Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008515.1 Hibiscus syriacus cultivar Beakdansim tig00111378_pilon, 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: 337978
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:198143 original size:150 final size:154
Alignment explanation
Indices: 197851--198357 Score: 528
Period size: 150 Copynumber: 3.3 Consensus size: 154
197841 CATTTTTCTC
* * * * *
197851 CAAATTTGAACCACATGCTCCTAAACCATAACACAATACATGTTTACTTTCAATTCCTATTTTTG
1 CAAATTTGAGCCACATGCTCCTAAACCATAATAGAATACATGTGTACTTTCAATTCCT-CTTTT-
* * * *
197916 ATGACAAAGTTTTATTTTTCAATTTAGTCCTTTAATTTTTCATAATCTCCTTATTTCTTCAATTC
64 AT---AAATTTTTATTTTTCAATTTAGTCCTTCAATTTTTTATAATCTCCTTATTTCCTCAATTC
* *
197981 ATCATTTATTTTAAATCCGTTTTTTTACT
126 GTCATTTATTTTAAATCCGTTTTTTTAAT
* ** * *
198010 -AGATTTGATTCGCATGCTCCTAAACCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTT-T
1 CAAATTTGAGCCACATGCTCCTAAACCATAATAGAATACATGTGTACTTTCAATTCCTCTTTTAT
* * *
198073 -AA-TTTTAATTTTCAATTTAATCCTTCAATTTTTTATAATCTCCTTATTTCCTCAACTCGTCAT
66 AAATTTTTATTTTTCAATTTAGTCCTTCAATTTTTTATAATCTCCTTATTTCCTCAATTCGTCAT
** *
198136 TTATTTTATGTCCCATTTTTTTTAAT
131 TTATTTTAAAT-CC-GTTTTTTTAAT
* * *
198162 CAAATTTGAGCCACATGCTCCTCAACCATATTGGAATACATGTGTACTTTCAATTCCTCTTTTTG
1 CAAATTTGAGCCACATGCTCCTAAACCATAATAGAATACATGTGTACTTTCAATTCCTC-TTTT-
198227 ATAACAATTTTTTATTTTTCAATTTAGTCCTTCAATTTTTCT-TAATCTCCTTA-TTCCTTCAAT
64 AT-A-AA-TTTTTATTTTTCAATTTAGTCCTTCAATTTTT-TATAATCTCCTTATTTCC-TCAAT
* * *
198290 TTGTCATTTATTTTAAGAT-CG--TTTTTCAC
124 TCGTCATTTATTTTAA-ATCCGTTTTTTTAAT
* * * *
198319 CAAATTTAAACCACATGCTCATATACCATAATAGAATAC
1 CAAATTTGAGCCACATGCTCCTAAACCATAATAGAATAC
198358 CTATGTAACC
Statistics
Matches: 291, Mismatches: 43, Indels: 30
0.80 0.12 0.08
Matches are distributed among these distances:
150 63 0.22
151 4 0.01
152 9 0.03
153 51 0.18
154 4 0.01
155 1 0.00
156 1 0.00
157 42 0.14
158 49 0.17
159 2 0.01
160 5 0.02
161 58 0.20
162 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.06, T:0.46
Consensus pattern (154 bp):
CAAATTTGAGCCACATGCTCCTAAACCATAATAGAATACATGTGTACTTTCAATTCCTCTTTTAT
AAATTTTTATTTTTCAATTTAGTCCTTCAATTTTTTATAATCTCCTTATTTCCTCAATTCGTCAT
TTATTTTAAATCCGTTTTTTTAAT
Found at i:199486 original size:78 final size:77
Alignment explanation
Indices: 199331--199478 Score: 253
Period size: 78 Copynumber: 1.9 Consensus size: 77
199321 CTCGATTCAA
199331 AAAAAATTTAAATCAAGTCCGAGTTGTAAAATATGACTCGTCAACTCGTATAACTCAAATTTTTT
1 AAAAAATTTAAATCAAGTCCGAGTTGTAAAATATGACTCGTCAACTCGTATAACTCAAATTTTTT
*
199396 TGACTCGACTCG
66 GGACTCGACTCG
*
199408 AAAAAATTTCAAATCAAGTCCGAGTTGTAAAATATGACTCGTCAACTCGTATAGCTCGAAA-TTT
1 AAAAAATTT-AAATCAAGTCCGAGTTGTAAAATATGACTCGTCAACTCGTATAACTC-AAATTTT
199472 TTGGACT
64 TTGGACT
199479 TGGCTCGATC
Statistics
Matches: 67, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
77 9 0.13
78 55 0.82
79 3 0.04
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (77 bp):
AAAAAATTTAAATCAAGTCCGAGTTGTAAAATATGACTCGTCAACTCGTATAACTCAAATTTTTT
GGACTCGACTCG
Found at i:202176 original size:267 final size:270
Alignment explanation
Indices: 201701--202241 Score: 1043
Period size: 267 Copynumber: 2.0 Consensus size: 270
201691 ATGCACGAGT
201701 ACTCATAATTCTATAATGTTATTGTTTATATATGGCATACGGGTTGATGGTTACGGTGGTTCTAG
1 ACTCATAATTCTATAATGTTATTGTTTATATATGGCATACGGGTTGATGGTTACGGTGGTTCTAG
201766 AAGTGGCAAATTAAGGCAGTGAGAATGGAAATAACGGTTCACCTCTTTTTGGAGCGGGCGAAGAG
66 AAGTGGCAAATTAAGGCAGTGAGAATGGAAATAACGGTTCACCTCTTTTTGGAGCGGGCGAAGAG
201831 CCGTTAAATGTGGTTTTAAGTTGTTTATACGATAAACTCATCGATCTCCGCCTATGAAACTGTGC
131 CCGTTAAATGTGGTTTTAAGTTGTTTATACGATAAACTCATCGATCTCCGCCTATGAAACTGTGC
201896 ATGAAAATATGTTTTGAACGTTGAGTT-AA-CTCGA-TTCACACAAATAACTCTACTATATTACA
196 ATGAAAATATGTTTTGAACGTTGAGTTAAAGCTCGATTTCACACAAATAACTCTACTATATTACA
201958 TGCATTCGTC
261 TGCATTCGTC
201968 ACTCATAATTCTATAATGTTATTGTTTATATATGGCATACGGGTTGATGGTTACGGTGGTTCTAG
1 ACTCATAATTCTATAATGTTATTGTTTATATATGGCATACGGGTTGATGGTTACGGTGGTTCTAG
202033 AAGTGGCAAATTAAGGCAGTGAGAATGGAAATAACGGTTCACCTCTTTTTGGAGCGGGCGAAGAG
66 AAGTGGCAAATTAAGGCAGTGAGAATGGAAATAACGGTTCACCTCTTTTTGGAGCGGGCGAAGAG
202098 CCGTTAAATGTGGTTTTAAGTTGTTTATACGATAAACTCATCGATCTCCGCCTATGAAACTGTGC
131 CCGTTAAATGTGGTTTTAAGTTGTTTATACGATAAACTCATCGATCTCCGCCTATGAAACTGTGC
202163 ATGAAAATATGTTTTGAACGTTGAGTTAACAAGCTCGATTTCACACAAATAACTCTACTATATTA
196 ATGAAAATATGTTTTGAACGTTGAGTT-A-AAGCTCGATTTCACACAAATAACTCTACTATATTA
202228 CATGCATTCGTC
259 CATGCATTCGTC
202240 AC
1 AC
202242 ATGAACATAA
Statistics
Matches: 269, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
267 222 0.83
270 2 0.01
271 5 0.02
272 40 0.15
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (270 bp):
ACTCATAATTCTATAATGTTATTGTTTATATATGGCATACGGGTTGATGGTTACGGTGGTTCTAG
AAGTGGCAAATTAAGGCAGTGAGAATGGAAATAACGGTTCACCTCTTTTTGGAGCGGGCGAAGAG
CCGTTAAATGTGGTTTTAAGTTGTTTATACGATAAACTCATCGATCTCCGCCTATGAAACTGTGC
ATGAAAATATGTTTTGAACGTTGAGTTAAAGCTCGATTTCACACAAATAACTCTACTATATTACA
TGCATTCGTC
Found at i:211923 original size:265 final size:273
Alignment explanation
Indices: 211570--212067 Score: 766
Period size: 270 Copynumber: 1.8 Consensus size: 273
211560 AATCACATTA
* * *
211570 GCTTAATCAAAATAATAATAATTTAAATTATTATTTGTTATTTAAATATTTTTATTTAATTGTGT
1 GCTTAATCAAAATAATAATAATTTAAATTATTATTCGGTATTTAAATATTTTTATTTAATTATGT
211635 ATTGAATATAATTTTAAAGTTCTATTTGATATTTTAA-TTTTTTCTCAATTAGATA-CCTAATTT
66 ATTGAATATAATTTTAAAGTTCTATTTGATATTTTAATTTTTTTCTCAATTAGATATCCTAATTT
* *
211698 AACCATTGTATTCGAATTG-GTCTA-GATTAATTTATTATTTAAATAAATCATTTATTAT-AATA
131 AACCATTGTATTCAAATTGAGT-TAGGATTAATTTATTATTTAAATAAACCATTTATTATGAATA
* *
211760 CTAATTTACAT-AAAAAT-AAAGTTTGAGTGTTTTTTATAATACTTTGCTATAATATTTTAAAAT
195 C-AATTTACATCAAAAATAAAAGTTCGAGTATTTTTTATAATACTTTGCTATAATATTTTAAAAT
211823 TGTACAAATATGATT
259 TGTACAAATATGATT
211838 GCTTAATC-AAA-AATAATAATTTAAA-TATT-TTCGGTATTTAAATATTTTTATTTAATTATGT
1 GCTTAATCAAAATAATAATAATTTAAATTATTATTCGGTATTTAAATATTTTTATTTAATTATGT
* *
211899 ATTTGAATATAATTTTAAAGTTCTATTTGATATTTTAATTTTTTTTCTGAATTAGATATCTTAAT
66 A-TTGAATATAATTTTAAAGTTCTATTTGATATTTTAA-TTTTTTTCTCAATTAGATATCCTAAT
* *
211964 TTAACCATTTTATTCAAATTGATGTTAGGTTTAATTTATTATTTAAATAAACCATTTATTATGAA
129 TTAACCATTGTATTCAAATTGA-GTTAGGATTAATTTATTATTTAAATAAACCATTTATTATGAA
*
212029 TACAATTTACATCTAAAATAAAAGTTCGAGTATTTTTTA
193 TACAATTTACATCAAAAATAAAAGTTCGAGTATTTTTTA
212068 ATATTTTAAA
Statistics
Matches: 208, Mismatches: 12, Indels: 16
0.88 0.05 0.07
Matches are distributed among these distances:
264 30 0.14
265 40 0.19
266 14 0.07
267 20 0.10
268 32 0.15
269 2 0.01
270 43 0.21
271 10 0.05
272 17 0.08
ACGTcount: A:0.37, C:0.06, G:0.07, T:0.49
Consensus pattern (273 bp):
GCTTAATCAAAATAATAATAATTTAAATTATTATTCGGTATTTAAATATTTTTATTTAATTATGT
ATTGAATATAATTTTAAAGTTCTATTTGATATTTTAATTTTTTTCTCAATTAGATATCCTAATTT
AACCATTGTATTCAAATTGAGTTAGGATTAATTTATTATTTAAATAAACCATTTATTATGAATAC
AATTTACATCAAAAATAAAAGTTCGAGTATTTTTTATAATACTTTGCTATAATATTTTAAAATTG
TACAAATATGATT
Found at i:214124 original size:20 final size:20
Alignment explanation
Indices: 214075--214210 Score: 105
Period size: 20 Copynumber: 6.8 Consensus size: 20
214065 CACTATCGCA
* **
214075 AATTCGCGTTGCGATAGTTGA
1 AATTCGCGTTGCGAT-TTTCC
*
214096 AAATCGCGTTGCGATTTTCC
1 AATTCGCGTTGCGATTTTCC
* * *
214116 ATTTCGCGTTGCGATAGTT-G
1 AATTCGCGTTGCGAT-TTTCC
*
214136 AAATCGCGTTGCGATTTTCC
1 AATTCGCGTTGCGATTTTCC
* * **
214156 -ATTCGCGTTGCTATAGTTGA
1 AATTCGCGTTGCGAT-TTTCC
*
214176 AAATCGCGTTGCGATTTTCC
1 AATTCGCGTTGCGATTTTCC
*
214196 ATTTCGCGTTGCGAT
1 AATTCGCGTTGCGAT
214211 AGTTGAAAAT
Statistics
Matches: 87, Mismatches: 24, Indels: 9
0.73 0.20 0.08
Matches are distributed among these distances:
19 14 0.16
20 45 0.52
21 28 0.32
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (20 bp):
AATTCGCGTTGCGATTTTCC
Found at i:214151 original size:40 final size:41
Alignment explanation
Indices: 214077--214229 Score: 274
Period size: 41 Copynumber: 3.8 Consensus size: 41
214067 CTATCGCAAA
214077 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
214118 TTCGCGTTGCGATAGTTG-AAATCGCGTTGCGATTTTCCA-
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
*
214157 TTCGCGTTGCTATAGTTGAAAATCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
*
214198 TTCGCGTTGCGATAGTTGAAAATCACGTTGCG
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCG
214230 CGTTGCGGTT
Statistics
Matches: 107, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
39 17 0.16
40 42 0.39
41 48 0.45
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (41 bp):
TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
Found at i:214209 original size:80 final size:81
Alignment explanation
Indices: 214076--214229 Score: 283
Period size: 80 Copynumber: 1.9 Consensus size: 81
214066 ACTATCGCAA
214076 ATTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTG-AAAT
1 ATTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAAT
*
214140 CGCGTTGCGATTTTCC
66 CACGTTGCGATTTTCC
*
214156 ATTCGCGTTGCTATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAAT
1 ATTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAAT
214221 CACGTTGCG
66 CACGTTGCG
214230 CGTTGCGGTT
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
80 59 0.83
81 12 0.17
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (81 bp):
ATTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAAT
CACGTTGCGATTTTCC
Found at i:214275 original size:22 final size:22
Alignment explanation
Indices: 214248--214301 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
214238 TTTTCCAAAT
214248 TCGTTGCGATAGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
* *
214270 TTGTTGCGAAAGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
214292 TCGTTGCGAT
1 TCGTTGCGAT
214302 TTTCCAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.19, C:0.17, G:0.28, T:0.37
Consensus pattern (22 bp):
TCGTTGCGATAGTCTACAGTTG
Found at i:214535 original size:5 final size:5
Alignment explanation
Indices: 214518--214553 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
214508 CCGCCGCCGC
*
214518 CGTC- CGTCC CGTCT CGTCT CGTCT CGTCT CGTCT CG
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CG
214554 GGTCGTGGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.00, C:0.44, G:0.22, T:0.33
Consensus pattern (5 bp):
CGTCT
Found at i:214685 original size:19 final size:19
Alignment explanation
Indices: 214661--214801 Score: 116
Period size: 19 Copynumber: 7.5 Consensus size: 19
214651 CAACGAATTT
214661 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
214680 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
*
214699 TCGCAACGCGAA-CTGGAAAA
1 TCGCAA--CGAATTTGGAAAA
*
214719 TCGCAACGCGATTT------
1 TCGCAACG-AATTTGGAAAA
*
214733 TCGCAACGAATTTAGAAAA
1 TCGCAACGAATTTGGAAAA
* * **
214752 TCGCAACGACAACTGTAGACTA
1 TCGCAACG--AA-TTTGGAAAA
214774 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
214793 TCGCAACGA
1 TCGCAACGA
214802 CAACTGTAGA
Statistics
Matches: 98, Mismatches: 11, Indels: 26
0.73 0.08 0.19
Matches are distributed among these distances:
13 4 0.04
14 8 0.08
18 2 0.02
19 48 0.49
20 16 0.16
21 6 0.06
22 14 0.14
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:214776 original size:22 final size:22
Alignment explanation
Indices: 214751--214822 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
214741 AATTTAGAAA
214751 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
214773 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
214792 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
214814 ATCGCAACG
1 ATCGCAACG
214823 CGATTTTCAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 13 0.33
20 2 0.05
21 2 0.05
22 22 0.56
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:214792 original size:41 final size:41
Alignment explanation
Indices: 214733--214822 Score: 171
Period size: 41 Copynumber: 2.2 Consensus size: 41
214723 AACGCGATTT
214733 TCGCAACGAATTTAGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTAGAAAATCGCAACGACAACTGTAGACTA
*
214774 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTAGAAAATCGCAACGACAACTGTAGACTA
214815 TCGCAACG
1 TCGCAACG
214823 CGATTTTCAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (41 bp):
TCGCAACGAATTTAGAAAATCGCAACGACAACTGTAGACTA
Found at i:214837 original size:21 final size:21
Alignment explanation
Indices: 214811--214928 Score: 96
Period size: 21 Copynumber: 5.7 Consensus size: 21
214801 ACAACTGTAG
214811 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGATTTTCA
** **
214832 ACTATCGCAACGCGAAATAGA
1 ACTATCGCAACGCGATTTTCA
* ** **
214853 A-AATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGATTTTCA
* **
214873 A-AATCAAAACGCGATTTTCA
1 ACTATCGCAACGCGATTTTCA
*
214893 ACTATCGCAATGCGATTTTCA
1 ACTATCGCAACGCGATTTTCA
*
214914 ATTATCGCAACGCGA
1 ACTATCGCAACGCGA
214929 ATTTGCGATA
Statistics
Matches: 78, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
20 32 0.41
21 46 0.59
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (21 bp):
ACTATCGCAACGCGATTTTCA
Found at i:214860 original size:20 final size:20
Alignment explanation
Indices: 214835--214877 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
214825 ATTTTCAACT
214835 ATCGCAACGCGAAATAGAAA
1 ATCGCAACGCGAAATAGAAA
*
214855 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATAGAAA
214875 ATC
1 ATC
214878 AAAACGCGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.12
Consensus pattern (20 bp):
ATCGCAACGCGAAATAGAAA
Found at i:214883 original size:20 final size:20
Alignment explanation
Indices: 214840--214886 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
214830 CAACTATCGC
**
214840 AACGCGAAATAGAAAATCGC
1 AACGCGAAATAGAAAATCAA
*
214860 AACGCGAAATGGAAAATCAA
1 AACGCGAAATAGAAAATCAA
214880 AACGCGA
1 AACGCGA
214887 TTTTCAACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.51, C:0.19, G:0.21, T:0.09
Consensus pattern (20 bp):
AACGCGAAATAGAAAATCAA
Found at i:225948 original size:18 final size:17
Alignment explanation
Indices: 225925--225958 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
225915 TTATTTGTAT
225925 ATAATATATAAATTATAA
1 ATAATATA-AAATTATAA
225943 ATAATATAAAATTATA
1 ATAATATAAAATTATA
225959 CTAAGTTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAATATAAAATTATAA
Found at i:253745 original size:20 final size:21
Alignment explanation
Indices: 253720--253771 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
253710 TTTTCCCAAT
*
253720 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
253740 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
253761 TCGCAATGCGA
1 TCGCAATGCGA
253772 TACTTACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:253784 original size:41 final size:41
Alignment explanation
Indices: 253757--253834 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
253747 GCGAATTGGG
* * *
253757 AAAATCGCAATGCGATACTTACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTTACTATCGCAACGCGATAATAA
*
253798 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTTACTATCGCAACGCGATA
253835 CTGACTTTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTTACTATCGCAACGCGATAATAA
Found at i:253785 original size:20 final size:20
Alignment explanation
Indices: 253760--253853 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
253750 AATTGGGAAA
*
253760 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * * **
253780 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-TACT
*
253801 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
253821 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
253841 TTCGCAACGCGAT
1 ATCGCAACGCGAT
253854 TTACATAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:254409 original size:19 final size:19
Alignment explanation
Indices: 254371--254437 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
254361 TTCGAGAATG
254371 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
254391 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
254410 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
254429 AAAATCGCA
1 AAAATCGCA
254438 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:254479 original size:20 final size:19
Alignment explanation
Indices: 254433--254598 Score: 127
Period size: 20 Copynumber: 9.1 Consensus size: 19
254423 GAAACCAAAA
*
254433 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
254452 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
254471 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
254491 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
254507 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
254524 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
254538 TCTCATTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
254557 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
254577 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
254597 TC
1 TC
254599 AACCAAAAGA
Statistics
Matches: 117, Mismatches: 17, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
14 19 0.16
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 41 0.35
20 48 0.41
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:254514 original size:39 final size:39
Alignment explanation
Indices: 254438--254514 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
254428 CAAAATCGCA
* **
254438 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
254477 TTGCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
254515 ATAGTCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.45
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
Found at i:254523 original size:33 final size:33
Alignment explanation
Indices: 254486--254573 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
254476 GTTGCGATTT
* **
254486 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
*
254519 TCATTTCGCGTTGCGATTCTCTCATTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
254552 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
254574 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 35 0.70
34 15 0.30
ACGTcount: A:0.12, C:0.25, G:0.24, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
Found at i:256681 original size:21 final size:21
Alignment explanation
Indices: 256657--256723 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
256647 TCATTTCTCG
256657 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * * * *
256678 AGAGGCCACTGCCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
256699 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
256720 AGAG
1 AGAG
256724 CCCGATTCAC
Statistics
Matches: 34, Mismatches: 11, Indels: 3
0.71 0.23 0.06
Matches are distributed among these distances:
20 1 0.03
21 32 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.37, G:0.21, T:0.18
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:256684 original size:42 final size:42
Alignment explanation
Indices: 256601--256684 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 42
256591 GCCCGACTCG
* * * *
256601 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAATAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
** * *
256643 CCTATCATTTCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
256685 ACTGCCATCG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.25
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:258100 original size:14 final size:14
Alignment explanation
Indices: 258081--258116 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
258071 ATTGTTTAAT
258081 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
258095 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
258109 TGATTTGT
1 TGATTTGT
258117 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:258264 original size:19 final size:19
Alignment explanation
Indices: 258240--258321 Score: 84
Period size: 19 Copynumber: 4.5 Consensus size: 19
258230 TGCGAAATGA
258240 GCATTGCGATTTTCATTTC
1 GCATTGCGATTTTCATTTC
*
258259 GCATTGCGA--TTC-TCTC
1 GCATTGCGATTTTCATTTC
258275 G--TTGCGATTTTCATTTC
1 GCATTGCGATTTTCATTTC
* *
258292 GCATTGCGATATTAATTTCC
1 GCATTGCGATTTTCATTT-C
*
258312 GCGTTGCGAT
1 GCATTGCGAT
258322 GGACATTAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
14 6 0.12
16 7 0.13
17 7 0.13
19 22 0.42
20 10 0.19
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.43
Consensus pattern (19 bp):
GCATTGCGATTTTCATTTC
Found at i:258267 original size:33 final size:34
Alignment explanation
Indices: 258224--258300 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 34
258214 AAAAGTACTA
*
258224 TCGCAATGCGAAAT-GAGCATTGCGATTTTCATT
1 TCGCATTGCGAAATCGAGCATTGCGATTTTCATT
* *** *
258257 TCGCATTGCG-ATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATCGAGCATTGCGATTTTCATT
258290 TCGCATTGCGA
1 TCGCATTGCGA
258301 TATTAATTTC
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
32 2 0.06
33 34 0.94
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (34 bp):
TCGCATTGCGAAATCGAGCATTGCGATTTTCATT
Found at i:260611 original size:12 final size:12
Alignment explanation
Indices: 260594--260618 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
260584 TCTTCGGGGA
260594 CTTTTTCTTCTT
1 CTTTTTCTTCTT
260606 CTTTTTCTTCTT
1 CTTTTTCTTCTT
260618 C
1 C
260619 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:260827 original size:24 final size:24
Alignment explanation
Indices: 260793--260846 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
260783 CTGAAACATC
* *
260793 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
260817 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
260841 ATCAAA
1 ATCAAA
260847 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:261931 original size:20 final size:20
Alignment explanation
Indices: 261906--261963 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
261896 ATTCATTTGA
261906 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
261926 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
261946 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
261964 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:262023 original size:19 final size:19
Alignment explanation
Indices: 261982--262049 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
261972 GAAATGAAAA
261982 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
261998 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
262015 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
262034 TCACATTGCGATTTTC
1 TCGCATTGCGATTTTC
262050 TCGTTGCGAT
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
19 29 0.63
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:264142 original size:14 final size:14
Alignment explanation
Indices: 264123--264180 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
264113 ATGCGAAATG
264123 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
264137 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
264153 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
264169 AAAATCGCAACG
1 AAAATCGCAACG
264181 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:264165 original size:32 final size:33
Alignment explanation
Indices: 264107--264197 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
264097 GGAAATGGCT
264107 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
264140 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
264172 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
264198 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:264191 original size:19 final size:19
Alignment explanation
Indices: 264049--264202 Score: 105
Period size: 19 Copynumber: 8.6 Consensus size: 19
264039 TAGTTTACTT
* *
264049 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
264069 TCGCAACGCGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
264088 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
264108 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
264127 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
*
264141 TCGCAATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
264159 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
264173 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
264192 TCGCAATGCGA
1 TCGCAACGCGA
264203 TTTGTGTTTC
Statistics
Matches: 108, Mismatches: 14, Indels: 25
0.73 0.10 0.17
Matches are distributed among these distances:
14 20 0.19
15 1 0.01
16 6 0.06
17 2 0.02
18 11 0.10
19 39 0.36
20 29 0.27
ACGTcount: A:0.43, C:0.23, G:0.20, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:264233 original size:14 final size:14
Alignment explanation
Indices: 264214--264271 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
264204 TTGTGTTTCG
264214 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
264228 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
264244 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
264260 CGTTGCGATTTT
1 CGTTGCGATTTT
264272 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:264248 original size:32 final size:33
Alignment explanation
Indices: 264209--264287 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
264199 GCGATTTGTG
264209 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
264241 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
264274 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
264288 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:264286 original size:19 final size:17
Alignment explanation
Indices: 264209--264287 Score: 62
Period size: 14 Copynumber: 4.8 Consensus size: 17
264199 GCGATTTGTG
264209 TTTCGCGTTGCGATTT--
1 TTTCGC-TTGCGATTTCA
*
264225 TGTCG-TTGCGATTTCA
1 TTTCGCTTGCGATTTCA
264241 TTTCGCGTTGCGATTT--
1 TTTCGC-TTGCGATTTCA
*
264257 TGTCG-TTGCGATTTTCA
1 TTTCGCTTGCGA-TTTCA
264274 TTTCGCATTGCGAT
1 TTTCGC-TTGCGAT
264288 AGCCATTTCC
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
14 15 0.30
15 3 0.06
16 12 0.24
17 4 0.08
18 10 0.20
19 6 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (17 bp):
TTTCGCTTGCGATTTCA
Found at i:264306 original size:20 final size:19
Alignment explanation
Indices: 264272--264326 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
264262 TTGCGATTTT
*
264272 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
264291 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
264311 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
264327 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:264824 original size:18 final size:18
Alignment explanation
Indices: 264798--264842 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
264788 GTCGATCAGA
*
264798 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
264816 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
264834 TGATGGCTC
1 TGATGGCTC
264843 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:266187 original size:20 final size:20
Alignment explanation
Indices: 266162--266199 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
266152 AATAGTTTCT
266162 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
266182 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
266200 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:266488 original size:22 final size:22
Alignment explanation
Indices: 266463--266506 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
266453 GATTTAGATA
266463 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
266485 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
266507 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:266719 original size:20 final size:20
Alignment explanation
Indices: 266694--266787 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
266684 GATTATGTAT
*
266694 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
266714 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
* *** * *
266734 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTAAG
* *
266755 TATCGCATTGCGATAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
266775 TATCGCATTGCGA
1 TATCGCGTTGCGA
266788 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:266788 original size:20 final size:20
Alignment explanation
Indices: 266674--266788 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
266664 AGCTTTGAAA
*
266674 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTAAGT
* * *
266695 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* *
266715 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* * ** * *
266735 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTAAGT
266756 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
266776 ATCGCATTGCGAT
1 ATCGCATTGCGAT
266789 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:266806 original size:21 final size:21
Alignment explanation
Indices: 266777--266869 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
266767 ATAGTAAGTA
266777 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
266798 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
266818 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
266839 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
266859 TCGCATTGCGA
1 TCGCATTGCGA
266870 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:266807 original size:41 final size:41
Alignment explanation
Indices: 266716--266850 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
266706 AAAGTCAGTA
* * * ** *
266716 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
266756 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
266798 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
266839 TCGCGTTGCGAT
1 TCGCGTTGCGAT
266851 TTACTTATTC
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 4 0.05
41 75 0.93
42 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:266851 original size:41 final size:41
Alignment explanation
Indices: 266777--266869 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
266767 ATAGTAAGTA
266777 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
266818 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
266859 TCGCATTGCGA
1 TCGCATTGCGA
266870 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:268870 original size:23 final size:23
Alignment explanation
Indices: 268832--268902 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
268822 AGATGCTTAT
* *
268832 TTGATGG-GCTTAGTGGCTATAC
1 TTGATGGACCTTAGTGGCTATGC
* *
268854 TTGGTGGACCTTAGTGGTTATGC
1 TTGATGGACCTTAGTGGCTATGC
** *
268877 TTGATGGGTCTTAGTGACTATGC
1 TTGATGGACCTTAGTGGCTATGC
268900 TTG
1 TTG
268903 TTGATGGGTT
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
22 6 0.15
23 33 0.85
ACGTcount: A:0.15, C:0.13, G:0.32, T:0.39
Consensus pattern (23 bp):
TTGATGGACCTTAGTGGCTATGC
Found at i:270445 original size:17 final size:16
Alignment explanation
Indices: 270419--270451 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
270409 CTAAACATGT
270419 CGATAGTTTTAATTTA
1 CGATAGTTTTAATTTA
270435 CGATGAGTTTTAATTTA
1 CGAT-AGTTTTAATTTA
270452 AAGTTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.48
Consensus pattern (16 bp):
CGATAGTTTTAATTTA
Found at i:276701 original size:19 final size:20
Alignment explanation
Indices: 276673--276718 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
276663 GGAAAAGGAG
*
276673 AATCGGTAAACGAACTTA-A
1 AATCGATAAACGAACTTATA
*
276692 AATCGATAAACGAGCTTATA
1 AATCGATAAACGAACTTATA
276712 AA-CGATA
1 AATCGATA
276719 TCATAAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 21 0.88
20 3 0.12
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (20 bp):
AATCGATAAACGAACTTATA
Found at i:279913 original size:26 final size:26
Alignment explanation
Indices: 279878--279929 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
279868 TAATTTGCAT
*
279878 GCAAATATTTTTATTTAATTTCCAAA
1 GCAAAAATTTTTATTTAATTTCCAAA
279904 GCAAAAATTTTTATTTAATTTCCAAA
1 GCAAAAATTTTTATTTAATTTCCAAA
279930 AAGAAAATAT
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:0.40, C:0.12, G:0.04, T:0.44
Consensus pattern (26 bp):
GCAAAAATTTTTATTTAATTTCCAAA
Found at i:279936 original size:26 final size:26
Alignment explanation
Indices: 279884--279937 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
279874 GCATGCAAAT
*
279884 ATTTTTATTTAATTTCCAAAGCAAAA
1 ATTTTTATTTAATTTCCAAAGAAAAA
279910 ATTTTTATTTAATTTCCAAA-AAGAAA
1 ATTTTTATTTAATTTCCAAAGAA-AAA
279936 AT
1 AT
279938 ATATCACGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 1 0.04
26 25 0.96
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (26 bp):
ATTTTTATTTAATTTCCAAAGAAAAA
Found at i:282011 original size:34 final size:34
Alignment explanation
Indices: 281970--282040 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
281960 TTTAAGGTAG
*
281970 TTTAAGTCATTTTAATATAATTGATAACATTTTC
1 TTTAAGTCATTTCAATATAATTGATAACATTTTC
* * *
282004 TTTAAGTCATTTCAATATGATTGGTAATATTTTC
1 TTTAAGTCATTTCAATATAATTGATAACATTTTC
282038 TTT
1 TTT
282041 TGACCTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.52
Consensus pattern (34 bp):
TTTAAGTCATTTCAATATAATTGATAACATTTTC
Found at i:283154 original size:24 final size:24
Alignment explanation
Indices: 283102--283157 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
283092 TGAACGTTCG
* *
283102 GTTATGTTCGTTTATATGCGTTTA
1 GTTATGTTCGTTTATATGCATTCA
*
283126 GTTATGTTCGTTTATGTGCATTCA
1 GTTATGTTCGTTTATATGCATTCA
*
283150 TTTATGTT
1 GTTATGTT
283158 TAACCTAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.16, C:0.09, G:0.20, T:0.55
Consensus pattern (24 bp):
GTTATGTTCGTTTATATGCATTCA
Found at i:284662 original size:16 final size:16
Alignment explanation
Indices: 284618--284670 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
284608 GGATCTCCAA
284618 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
284634 C-ATT-TGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
284648 CGTTTATGTTTGTGTT
1 CGTTTATGTTCGTGTT
284664 CGTTTAT
1 CGTTTAT
284671 TTATTAAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 11 0.34
15 4 0.12
16 17 0.53
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.58
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:284758 original size:16 final size:16
Alignment explanation
Indices: 284737--284768 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
284727 AAAAAAATTT
284737 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
284753 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
284769 CTTATTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.12, G:0.25, T:0.56
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:289985 original size:14 final size:14
Alignment explanation
Indices: 289966--289998 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
289956 GAGATAGACC
289966 ATATTTTAAAATA-T
1 ATATTTT-AAATACT
289980 ATATTTTAAATACT
1 ATATTTTAAATACT
289994 ATATT
1 ATATT
289999 ATTACCCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATTTTAAATACT
Found at i:296972 original size:19 final size:19
Alignment explanation
Indices: 296945--296988 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
296935 GTTTTTTTCC
*
296945 ATATATATAT-ATAATAT-
1 ATATATTTATAATAATATA
*
296962 ATATATTTATAGTAATATA
1 ATATATTTATAATAATATA
296981 ATATATTT
1 ATATATTT
296989 TTTTTTGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 9 0.39
18 6 0.26
19 8 0.35
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
ATATATTTATAATAATATA
Found at i:297014 original size:10 final size:10
Alignment explanation
Indices: 297001--297034 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
296991 TTTTGAATTT
297001 TTATATATTA
1 TTATATATTA
297011 TTATATATTA
1 TTATATATTA
*
297021 TTATTATACTA
1 TTA-TATATTA
297032 TTA
1 TTA
297035 ATTTTGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (10 bp):
TTATATATTA
Found at i:298643 original size:38 final size:39
Alignment explanation
Indices: 298592--298670 Score: 142
Period size: 38 Copynumber: 2.1 Consensus size: 39
298582 GTTACAGCCA
*
298592 ATAACTCTAGCTTTAGTTCAACTC-TAAGGATATTTATG
1 ATAACTCTAGCTTTAATTCAACTCTTAAGGATATTTATG
298630 ATAACTCTAGCTTTAATTCAACTCTTAAGGATATTTATG
1 ATAACTCTAGCTTTAATTCAACTCTTAAGGATATTTATG
298669 AT
1 AT
298671 GTGATACATG
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 23 0.59
39 16 0.41
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (39 bp):
ATAACTCTAGCTTTAATTCAACTCTTAAGGATATTTATG
Found at i:302689 original size:106 final size:106
Alignment explanation
Indices: 302504--303824 Score: 2183
Period size: 106 Copynumber: 12.4 Consensus size: 106
302494 TACAGCCTTT
302504 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
302569 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
*
302610 AGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
302675 CGAAGAGACTGCTGGTTGTCAATAACCAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
* *
302716 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAAGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
302781 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
* *
302822 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGATAACGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
302887 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
302928 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
302993 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
*
303034 AGAGCCAATTTCAACTTCGCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
303099 CGAAGGGACCACTGGTTGTCAATAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
*
303140 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
303205 CGAAGGGACCACTGTTTGTCAATAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
* *
303246 ATAGCCAATTTCAACTTCACAACGAAGGATGTTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
303311 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
* * *
303352 AGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTGCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* ** * *
303417 CGAAGGGACCGCTGGTTGTCAATAATCAGTTTCCCAATCTCAGGGCCGATT
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAAT-T---------TC
* *
303468 AGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
303533 CGAAAGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
*
303574 AAAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
303639 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
* * * *
303680 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCATGTTCAACTGCACAA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
** * *
303745 CGAAGGGACCGCTGGTTGTCAATAAACAGTTTCCCAATCTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
* * *
303786 AGGGCCAATTTCAACTTCACGACGGAGGATATTGGACTC
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
303825 GGAACAATGC
Statistics
Matches: 1143, Mismatches: 62, Indels: 20
0.93 0.05 0.02
Matches are distributed among these distances:
106 1047 0.92
107 1 0.00
115 1 0.00
116 94 0.08
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
Found at i:304358 original size:84 final size:85
Alignment explanation
Indices: 304027--304355 Score: 410
Period size: 85 Copynumber: 3.9 Consensus size: 85
304017 CGAAAACCCC
* * * * * *
304027 CGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAAGGTT
1 CGAGTTCGATTTCACTCAGC-TCCAAGGCGCATCATTTGCAGCATAACTTAAGGCGAGAAGGGTT
*
304092 ATTTGCCAACCAAAGAGCCTT
65 ATCTGCCAACCAAAGAGCCTT
* *
304113 CGAGTTCGATTTCATTCAGCTCCAAGGCGCATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTA
1 CGAGTTCGATTTCACTCAGCTCCAAGGCGCATCATTTGCAGCATAACTTAAGGCGAGAAGGGTTA
304178 TCTGCCAACCAAAGAGCCTT
66 TCTGCCAACCAAAGAGCCTT
* * * *
304198 CGAGTTCGATTTCATTCAGCTCCAAGGCGCATCATTTGCAGCATAACTCAAGGCTAGAAGAGTTA
1 CGAGTTCGATTTCACTCAGCTCCAAGGCGCATCATTTGCAGCATAACTTAAGGCGAGAAGGGTTA
* *
304263 TCTGTCAA-CAAATA-CCTT
66 TCTGCCAACCAAAGAGCCTT
* * * * * * * *
304281 CGAGTTTGATTCCACTCAGCTCCAAGGCACCATCATTTGCAGCACAGCTGAAGGCAAGAAGGGCT
1 CGAGTTCGATTTCACTCAGCTCCAAGGC-GCATCATTTGCAGCATAACTTAAGGCGAGAAGGGTT
*
304346 ATCTGTCAAC
65 ATCTGCCAAC
304356 AAAATTATCG
Statistics
Matches: 218, Mismatches: 23, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
83 29 0.13
84 43 0.20
85 128 0.59
86 18 0.08
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (85 bp):
CGAGTTCGATTTCACTCAGCTCCAAGGCGCATCATTTGCAGCATAACTTAAGGCGAGAAGGGTTA
TCTGCCAACCAAAGAGCCTT
Found at i:304879 original size:2 final size:2
Alignment explanation
Indices: 304874--304933 Score: 79
Period size: 2 Copynumber: 30.5 Consensus size: 2
304864 GTTTTTTTCC
*
304874 AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
304916 TT AT AGT A- AT AT A- AT AT A
1 AT AT A-T AT AT AT AT AT AT A
304934 ATTTTTTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
1 2 0.04
2 47 0.92
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:304971 original size:3 final size:3
Alignment explanation
Indices: 304963--304995 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
304953 TATATAATAG
304963 ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
304996 ATACTATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:305003 original size:20 final size:20
Alignment explanation
Indices: 304965--305004 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
304955 TATAATAGAT
* *
304965 TATTATTATTATTATTATTA
1 TATTATTATTAATACTATTA
304985 TATTATTATTAATACTATTA
1 TATTATTATTAATACTATTA
305005 ATTTTGTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTATTATTAATACTATTA
Found at i:306645 original size:17 final size:17
Alignment explanation
Indices: 306623--306683 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
306613 TACAGCCAAT
306623 AACTCTAGCTTTAGTTC
1 AACTCTAGCTTTAGTTC
* *
306640 AACTCTAAGGATATTTATGAT-
1 AACTCT-A-G--CTTTA-GTTC
306661 AACTCTAGCTTTAGTTC
1 AACTCTAGCTTTAGTTC
306678 AACTCT
1 AACTCT
306684 TAAGGATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
16 2 0.06
17 16 0.47
18 1 0.03
19 2 0.06
20 1 0.03
21 10 0.29
22 2 0.06
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (17 bp):
AACTCTAGCTTTAGTTC
Found at i:306672 original size:38 final size:39
Alignment explanation
Indices: 306621--306699 Score: 151
Period size: 38 Copynumber: 2.1 Consensus size: 39
306611 GTTACAGCCA
306621 ATAACTCTAGCTTTAGTTCAACTC-TAAGGATATTTATG
1 ATAACTCTAGCTTTAGTTCAACTCTTAAGGATATTTATG
306659 ATAACTCTAGCTTTAGTTCAACTCTTAAGGATATTTATG
1 ATAACTCTAGCTTTAGTTCAACTCTTAAGGATATTTATG
306698 AT
1 AT
306700 GTGATACATG
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 24 0.60
39 16 0.40
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.41
Consensus pattern (39 bp):
ATAACTCTAGCTTTAGTTCAACTCTTAAGGATATTTATG
Found at i:310613 original size:13 final size:13
Alignment explanation
Indices: 310595--310619 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
310585 TCGAATATAC
310595 TTAGAAAATCTTT
1 TTAGAAAATCTTT
310608 TTAGAAAATCTT
1 TTAGAAAATCTT
310620 AAAATTCATT
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:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TTAGAAAATCTTT
Found at i:311100 original size:17 final size:17
Alignment explanation
Indices: 311047--311112 Score: 59
Period size: 16 Copynumber: 4.1 Consensus size: 17
311037 GAAATATAAG
*
311047 TTCAAAC-ATCCATAAA
1 TTCAAACAATCCACAAA
*
311063 TTCAAACAAAT--TCAAA
1 TTCAAAC-AATCCACAAA
*
311079 GTCAAACAATCCACAAA
1 TTCAAACAATCCACAAA
*
311096 TTCAAACATTCCA-AAA
1 TTCAAACAATCCACAAA
311112 T
1 T
311113 ATCCAAAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
15 3 0.08
16 20 0.50
17 15 0.38
18 2 0.05
ACGTcount: A:0.52, C:0.24, G:0.02, T:0.23
Consensus pattern (17 bp):
TTCAAACAATCCACAAA
Found at i:312321 original size:22 final size:22
Alignment explanation
Indices: 312245--312326 Score: 94
Period size: 23 Copynumber: 3.7 Consensus size: 22
312235 ACAGAACCCC
* *
312245 AGGGGGTATCGATTCCCCTAC-
1 AGGGGGAATCGATTCCCCTTCA
*
312266 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGATTCCCCTTC-A
*
312289 AGGGGGAATCGGTTCCCCTTCA
1 AGGGGGAATCGATTCCCCTTCA
* *
312311 AGGGAGTATCGATTCC
1 AGGGGGAATCGATTCC
312327 ATCTGCACCA
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
21 18 0.34
22 14 0.26
23 21 0.40
ACGTcount: A:0.21, C:0.26, G:0.30, T:0.23
Consensus pattern (22 bp):
AGGGGGAATCGATTCCCCTTCA
Found at i:313626 original size:19 final size:19
Alignment explanation
Indices: 313602--313652 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
313592 ATGCAATTAG
313602 TGCATCGATGCATAAGGCA
1 TGCATCGATGCATAAGGCA
313621 TGCATCGATGCATAAGGCA
1 TGCATCGATGCATAAGGCA
313640 TGCATCGATGCAT
1 TGCATCGATGCAT
313653 CCCAGTGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (19 bp):
TGCATCGATGCATAAGGCA
Found at i:314781 original size:30 final size:30
Alignment explanation
Indices: 314741--314813 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
314731 GGTTCTTCGG
* *
314741 GACCTATGGATAGTTATCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
314771 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
314801 GACCTCTGGATAG
1 GACCTCTGGATAG
314814 GTCCTTCAGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:318888 original size:22 final size:21
Alignment explanation
Indices: 318846--318885 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
318836 GAGTTTATTT
*
318846 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
318867 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
318886 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:320920 original size:19 final size:20
Alignment explanation
Indices: 320882--320924 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
320872 AAACCATTTA
*
320882 GGGGGGAATCGGTTCCCCCTT
1 GGGGGGAATCAGTT-CCCCTT
*
320903 GGGGGGAATCAGTTCCCTTT
1 GGGGGGAATCAGTTCCCCTT
320923 GG
1 GG
320925 ACATTTTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.12, C:0.23, G:0.40, T:0.26
Consensus pattern (20 bp):
GGGGGGAATCAGTTCCCCTT
Found at i:323221 original size:26 final size:26
Alignment explanation
Indices: 323192--323243 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
323182 ATGTTGCATT
323192 TTCGTATCAGTATTATGTGTACTTTC
1 TTCGTATCAGTATTATGTGTACTTTC
323218 TTCGTATCAGTATTATGTGTACTTTC
1 TTCGTATCAGTATTATGTGTACTTTC
323244 GGCACTAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.50
Consensus pattern (26 bp):
TTCGTATCAGTATTATGTGTACTTTC
Found at i:324091 original size:4 final size:4
Alignment explanation
Indices: 324082--324107 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
324072 TGATAAGAAT
324082 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
324108 AACTCGAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:328834 original size:20 final size:20
Alignment explanation
Indices: 328797--328839 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
328787 AGCCTTTTAA
*
328797 AAAATACAGAAAAAAAAATC
1 AAAATACAGAAAAAAAAAAC
*
328817 AAAATACA-AACAACAAAAAC
1 AAAATACAGAA-AAAAAAAAC
328837 AAA
1 AAA
328840 CAAACAAGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.77, C:0.14, G:0.02, T:0.07
Consensus pattern (20 bp):
AAAATACAGAAAAAAAAAAC
Found at i:329581 original size:29 final size:29
Alignment explanation
Indices: 329539--329611 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
329529 AAATCCAAGC
329539 GGCCAATCAAATGAGAGCGTTCTTAGTTT
1 GGCCAATCAAATGAGAGCGTTCTTAGTTT
*
329568 GGCCAATCAAATGAGAGCGTTTTTAGTTT
1 GGCCAATCAAATGAGAGCGTTCTTAGTTT
*
329597 GGCCAATGAAATGAG
1 GGCCAATCAAATGAG
329612 GCCAATTTCC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (29 bp):
GGCCAATCAAATGAGAGCGTTCTTAGTTT
Found at i:330245 original size:4 final size:4
Alignment explanation
Indices: 330236--330262 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
330226 AAAAAAGTAA
330236 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
330263 GATTAAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Done.