score: 327
Period size: 96 Copynumber: 3.3 Consensus size: 96
630093 TTTGATATGA
* *
630103 TCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCAATTTATAGCTTCAATTTGTTTCACTGCA
1 TCTGCTCCACTGCAACTTCAGAGAAATAAGATCTGCAATTTATAGCTTCAATTTGTTTCACTGCA
* *
630168 ACTTCAGGGGAATAAGATTCACTATCTTCAG
66 AATTCAGGGAAATAAGATTCACTATCTTCAG
* * *** * * *
630199 TCTGTTCCACTGCAACTTCAGAGAAATAAGA-CT----TGTA-A-CTTCAACCCGCTCCACTACA
1 TCTGCTCCACTGCAACTTCAGAGAAATAAGATCTGCAATTTATAGCTTCAATTTGTTTCACTGCA
* * * *
630257 AATTCAGGGAGATAAGGTT---TGAT-ATGA-
66 AATTCAGGGAAATAAGATTCACT-ATCTTCAG
*
630284 TCTGCTCTACTGCAACTTCAGA-AAGATAAGATCTGCAATTTATAGCTTCAATTTGTTTCACTGC
1 TCTGCTCCACTGCAACTTCAGAGAA-ATAAGATCTGCAATTTATAGCTTCAATTTGTTTCACTGC
*
630348 AATTTCAGGGAAATAAGATTCACTATCTTCAG
65 AAATTCAGGGAAATAAGATTCACTATCTTCAG
* *
630380 TCTCCTCCACTGCAACTTCAGGGAAATAAGA
1 TCTGCTCCACTGCAACTTCAGAGAAATAAGA
630411 CTTGTAACTA
Statistics
Matches: 164, Mismatches: 33, Indels: 30
0.72 0.15 0.13
Matches are distributed among these distances:
84 2 0.01
85 26 0.16
86 5 0.03
87 2 0.01
89 29 0.18
90 4 0.02
91 4 0.02
92 30 0.18
94 2 0.01
95 5 0.03
96 53 0.32
97 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (96 bp):
TCTGCTCCACTGCAACTTCAGAGAAATAAGATCTGCAATTTATAGCTTCAATTTGTTTCACTGCA
AATTCAGGGAAATAAGATTCACTATCTTCAG
Found at i:630701 original size:223 final size:224
Alignment explanation
Indices: 630161--630719 Score: 647
Period size: 223 Copynumber: 2.5 Consensus size: 224
630151 CAATTTGTTT
* * * * * * * *
630161 CACTGCAACTTCAGGGGAATAAGATTCACTATCTTCAGTCTGTTCCACTGCAACTTCAGAGAAAT
1 CACTGCAACTTCAGGGAAATAAGACT-AGTAACTACA-ACTGTTCCACTGCAACTTCAGGGAGAT
* * * * *
630226 AAGACTTGTAACTTCAACCCGCTCCACTACAAATTCAGGGAGATAAGGTTTGATATGATCTGCTC
64 AAGACTAGTAACTTCAACCTGCTCCACTACAACTTCAAGGAGATAACGTTTGATATGATCTGCTC
* ** * * *
630291 TACTGCAACTTCAGAAAGATAAGATCTGCAATTTATAGCTTCAATTTGTTTCACTGCAATTTCAG
129 CACTGCAACTTCAGAAAGATAAGATCTGCAATTTATAGCTTCAATCCGTTCCACTACAACTTCAG
630356 GGAAATAAGATTCACTATCTTCAGTCTCCTC
194 GGAAATAAGATTCACTATCTTCAGTCTCCTC
* * * *
630387 CACTGCAACTTCAGGGAAATAAGACTTGTAACTACAACTGGCTCCACTACAACTTCAAGGAGATA
1 CACTGCAACTTCAGGGAAATAAGACTAGTAACTACAACT-GTTCCACTGCAACTTCAGGGAGATA
* * ** *
630452 AGGCTTA-CAACTTCAACCTGCTCCACTGTAACTTCAAGGAGATAACGTTTGCTATGATCTGCTC
65 AGAC-TAGTAACTTCAACCTGCTCCACTACAACTTCAAGGAGATAACGTTTGATATGATCTGCTC
* ** *
630516 CACTGCAACTTCAGATAGATAAGATCTGTTA-TT-TAGCTTTAATCCGTTCCACTACAACTTCAG
129 CACTGCAACTTCAGAAAGATAAGATCTGCAATTTATAGCTTCAATCCGTTCCACTACAACTTCAG
* * *
630579 GGAAATAATATTCGCTATCTTCAGTCTGCTC
194 GGAAATAAGATTCACTATCTTCAGTCTCCTC
* ** * *
630610 CACTGCAACTTCGGGGAGCTAAGAGTAGTAACTTCAACCTGTTCCACTGCAACTTCAGGGAGATA
1 CACTGCAACTTCAGGGAAATAAGACTAGTAACTACAA-CTGTTCCACTGCAACTTCAGGGAGATA
* ** * *
630675 CGACTAGTGGCTTCAATCTACTCCACTACAACTTCAAGGAGATAA
65 AGACTAGTAACTTCAACCTGCTCCACTACAACTTCAAGGAGATAA
630720 GATTCGCCAT
Statistics
Matches: 276, Mismatches: 53, Indels: 11
0.81 0.16 0.03
Matches are distributed among these distances:
222 2 0.01
223 138 0.50
224 6 0.02
225 105 0.38
226 25 0.09
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (224 bp):
CACTGCAACTTCAGGGAAATAAGACTAGTAACTACAACTGTTCCACTGCAACTTCAGGGAGATAA
GACTAGTAACTTCAACCTGCTCCACTACAACTTCAAGGAGATAACGTTTGATATGATCTGCTCCA
CTGCAACTTCAGAAAGATAAGATCTGCAATTTATAGCTTCAATCCGTTCCACTACAACTTCAGGG
AAATAAGATTCACTATCTTCAGTCTCCTC
Found at i:631613 original size:5 final size:5
Alignment explanation
Indices: 631594--631641 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
631584 GGCCTCTCCT
* *
631594 TTTTCC TTTCC TTTTC -TTT- TTTTC TTTTT TTTTC TTTTC TTTTC TTTT
1 TTTT-C TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
631642 TTAAAAGTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
4 6 0.17
5 27 0.75
6 3 0.08
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:631614 original size:18 final size:18
Alignment explanation
Indices: 631593--631631 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
631583 TGGCCTCTCC
631593 TTTTTCCTTTCCTTTTCT
1 TTTTTCCTTTCCTTTTCT
* **
631611 TTTTTTCTTTTTTTTTCT
1 TTTTTCCTTTCCTTTTCT
631629 TTT
1 TTT
631632 CTTTTCTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTCCTTTCCTTTTCT
Found at i:635068 original size:17 final size:17
Alignment explanation
Indices: 635042--635079 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
635032 GTAGTGAAAT
*
635042 TAAAATAAAA-AATACAA
1 TAAAAGAAAATAATA-AA
635059 TAAAAGAAAATAATAAA
1 TAAAAGAAAATAATAAA
635076 TAAA
1 TAAA
635080 TAAATGTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (17 bp):
TAAAAGAAAATAATAAA
Found at i:635071 original size:22 final size:21
Alignment explanation
Indices: 635043--635083 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
635033 TAGTGAAATT
635043 AAAATAAAAAATACAATAAAAG
1 AAAATAAAAAATA-AATAAAAG
*
635065 AAAATAATAAATAAATAAA
1 AAAATAAAAAATAAATAAA
635084 TGTGAAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.17
Consensus pattern (21 bp):
AAAATAAAAAATAAATAAAAG
Found at i:637533 original size:12 final size:12
Alignment explanation
Indices: 637513--637559 Score: 67
Period size: 12 Copynumber: 3.8 Consensus size: 12
637503 GTAGTGAAAT
637513 TAAAATAAAAAA
1 TAAAATAAAAAA
* *
637525 TACAATAAAAAG
1 TAAAATAAAAAA
637537 TAAAATAAAAAAA
1 TAAAAT-AAAAAA
637550 TAAAATAAAA
1 TAAAATAAAA
637560 GGAAATAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
12 19 0.63
13 11 0.37
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (12 bp):
TAAAATAAAAAA
Done.