Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009029.1 Hibiscus syriacus cultivar Beakdansim tig00112429_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: 496945
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 2 of 3
Found at i:167698 original size:4 final size:4
Alignment explanation
Indices: 167689--167954 Score: 532
Period size: 4 Copynumber: 66.5 Consensus size: 4
167679 TTTATGTATC
167689 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
167737 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
167785 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
167833 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
167881 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
167929 ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT AT
167955 ATACTTTTCT
Statistics
Matches: 262, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 262 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:169159 original size:12 final size:11
Alignment explanation
Indices: 169131--169168 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
169121 CCTCTTTTTG
*
169131 TTCTTTGCTTT
1 TTCTTTGATTT
169142 TTCTTTGATTT
1 TTCTTTGATTT
169153 TTGCTTTGATTT
1 TT-CTTTGATTT
169165 TTCT
1 TTCT
169169 CTTTGCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.05, C:0.13, G:0.11, T:0.71
Consensus pattern (11 bp):
TTCTTTGATTT
Found at i:169172 original size:13 final size:12
Alignment explanation
Indices: 169126--169173 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
169116 TTTGTCCTCT
169126 TTTTGTTCTTTG-
1 TTTT-TTCTTTGA
*
169138 CTTTTTCTTTGA
1 TTTTTTCTTTGA
*
169150 TTTTTGCTTTGA
1 TTTTTTCTTTGA
169162 TTTTTCTCTTTG
1 TTTTT-TCTTTG
169174 CTCTTCTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 7 0.23
12 18 0.60
13 5 0.17
ACGTcount: A:0.04, C:0.12, G:0.12, T:0.71
Consensus pattern (12 bp):
TTTTTTCTTTGA
Found at i:169856 original size:20 final size:20
Alignment explanation
Indices: 169828--169868 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
169818 CAAAGAGAGG
*
169828 GAATGTTTCAAGGTCTAAAA
1 GAATATTTCAAGGTCTAAAA
*
169848 GAATATTTCAAGGTCTCAAA
1 GAATATTTCAAGGTCTAAAA
169868 G
1 G
169869 TGATAGAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (20 bp):
GAATATTTCAAGGTCTAAAA
Found at i:169876 original size:26 final size:24
Alignment explanation
Indices: 169800--169879 Score: 78
Period size: 26 Copynumber: 3.3 Consensus size: 24
169790 TCAAGGTGGA
169800 AAGAATGTTTCAAGGTCTCAAAGAG
1 AAGAATGTTTCAAGGTCTCAAAG-G
*
169825 AGGGAATGTTTCAAGGTCT--AA--
1 A-AGAATGTTTCAAGGTCTCAAAGG
*
169846 AAGAATATTTCAAGGTCTCAAAGTG
1 AAGAATGTTTCAAGGTCTCAAAG-G
169871 ATAGAATGT
1 A-AGAATGT
169880 CAAAAATTGG
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
20 15 0.34
21 1 0.02
22 2 0.05
24 2 0.05
25 2 0.05
26 22 0.50
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.28
Consensus pattern (24 bp):
AAGAATGTTTCAAGGTCTCAAAGG
Found at i:169878 original size:46 final size:45
Alignment explanation
Indices: 169786--169879 Score: 125
Period size: 46 Copynumber: 2.1 Consensus size: 45
169776 ATAAATGCAG
* * *
169786 TGTTTCAAGGTGGAAAGAATGTTTCAAGGTCTCAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
* * *
169831 TGTTTCAAGGTCTAAAAGAATATTTCAAGGTCTCAAAGTGATAGAA
1 TGTTTCAAGGT-GAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
169877 TGT
1 TGT
169880 CAAAAATTGG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 11 0.26
46 31 0.74
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.29
Consensus pattern (45 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
Found at i:174745 original size:3 final size:3
Alignment explanation
Indices: 174737--174782 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
174727 ATGTAAATTA
* *
174737 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC GAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
174783 TACAAAAAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:176464 original size:2 final size:2
Alignment explanation
Indices: 176457--176487 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
176447 ATTTATAATT
176457 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
176488 TTAATAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:176750 original size:51 final size:51
Alignment explanation
Indices: 176619--176762 Score: 168
Period size: 50 Copynumber: 2.9 Consensus size: 51
176609 AGATATACAT
* * *
176619 ACTTACACC-AGTGTAAGTATGTGTTAAGTGTTATACTTTTTTATTTTATTT
1 ACTTACACCGA-TGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
* * * *
176670 ACTTACACCGGTATAA-TAGGTGTTAAGTGCTACACTTGTTTATTTTATTC
1 ACTTACACCGATGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
** *
176720 ACTTGTATCGATGTAAGTATGTGTTAAGTGCTACA-TTTTTTAT
1 ACTTACACCGATGTAAGTATGTGTTAAGTGCTACACTTTTTTAT
176763 AGTATGAATT
Statistics
Matches: 77, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
50 47 0.61
51 30 0.39
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.47
Consensus pattern (51 bp):
ACTTACACCGATGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
Found at i:177556 original size:19 final size:18
Alignment explanation
Indices: 177514--177556 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
177504 CAGTAATCCT
**
177514 ATTCCCTGATAATCTTTT
1 ATTCCCTGATAATCTTAC
177532 ATTTCCACTGATAATCTTAC
1 A-TTCC-CTGATAATCTTAC
177552 ATTCC
1 ATTCC
177557 GTGAACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 8 0.38
20 12 0.57
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.44
Consensus pattern (18 bp):
ATTCCCTGATAATCTTAC
Found at i:179437 original size:15 final size:16
Alignment explanation
Indices: 179416--179463 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
179406 GAGTATTTAA
179416 AATTATTTTATATTTT
1 AATTATTTTATATTTT
* *
179432 AA-TATTTAATATATT
1 AATTATTTTATATTTT
179447 AATTATTTGTA-ATTTT
1 AATTATTT-TATATTTT
179463 A
1 A
179464 TGAGGTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 13 0.50
16 12 0.46
17 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
AATTATTTTATATTTT
Found at i:179494 original size:17 final size:17
Alignment explanation
Indices: 179472--179512 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
179462 TATGAGGTTA
179472 AAAAATAAT-ATTATTAT
1 AAAAATAATAATTATT-T
179489 AAAAAT-ATAATTATTT
1 AAAAATAATAATTATTT
179505 -AAAATAAT
1 AAAAATAAT
179513 TTTTAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 5 0.23
16 5 0.23
17 12 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAAATAATAATTATTT
Found at i:181037 original size:11 final size:11
Alignment explanation
Indices: 181021--181048 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
181011 GAGACATTAC
181021 CCGCCCCGCAT
1 CCGCCCCGCAT
181032 CCGCCCCGCAT
1 CCGCCCCGCAT
181043 CCGCCC
1 CCGCCC
181049 GCCCCACATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.68, G:0.18, T:0.07
Consensus pattern (11 bp):
CCGCCCCGCAT
Found at i:185099 original size:24 final size:22
Alignment explanation
Indices: 185052--185093 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
185042 TATAGATACG
185052 ATGGTATAAGAACAATTTTTAA
1 ATGGTATAAGAACAATTTTTAA
185074 ATGGTATAAGAACAATTTTT
1 ATGGTATAAGAACAATTTTT
185094 TAAAATTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (22 bp):
ATGGTATAAGAACAATTTTTAA
Found at i:187256 original size:15 final size:16
Alignment explanation
Indices: 187222--187264 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
187212 CTTATTTGAA
*
187222 ATAAAAAAAAGACTCG
1 ATAAAAAAAAGACTAG
*
187238 ATAAAAAAAAGA-TAT
1 ATAAAAAAAAGACTAG
*
187253 ATAAAAACAAGA
1 ATAAAAAAAAGA
187265 GAACTAATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.70, C:0.07, G:0.09, T:0.14
Consensus pattern (16 bp):
ATAAAAAAAAGACTAG
Found at i:187665 original size:24 final size:24
Alignment explanation
Indices: 187633--187718 Score: 102
Period size: 24 Copynumber: 3.6 Consensus size: 24
187623 TAAATAAAAA
*
187633 AACATAAACGAACAAGAACGGACG
1 AACATAAACGAACAAGAACGAACG
*
187657 AACATAAACGAACACGAACGAACG
1 AACATAAACGAACAAGAACGAACG
* * **
187681 AACATAAACAAAC-ACAATAAACG
1 AACATAAACGAACAAGAACGAACG
*
187704 GACATAAACGAACAA
1 AACATAAACGAACAA
187719 CACAGACAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 17 0.33
24 35 0.67
ACGTcount: A:0.58, C:0.22, G:0.14, T:0.06
Consensus pattern (24 bp):
AACATAAACGAACAAGAACGAACG
Found at i:187995 original size:14 final size:16
Alignment explanation
Indices: 187976--188007 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
187966 GCCCTCTGTT
187976 CGAACATA-AAT-GAA
1 CGAACATATAATCGAA
187990 CGAACATATAATCGAA
1 CGAACATATAATCGAA
188006 CG
1 CG
188008 TTCACGAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.50, C:0.19, G:0.16, T:0.16
Consensus pattern (16 bp):
CGAACATATAATCGAA
Found at i:192298 original size:31 final size:31
Alignment explanation
Indices: 192260--192321 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
192250 AAGAGTTCTA
192260 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
1 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
*
192291 TACGAGCTGTGGTGAGAGGATGAAGCTTTGC
1 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
192322 ATGCGTCATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.15, G:0.39, T:0.24
Consensus pattern (31 bp):
TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
Found at i:196029 original size:30 final size:30
Alignment explanation
Indices: 195986--196129 Score: 97
Period size: 30 Copynumber: 5.0 Consensus size: 30
195976 TTTTTAAAGC
* *
195986 CATATACCTTTCACTTTATTCATTTCATAG
1 CATATATCATTCACTTTATTCATTTCATAG
* * * *
196016 CATGTGTCATTCACTTCATTTATTTC--AG
1 CATATATCATTCACTTTATTCATTTCATAG
* *
196044 CACATATCATTCA-TTTAATTCATTTCGTAG
1 CATATATCATTCACTTT-ATTCATTTCATAG
* * *
196074 TC-TGTACCATTCA--TT-TTCATCTCATAG
1 -CATATATCATTCACTTTATTCATTTCATAG
**
196101 CATATATTTTTCACTTT-TTCATTTCATAG
1 CATATATCATTCACTTTATTCATTTCATAG
196130 TTCAATGTAA
Statistics
Matches: 86, Mismatches: 21, Indels: 15
0.70 0.17 0.12
Matches are distributed among these distances:
26 1 0.01
27 19 0.22
28 20 0.23
29 15 0.17
30 30 0.35
31 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.06, T:0.47
Consensus pattern (30 bp):
CATATATCATTCACTTTATTCATTTCATAG
Found at i:196371 original size:49 final size:50
Alignment explanation
Indices: 196241--196372 Score: 178
Period size: 49 Copynumber: 2.7 Consensus size: 50
196231 TTGATAATAT
* * *
196241 CATCACCGTCACACAGACGTCAGACATGCT-AATTATCATTTATTAGTAG
1 CATCACCGTCACAAAGACGTCAGACATGCTAAATCATCATTTAATAGTAG
* * *
196290 CACCACCGTCACAAAGATGTCAGACGTGCTAAATCATCA-TTAATAGTAG
1 CATCACCGTCACAAAGACGTCAGACATGCTAAATCATCATTTAATAGTAG
* *
196339 CATCACCATCACAAAGACGTCATACATGCTAAAT
1 CATCACCGTCACAAAGACGTCAGACATGCTAAAT
196373 GCTCCACCTC
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
49 64 0.90
50 7 0.10
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24
Consensus pattern (50 bp):
CATCACCGTCACAAAGACGTCAGACATGCTAAATCATCATTTAATAGTAG
Found at i:196507 original size:52 final size:52
Alignment explanation
Indices: 196435--196539 Score: 138
Period size: 52 Copynumber: 2.0 Consensus size: 52
196425 TAAATCATTT
* * * * * *
196435 ATCATTCACTTATCAGAATCTTTTCAAATATCATCACAATCAAGTATCATAC
1 ATCATTCACTCATCAAAATCTTTTCAAACATCAACAAAATCAAGTATAATAC
* *
196487 ATCATTCACTCATCAAAATCTTTTTAAACATTAACAAAATCAAGTATAATAC
1 ATCATTCACTCATCAAAATCTTTTCAAACATCAACAAAATCAAGTATAATAC
196539 A
1 A
196540 CTATAAATCT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.43, C:0.21, G:0.03, T:0.33
Consensus pattern (52 bp):
ATCATTCACTCATCAAAATCTTTTCAAACATCAACAAAATCAAGTATAATAC
Found at i:201770 original size:160 final size:160
Alignment explanation
Indices: 201536--201891 Score: 514
Period size: 160 Copynumber: 2.2 Consensus size: 160
201526 TATTCTATTG
* * *
201536 TGGTATAAGAGCATGTGGTTCAAATTTGGTAAAAAAAAATGGACTTAAAATAAATCATAAATTGA
1 TGGTTTAAGAGCATGTGGTTCAAATTTGGT-AAAAAAAATAGACTTAAAATAAATCACAAATTGA
* * *
201601 AGGAATAAGGAGATTATGAAAAATTGAATAACTAAATTGAAAAATAAAAAAATTGTTATAAAAAA
65 AGAAATAAGGAGATTATGAAAAATTGAAGAACTAAATTGAAAAATAAAAAAATTATTATAAAAAA
* *
201666 GATGAATTGAAGGTACACATGTATTTTACAA
130 GATGAATTGAAAGTACACATGTATTCTACAA
* * * * * *
201697 TGGTTTAGGAGCATGTAGATCAAATTTCGTAAAAAAAATAGACTTAAAATAAATGACGAATTGAA
1 TGGTTTAAGAGCATGTGGTTCAAATTTGGTAAAAAAAATAGACTTAAAATAAATCACAAATTGAA
* * * *
201762 GAAATAAGGAGATTATGAAAAATTGAAGGACTAAATTGAAAAATAGAAAATTTATTATCAAAAAG
66 GAAATAAGGAGATTATGAAAAATTGAAGAACTAAATTGAAAAATAAAAAAATTATTATAAAAAAG
* * *
201827 ATGAATTGAAATTATACATGTATTCTACTA
131 ATGAATTGAAAGTACACATGTATTCTACAA
201857 TGGTTTAAGAGCATGTGGTTCAAATTTGGTAAAAA
1 TGGTTTAAGAGCATGTGGTTCAAATTTGGTAAAAA
201892 TGAACTTAAA
Statistics
Matches: 170, Mismatches: 25, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
160 145 0.85
161 25 0.15
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.29
Consensus pattern (160 bp):
TGGTTTAAGAGCATGTGGTTCAAATTTGGTAAAAAAAATAGACTTAAAATAAATCACAAATTGAA
GAAATAAGGAGATTATGAAAAATTGAAGAACTAAATTGAAAAATAAAAAAATTATTATAAAAAAG
ATGAATTGAAAGTACACATGTATTCTACAA
Found at i:206007 original size:15 final size:15
Alignment explanation
Indices: 205987--206018 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
205977 AAAATCTTTC
*
205987 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTGGAT
206002 TTTCCCGTTCTGGAT
1 TTTCCCGTTCTGGAT
206017 TT
1 TT
206019 CAATCTGCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.25, G:0.16, T:0.53
Consensus pattern (15 bp):
TTTCCCGTTCTGGAT
Found at i:210281 original size:669 final size:669
Alignment explanation
Indices: 209001--210341 Score: 2506
Period size: 669 Copynumber: 2.0 Consensus size: 669
208991 TCGAGAGCAA
*
209001 AGTTTGTCAAATTTCCTCTATTGTTGCATCTTTGATAAGAAGCTCCAATTGATTCTCCTGCACAT
1 AGTTTGTCAAATTTCCTCTATTGTTGCATCTCTGATAAGAAGCTCCAATTGATTCTCCTGCACAT
209066 GTTGAAAGCCGCCTATGAATTCTGCAAGCAACATTTGTCTACCATTTGATGTAAACAAATTACGA
66 GTTGAAAGCCGCCTATGAATTCTGCAAGCAACATTTGTCTACCATTTGATGTAAACAAATTACGA
209131 AAAGAATTAGAGGCATGTTACCGCAAAACCTCAAGATCATCACACCACTTATTATCATCAGTCTT
131 AAAGAATTAGAGGCATGTTACCGCAAAACCTCAAGATCATCACACCACTTATTATCATCAGTCTT
209196 CAACATACAAACACTATTCCTTCTTCTTCTATTCAGCATGGACGCATGGAAAAATCTAGTGTTAC
196 CAACATACAAACACTATTCCTTCTTCTTCTATTCAGCATGGACGCATGGAAAAATCTAGTGTTAC
*
209261 AATCTTCTTGTTTGATCCATTTGCTACGAGACTTCTGGTACCACAGACTTTCCTCTTTCTTAAGA
261 AATCTTCTTGTTTGATCCATTTGCTACGAGACTTCTGGTACCACAGACTTTCCTCTTGCTTAAGA
*
209326 ACTATATCGAGTTCCTGCTTAAGGTTATCATATAGGTCCAAAATAAAAGGTGTCTCGGACTTTTC
326 ACTATATCGAGTTCCTGCTTAAGGTTATCATATAGGTCCAAAATAAAAGGTGACTCGGACTTTTC
209391 AAGGGCGATTTCAATTCCCAGTATCTGAGAGAGGAGAAGAGTCTTCTGTTTTCCAATATGGCCAA
391 AAGGGCGATTTCAATTCCCAGTATCTGAGAGAGGAGAAGAGTCTTCTGTTTTCCAATATGGCCAA
209456 AAACTTCAAGTTTCCATCTTCGAATTTTCTCTTAAAAGGTGAATAGATTATCAAAAATAGAAGCT
456 AAACTTCAAGTTTCCATCTTCGAATTTTCTCTTAAAAGGTGAATAGATTATCAAAAATAGAAGCT
* **
209521 TGATTGTTCCAATTGCTAGCCAAGAAATAACAAAAGTCAAGGTTACTAATAAAATTAAAACAGTG
521 TGATTGTTCCAATTGCTAGCCAAGAAAGAACAAAAGTCAAGGTTACTAATAAAATTAAAACAACG
209586 CAATGCATGATCAAACCTCCCGATTTTCGTTCGAATCCCCTTCGAAGGTTGTGTTCGTATGCCAT
586 CAATGCATGATCAAACCTCCCGATTTTCGTTCGAATCCCCTTCGAAGGTTGTGTTCGTATGCCAT
209651 TGTACATCACCTCCTTCAG
651 TGTACATCACCTCCTTCAG
*
209670 AGTTTGTCGAATTTCCTCTATTGTTGCATCTCTGATAAGAAGCTCCAATTGATTCTCCTGCACAT
1 AGTTTGTCAAATTTCCTCTATTGTTGCATCTCTGATAAGAAGCTCCAATTGATTCTCCTGCACAT
209735 GTTGAAAGCCGCCTATGAATTCTGCAAGCAACATTTGTCTACCATTTGATGTAAACAAATTACGA
66 GTTGAAAGCCGCCTATGAATTCTGCAAGCAACATTTGTCTACCATTTGATGTAAACAAATTACGA
*
209800 AAAGAATTAGAGGCATGTTACCGCAAAACCTCAAGATCATCACACCACTTATTATCATCCGTCTT
131 AAAGAATTAGAGGCATGTTACCGCAAAACCTCAAGATCATCACACCACTTATTATCATCAGTCTT
*
209865 CAACATACAAACATTATTCCTTCTTCTTCTATTCAGCATGGACGCATGGAAAAATCTAGTGTTAC
196 CAACATACAAACACTATTCCTTCTTCTTCTATTCAGCATGGACGCATGGAAAAATCTAGTGTTAC
* *
209930 AATCTTCTTGTTTGATCCATTTGCTACGAGACTTCTGGTACCATAGACTTTCCTCTTGCTTAAGG
261 AATCTTCTTGTTTGATCCATTTGCTACGAGACTTCTGGTACCACAGACTTTCCTCTTGCTTAAGA
209995 ACTATATCGAGTTCCTGCTTAAGGTTATCATATAGGTCCAAAATAAAAGGTGACTCGGACTTTTC
326 ACTATATCGAGTTCCTGCTTAAGGTTATCATATAGGTCCAAAATAAAAGGTGACTCGGACTTTTC
*
210060 AAGGGCGATTTCAATTCCTAGTAATC-GAGAGAGGAGAAGAGTCTT-TCGTTTTCCAATATGGCC
391 AAGGGCGATTTCAATTCCCAGT-ATCTGAGAGAGGAGAAGAGTCTTCT-GTTTTCCAATATGGCC
** *
210123 AAAAACTTCAAGTTTCCATCTTCGGCTTTTCTCTTAAAAGGTGAATAGATTATCAAAAATAGAAT
454 AAAAACTTCAAGTTTCCATCTTCGAATTTTCTCTTAAAAGGTGAATAGATTATCAAAAATAGAAG
210188 CTTGATTGTTCCAATTGCTAGCCAAGAAAGAACAAAAGTCAAGGTTACTAATAAAATTAAAACAA
519 CTTGATTGTTCCAATTGCTAGCCAAGAAAGAACAAAAGTCAAGGTTACTAATAAAATTAAAACAA
*
210253 CGCAATGCATGATCAAACCTCTCGATTTTCGTTCGAATCCCCTTCGAAGGTTGTGTTCGTATGCC
584 CGCAATGCATGATCAAACCTCCCGATTTTCGTTCGAATCCCCTTCGAAGGTTGTGTTCGTATGCC
210318 ATTGTACATCACCTCCTTCAG
649 ATTGTACATCACCTCCTTCAG
210339 AGT
1 AGT
210342 GAATCAGCTC
Statistics
Matches: 654, Mismatches: 16, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
668 1 0.00
669 650 0.99
670 3 0.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (669 bp):
AGTTTGTCAAATTTCCTCTATTGTTGCATCTCTGATAAGAAGCTCCAATTGATTCTCCTGCACAT
GTTGAAAGCCGCCTATGAATTCTGCAAGCAACATTTGTCTACCATTTGATGTAAACAAATTACGA
AAAGAATTAGAGGCATGTTACCGCAAAACCTCAAGATCATCACACCACTTATTATCATCAGTCTT
CAACATACAAACACTATTCCTTCTTCTTCTATTCAGCATGGACGCATGGAAAAATCTAGTGTTAC
AATCTTCTTGTTTGATCCATTTGCTACGAGACTTCTGGTACCACAGACTTTCCTCTTGCTTAAGA
ACTATATCGAGTTCCTGCTTAAGGTTATCATATAGGTCCAAAATAAAAGGTGACTCGGACTTTTC
AAGGGCGATTTCAATTCCCAGTATCTGAGAGAGGAGAAGAGTCTTCTGTTTTCCAATATGGCCAA
AAACTTCAAGTTTCCATCTTCGAATTTTCTCTTAAAAGGTGAATAGATTATCAAAAATAGAAGCT
TGATTGTTCCAATTGCTAGCCAAGAAAGAACAAAAGTCAAGGTTACTAATAAAATTAAAACAACG
CAATGCATGATCAAACCTCCCGATTTTCGTTCGAATCCCCTTCGAAGGTTGTGTTCGTATGCCAT
TGTACATCACCTCCTTCAG
Found at i:218714 original size:37 final size:36
Alignment explanation
Indices: 218656--218774 Score: 161
Period size: 35 Copynumber: 3.3 Consensus size: 36
218646 TCTCATTACA
* *
218656 ATTTTTC-AACAAATATCTACCAAACTTTGAAAAAAC
1 ATTTTTCAAAGAAATATTTACCAAACTTTG-AAAAAC
*
218692 ATTTTTCAAAGAAATATTTACCAAACTTTGAAAACC
1 ATTTTTCAAAGAAATATTTACCAAACTTTGAAAAAC
* *
218728 A-TTTTCAAAGAAACATTTACCAAACTTTGAAAATC
1 ATTTTTCAAAGAAATATTTACCAAACTTTGAAAAAC
218763 ATTTTTTCAAAG
1 A-TTTTTCAAAG
218775 TTGGTTGCCA
Statistics
Matches: 75, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 33 0.44
36 13 0.17
37 29 0.39
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.34
Consensus pattern (36 bp):
ATTTTTCAAAGAAATATTTACCAAACTTTGAAAAAC
Found at i:218731 original size:21 final size:20
Alignment explanation
Indices: 218707--218766 Score: 51
Period size: 21 Copynumber: 3.2 Consensus size: 20
218697 TCAAAGAAAT
218707 ATTTACCAAACTTTGAAAACC
1 ATTTACCAAACTTTGAAAA-C
*
218728 ATTT-TCAAA----G-AAAC
1 ATTTACCAAACTTTGAAAAC
218742 ATTTACCAAACTTTGAAAATC
1 ATTTACCAAACTTTGAAAA-C
218763 ATTT
1 ATTT
218767 TTTCAAAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
14 5 0.17
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 9 0.30
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.33
Consensus pattern (20 bp):
ATTTACCAAACTTTGAAAAC
Found at i:223311 original size:37 final size:37
Alignment explanation
Indices: 223256--223373 Score: 163
Period size: 35 Copynumber: 3.3 Consensus size: 37
223246 TCTCATTACA
*
223256 ATTTTTC-AACAAACATTTACCAAACTTTGAAAAACC
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACC
*
223292 ATTTTTCAAAGAAACATTTATCAAACTTTG-AAAACC
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACC
* *
223328 A-TTTTCAAAGAAACATTTACCAAA-TTTTAAAAATC
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACC
223363 ATTTTTTCAAA
1 A-TTTTTCAAA
223374 ATTAATTGCC
Statistics
Matches: 73, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
34 3 0.04
35 28 0.38
36 14 0.19
37 28 0.38
ACGTcount: A:0.45, C:0.17, G:0.03, T:0.35
Consensus pattern (37 bp):
ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACC
Found at i:224479 original size:60 final size:61
Alignment explanation
Indices: 224363--224488 Score: 139
Period size: 60 Copynumber: 2.1 Consensus size: 61
224353 ATCATTCTGA
* * * * *
224363 AACTTTTAATAGTCGAGGGACTCGACAAAGCAACACTCTATAGTCAGAGGATCATTT-TGT
1 AACTTTTAATAGTCGAGGGACTCAAAAAAGCAACACCCTATAATCAGAGGACCATTTGTGT
* * ** * *
224423 AACTTTTAATAGTCGAGGGACTTAAAAAAGTAGTACCCTGTAATCAGTGGACCATTTGTGT
1 AACTTTTAATAGTCGAGGGACTCAAAAAAGCAACACCCTATAATCAGAGGACCATTTGTGT
224484 -ACTTT
1 AACTTT
224489 ACCCTTAATA
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 51 0.94
61 3 0.06
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.31
Consensus pattern (61 bp):
AACTTTTAATAGTCGAGGGACTCAAAAAAGCAACACCCTATAATCAGAGGACCATTTGTGT
Found at i:233214 original size:2 final size:2
Alignment explanation
Indices: 233207--233245 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
233197 ACTTCTACTA
233207 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
233246 CTCGCGCATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:241117 original size:28 final size:28
Alignment explanation
Indices: 241084--241146 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
241074 GATACACCCT
241084 GAAATTTTATTTGTGTCCATCTATTAAA
1 GAAATTTTATTTGTGTCCATCTATTAAA
241112 GAAATTTTATTTGTGTCCATCTATTAAA
1 GAAATTTTATTTGTGTCCATCTATTAAA
*
241140 AAAATTT
1 GAAATTT
241147 GTGTTACTGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.46
Consensus pattern (28 bp):
GAAATTTTATTTGTGTCCATCTATTAAA
Found at i:244310 original size:24 final size:24
Alignment explanation
Indices: 244278--244324 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
244268 AATCCTGAAT
244278 TTTAGAACATATTTAAGGAAAAAC
1 TTTAGAACATATTTAAGGAAAAAC
244302 TTTAGAACATATTTAAGGAAAAA
1 TTTAGAACATATTTAAGGAAAAA
244325 TTGTGGGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.51, C:0.06, G:0.13, T:0.30
Consensus pattern (24 bp):
TTTAGAACATATTTAAGGAAAAAC
Found at i:248132 original size:20 final size:20
Alignment explanation
Indices: 248107--248144 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
248097 TATGAAAAAA
248107 AATATTATATATTTTTAATT
1 AATATTATATATTTTTAATT
* *
248127 AATATTTTTTATTTTTAA
1 AATATTATATATTTTTAA
248145 AAATGGTTAA
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
AATATTATATATTTTTAATT
Found at i:248549 original size:18 final size:19
Alignment explanation
Indices: 248514--248550 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
248504 CACGGAATGT
248514 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
248534 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
248551 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:258423 original size:16 final size:18
Alignment explanation
Indices: 258386--258428 Score: 56
Period size: 16 Copynumber: 2.5 Consensus size: 18
258376 AATAACTTAA
258386 AATAATTTTATATTGTTT
1 AATAATTTTATATTGTTT
258404 -ATAA-TTTATATT-TTT
1 AATAATTTTATATTGTTT
258419 AATAAATTTT
1 AAT-AATTTT
258429 GTATACAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 3 0.14
16 10 0.45
17 6 0.27
18 3 0.14
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
AATAATTTTATATTGTTT
Found at i:260485 original size:35 final size:37
Alignment explanation
Indices: 260433--260504 Score: 130
Period size: 35 Copynumber: 2.0 Consensus size: 37
260423 TTAAATTCCG
260433 ATAAATATTTTGGTATAATCACATATTTGG-CCTTGT
1 ATAAATATTTTGGTATAATCACATATTTGGTCCTTGT
260469 ATAAATA-TTTGGTATAATCACATATTTGGTCCTTGT
1 ATAAATATTTTGGTATAATCACATATTTGGTCCTTGT
260505 TATTTATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 22 0.63
36 13 0.37
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (37 bp):
ATAAATATTTTGGTATAATCACATATTTGGTCCTTGT
Found at i:260495 original size:17 final size:17
Alignment explanation
Indices: 260441--260498 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
260431 CGATAAATAT
260441 TTTGGTATAATCACATA
1 TTTGGTATAATCACATA
* *
260458 TTTGGCCT-TGTAT-AAATA
1 TTTGG--TAT-AATCACATA
260476 TTTGGTATAATCACATA
1 TTTGGTATAATCACATA
260493 TTTGGT
1 TTTGGT
260499 CCTTGTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
16 3 0.09
17 16 0.50
18 10 0.31
19 3 0.09
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45
Consensus pattern (17 bp):
TTTGGTATAATCACATA
Found at i:263761 original size:21 final size:21
Alignment explanation
Indices: 263731--263778 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
263721 AAAAAAATTT
* *
263731 GGGTTCGGGTCAGGTCGAGTC
1 GGGTTTGGGTCAAGTCGAGTC
263752 GGGTTTGGGTCAAGTCGAGTC
1 GGGTTTGGGTCAAGTCGAGTC
*
263773 GTGTTT
1 GGGTTT
263779 TTTTTAATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.10, C:0.15, G:0.44, T:0.31
Consensus pattern (21 bp):
GGGTTTGGGTCAAGTCGAGTC
Found at i:277625 original size:15 final size:15
Alignment explanation
Indices: 277605--277636 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
277595 ACAGATAGAA
277605 TTTTTATATAAATAT
1 TTTTTATATAAATAT
*
277620 TTTTTATTTAAATAT
1 TTTTTATATAAATAT
277635 TT
1 TT
277637 AGAATTTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTTATATAAATAT
Found at i:291057 original size:46 final size:45
Alignment explanation
Indices: 290997--291085 Score: 126
Period size: 46 Copynumber: 2.0 Consensus size: 45
290987 AAAATAGCCA
*
290997 GAGTGCATCGATGCATAGCT-TGTGCATCGATGCATCAAAATGCACT
1 GAGTGCATCAATGCAT-GCTATGTGCATCGATGCAT-AAAATGCACT
* *
291043 GAGTGCATCAATGCATGGTATGTGCATCGATGTATAAAATGCA
1 GAGTGCATCAATGCATGCTATGTGCATCGATGCATAAAATGCA
291086 TTCGATGTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
45 10 0.26
46 29 0.74
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (45 bp):
GAGTGCATCAATGCATGCTATGTGCATCGATGCATAAAATGCACT
Found at i:292204 original size:21 final size:21
Alignment explanation
Indices: 292170--292213 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
292160 CCGGAGGAGG
* *
292170 AGGAGGAGCACGAGAAGAGCT
1 AGGAGCAGCACGAGAAGAACT
*
292191 AGGAGCAGCTCGAGAAGAACT
1 AGGAGCAGCACGAGAAGAACT
292212 AG
1 AG
292214 CTCCCGGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.16, G:0.39, T:0.07
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAACT
Found at i:300081 original size:37 final size:37
Alignment explanation
Indices: 300031--300106 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
300021 GGTCGAAAAG
* *
300031 CTAAACAAAGCAATGCCCTTAGTCGAGGGATTATGTA
1 CTAAACAAAGCAATGCCCTTAGTCGAGAGACTATGTA
*
300068 CTAAAGAAAGCAATGCCCTTAGTCGAGAGACTATGTA
1 CTAAACAAAGCAATGCCCTTAGTCGAGAGACTATGTA
300105 CT
1 CT
300107 CAATAAGATG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.24
Consensus pattern (37 bp):
CTAAACAAAGCAATGCCCTTAGTCGAGAGACTATGTA
Found at i:306441 original size:128 final size:127
Alignment explanation
Indices: 306209--306466 Score: 507
Period size: 128 Copynumber: 2.0 Consensus size: 127
306199 CCTAAAAAAC
306209 GGTTAATATACGATGTGATAGGTTAAATAAATGATCGGTTAAAATTTAAACCAGTTATGTTATAT
1 GGTTAATATACGATGTGATAGGTTAAATAAATGATCGGTTAAAATTTAAACCAGTTATGTTATAT
306274 TATTTAACCGGAAATATTATAAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATA
66 TATTTAACCGGAAATATTATAAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATA
306336 GGTTAAATATACGATGTGATAGGTTAAATAAATGATCGGTTAAAATTTAAACCAGTTATGTTATA
1 GGTT-AATATACGATGTGATAGGTTAAATAAATGATCGGTTAAAATTTAAACCAGTTATGTTATA
306401 TTATTTAACCGGAAATATTATAAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATA
65 TTATTTAACCGGAAATATTATAAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATA
306464 GGT
1 GGT
306467 GGCGCTTATA
Statistics
Matches: 130, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
127 4 0.03
128 126 0.97
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (127 bp):
GGTTAATATACGATGTGATAGGTTAAATAAATGATCGGTTAAAATTTAAACCAGTTATGTTATAT
TATTTAACCGGAAATATTATAAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATA
Found at i:308014 original size:60 final size:60
Alignment explanation
Indices: 307901--308014 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
307891 AATAGTGGGG
* * * * * **
307901 TGACCATTTTCTAACTTTTAATAATCTAGGGACTTAACAAATCAACATTCTATAATCGAA
1 TGACCATTTTATAAATTTTAATAACCGAGGGACTTAACAAAGCAACACCCTATAATCGAA
* * *
307961 TGACGATTTTATAAATTTTAATAACCGAGGGACTTAATAAAGCAATACCCTATA
1 TGACCATTTTATAAATTTTAATAACCGAGGGACTTAACAAAGCAACACCCTATA
308015 GACATGAGAT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 44 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (60 bp):
TGACCATTTTATAAATTTTAATAACCGAGGGACTTAACAAAGCAACACCCTATAATCGAA
Found at i:311060 original size:2 final size:2
Alignment explanation
Indices: 311053--311085 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
311043 CACGCACTCC
311053 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
311086 CTGTTCGAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:315337 original size:30 final size:30
Alignment explanation
Indices: 314801--315320 Score: 1013
Period size: 30 Copynumber: 17.3 Consensus size: 30
314791 GAAGGACCTA
*
314801 TCCAGAGGTCATAAAGATCCTCAGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
314831 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
314861 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
314891 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
314921 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
314951 TCCAGAGGTCATAAAGATCCTCAGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
314981 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
315011 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
315041 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
315071 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
315101 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
315131 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
315161 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
315191 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
315221 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
315251 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
315281 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
315311 TCCATAGGTC
1 TCCAGAGGTC
315321 CCGAAGAACC
Statistics
Matches: 486, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 486 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:315393 original size:31 final size:30
Alignment explanation
Indices: 315303--315398 Score: 95
Period size: 31 Copynumber: 3.1 Consensus size: 30
315293 AAAGATCCTC
* * *
315303 GGTAACTGTCCATAGGTCCCGAAGAACCTA
1 GGTAACTGTCCATATGTCTCGAAGAACATA
* **
315333 GGTAAACTATCCATATGT-TCCTTAGAACATA
1 GGT-AACTGTCCATATGTCT-CGAAGAACATA
*
315364 GGTATACTGTCCATATGTCTCGAAAAACATA
1 GGTA-ACTGTCCATATGTCTCGAAGAACATA
315395 GGTA
1 GGTA
315399 GTCCTTTGAC
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
30 4 0.08
31 47 0.90
32 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (30 bp):
GGTAACTGTCCATATGTCTCGAAGAACATA
Found at i:315761 original size:2 final size:2
Alignment explanation
Indices: 315749--315783 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
315739 TACACAACTC
315749 AT AT A- 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
315784 TGTAACATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:320238 original size:30 final size:30
Alignment explanation
Indices: 319642--320221 Score: 1142
Period size: 30 Copynumber: 19.3 Consensus size: 30
319632 GAAAGACCTA
*
319642 TCCAGAGGTCATAAAGATCCTCAGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
319672 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
319702 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
319732 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
319762 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
319792 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
319822 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
319852 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
319882 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
319912 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
319942 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
319972 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
320002 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
320032 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
320062 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
320092 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
320122 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
320152 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
320182 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
320212 TCCATAGGTC
1 TCCAGAGGTC
320222 CCGAAGAACC
Statistics
Matches: 548, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 548 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:320294 original size:31 final size:30
Alignment explanation
Indices: 320204--320299 Score: 95
Period size: 31 Copynumber: 3.1 Consensus size: 30
320194 AAAGATCCTC
* * *
320204 GGTAACTGTCCATAGGTCCCGAAGAACCTA
1 GGTAACTGTCCATATGTCTCGAAGAACATA
* **
320234 GGTAAACTATCCATATGT-TCCTTAGAACATA
1 GGT-AACTGTCCATATGTCT-CGAAGAACATA
*
320265 GGTATACTGTCCATATGTCTCGAAAAACATA
1 GGTA-ACTGTCCATATGTCTCGAAGAACATA
320296 GGTA
1 GGTA
320300 GTTCTTTGAC
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
30 4 0.08
31 47 0.90
32 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (30 bp):
GGTAACTGTCCATATGTCTCGAAGAACATA
Found at i:322196 original size:23 final size:22
Alignment explanation
Indices: 322169--322218 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
322159 CCAAACGACA
322169 AAAAAACGTG-TCATAAAGGTAG
1 AAAAAACGTGCT-ATAAAGGTAG
*
322191 AGAAAAACTTGCTATAAAGGTAG
1 A-AAAAACGTGCTATAAAGGTAG
322214 AAAAA
1 AAAAA
322219 GACCATAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 5 0.20
23 19 0.76
24 1 0.04
ACGTcount: A:0.54, C:0.08, G:0.20, T:0.18
Consensus pattern (22 bp):
AAAAAACGTGCTATAAAGGTAG
Found at i:323350 original size:31 final size:29
Alignment explanation
Indices: 323315--323373 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
323305 GTTGATGGCT
*
323315 TGATTAACATCATTTAAATAGTTAAGTGGTA
1 TGATTAACA-CAATTAAA-AGTTAAGTGGTA
* *
323346 TGATTGACACAATTAAAAGTTGAGTGGT
1 TGATTAACACAATTAAAAGTTAAGTGGT
323374 CGGATTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 10 0.40
30 7 0.28
31 8 0.32
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.36
Consensus pattern (29 bp):
TGATTAACACAATTAAAAGTTAAGTGGTA
Found at i:327332 original size:36 final size:38
Alignment explanation
Indices: 327292--327367 Score: 93
Period size: 40 Copynumber: 2.0 Consensus size: 38
327282 ACTTAGCGTT
327292 AAGTTTTGAACG-GA-TACTAAAATGAAACAAAAACTA
1 AAGTTTTGAACGAGAGTACTAAAATGAAACAAAAACTA
* * *
327328 AAGTTTTTAATGACGATGTACTAAAATGAAACACAAACTA
1 AAGTTTTGAACGA-GA-GTACTAAAATGAAACAAAAACTA
327368 CACTATAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 10 0.30
38 2 0.06
40 21 0.64
ACGTcount: A:0.50, C:0.12, G:0.13, T:0.25
Consensus pattern (38 bp):
AAGTTTTGAACGAGAGTACTAAAATGAAACAAAAACTA
Found at i:327575 original size:16 final size:16
Alignment explanation
Indices: 327554--327601 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
327544 AAAAAAGCAA
327554 TTTATTCACTGAATTT
1 TTTATTCACTGAATTT
*
327570 TTTATTTACT--ATTAT
1 TTTATTCACTGAATT-T
*
327585 TTTAGTCACTGAATTT
1 TTTATTCACTGAATTT
327601 T
1 T
327602 AAAAATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
14 3 0.12
15 9 0.35
16 11 0.42
17 3 0.12
ACGTcount: A:0.25, C:0.10, G:0.06, T:0.58
Consensus pattern (16 bp):
TTTATTCACTGAATTT
Found at i:328124 original size:13 final size:13
Alignment explanation
Indices: 328091--328126 Score: 51
Period size: 11 Copynumber: 3.0 Consensus size: 13
328081 TTAATTAGGT
328091 TTCTATATT-TTA
1 TTCTATATTATTA
328103 TT-TAT-TTATTA
1 TTCTATATTATTA
328114 TTCTATATTATTA
1 TTCTATATTATTA
328127 ATTAATTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 2 0.10
11 8 0.38
12 5 0.24
13 6 0.29
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.67
Consensus pattern (13 bp):
TTCTATATTATTA
Found at i:328134 original size:21 final size:22
Alignment explanation
Indices: 328091--328134 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
328081 TTAATTAGGT
* *
328091 TTCTATATTTTATTTATTTATTA
1 TTCTATA-TTTATTAATTAATTA
328114 TTCTATA-TTATTAATTAATTA
1 TTCTATATTTATTAATTAATTA
328135 GATATTAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.63
23 7 0.37
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (22 bp):
TTCTATATTTATTAATTAATTA
Found at i:331158 original size:45 final size:44
Alignment explanation
Indices: 331102--331226 Score: 118
Period size: 45 Copynumber: 2.9 Consensus size: 44
331092 CTTAAATTTT
*
331102 AAATATTATTTTATTTTTATCTTAATTTTAAAATAGTATAATA-A
1 AAATA-TATTTTATTTTTATCTTAATTTTAAAATATTATAATATA
* * *
331146 TAAA-ATA---TA-TTTTCTCTTAATTTTAAAATATTTTAATTTAA
1 -AAATATATTTTATTTTTATCTTAATTTTAAAATATTATAATAT-A
* * *
331187 AAATGTATTTTATTTTAATTTTAATTTTAAAATATTATAA
1 AAATATATTTTATTTTTATCTTAATTTTAAAATATTATAA
331227 GATTAAAGTA
Statistics
Matches: 64, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
39 25 0.39
40 5 0.08
41 3 0.05
43 2 0.03
44 3 0.05
45 26 0.41
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (44 bp):
AAATATATTTTATTTTTATCTTAATTTTAAAATATTATAATATA
Found at i:331172 original size:75 final size:75
Alignment explanation
Indices: 331027--331172 Score: 188
Period size: 75 Copynumber: 1.9 Consensus size: 75
331017 TTAACATTAA
* * * *
331027 AAATATATATTTATTTTTATCTTAATTTTAAAATGTTATAAGAATAAATTGCATTTTATTTTTAT
1 AAATATATATTTATTTTTATCTTAATTTTAAAATGTTATAAGAATAAAATACATTTTATCTTAAT
331092 CTTAAATTTT
66 CTTAAATTTT
* * *
331102 AAATAT-TATTTTATTTTTATCTTAATTTTAAAATAG-TATAATAATAAAATATATTTTCTCTTA
1 AAATATATA-TTTATTTTTATCTTAATTTTAAAAT-GTTATAAGAATAAAATACATTTTATCTTA
*
331165 ATTTTAAA
64 ATCTTAAA
331173 ATATTTTAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
74 2 0.03
75 58 0.95
76 1 0.02
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.53
Consensus pattern (75 bp):
AAATATATATTTATTTTTATCTTAATTTTAAAATGTTATAAGAATAAAATACATTTTATCTTAAT
CTTAAATTTT
Found at i:331175 original size:39 final size:39
Alignment explanation
Indices: 331116--331210 Score: 120
Period size: 39 Copynumber: 2.4 Consensus size: 39
331106 ATTATTTTAT
331116 TTTTATCTTAATTTTAAAATAGTATAATA-ATAAAATATA
1 TTTTATCTTAATTTTAAAATAGTATAATATA-AAAATATA
* * * * *
331155 TTTTCTCTTAATTTTAAAATATTTTAATTTAAAAATGTA
1 TTTTATCTTAATTTTAAAATAGTATAATATAAAAATATA
*
331194 TTTTATTTTAATTTTAA
1 TTTTATCTTAATTTTAA
331211 TTTTAAAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 47 0.98
40 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (39 bp):
TTTTATCTTAATTTTAAAATAGTATAATATAAAAATATA
Found at i:331197 original size:18 final size:16
Alignment explanation
Indices: 331162--331204 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
331152 ATATTTTCTC
*
331162 TTAATTTTAAAATATT
1 TTAATTTAAAAATATT
331178 TTAATTTAAAAATGTATT
1 TTAATTTAAAAA--TATT
*
331196 TTATTTTAA
1 TTAATTTAA
331205 TTTTAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 11 0.48
18 12 0.52
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
TTAATTTAAAAATATT
Found at i:331251 original size:17 final size:19
Alignment explanation
Indices: 331217--331254 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
331207 TTAATTTTAA
331217 AATATTATAAGATTAAAGT
1 AATATTATAAGATTAAAGT
331236 AATATT-TAAG-TTAAAGT
1 AATATTATAAGATTAAAGT
331253 AA
1 AA
331255 GAATAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
18 4 0.21
19 6 0.32
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.37
Consensus pattern (19 bp):
AATATTATAAGATTAAAGT
Found at i:334755 original size:19 final size:19
Alignment explanation
Indices: 334698--334755 Score: 75
Period size: 17 Copynumber: 3.1 Consensus size: 19
334688 TTAGAGATAT
*
334698 TTTATAGTAATAATTCTAAA
1 TTTATA-TAATAATTTTAAA
334718 TTTATATAAT-ATTTT-AA
1 TTTATATAATAATTTTAAA
*
334735 TTTTTATAATAATTTTAAA
1 TTTATATAATAATTTTAAA
334754 TT
1 TT
334756 GGGTAAACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
17 11 0.32
18 9 0.26
19 8 0.24
20 6 0.18
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (19 bp):
TTTATATAATAATTTTAAA
Found at i:335238 original size:25 final size:25
Alignment explanation
Indices: 335186--335238 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
335176 ATTATGTATG
*
335186 AATTTTTAAAATTTTAAAATAATTA
1 AATTTTTAAAATTTTAAAATAATAA
335211 AATTTATT-AAATTTTAAAAATAA-AA
1 AATTT-TTAAAATTTT-AAAATAATAA
335236 AAT
1 AAT
335239 AAATTATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 16 0.64
26 9 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
AATTTTTAAAATTTTAAAATAATAA
Found at i:335244 original size:25 final size:25
Alignment explanation
Indices: 335194--335244 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
335184 TGAATTTTTA
* **
335194 AAATTTTAAAATAATTAAATTTATT
1 AAATTTTAAAATAATAAAATAAATT
335219 AAATTTTAAAAATAA-AAAATAAATT
1 AAATTTT-AAAATAATAAAATAAATT
335244 A
1 A
335245 TCAATTGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
AAATTTTAAAATAATAAAATAAATT
Found at i:343484 original size:17 final size:17
Alignment explanation
Indices: 343462--343495 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
343452 ACAATTATTT
343462 TAAATAATATCTAATTA
1 TAAATAATATCTAATTA
343479 TAAATAATATCTAATTA
1 TAAATAATATCTAATTA
343496 ATTTGATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATAATATCTAATTA
Found at i:346470 original size:17 final size:17
Alignment explanation
Indices: 346448--346482 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
346438 GAGAGACTTC
346448 GAGGATTTGTATAACAG
1 GAGGATTTGTATAACAG
346465 GAGGATTTGTATAACAG
1 GAGGATTTGTATAACAG
346482 G
1 G
346483 TTCTCGTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.06, G:0.31, T:0.29
Consensus pattern (17 bp):
GAGGATTTGTATAACAG
Found at i:356423 original size:16 final size:16
Alignment explanation
Indices: 356402--356436 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
356392 TTTTTTTAAG
356402 GATTATGTTGGGTCGA
1 GATTATGTTGGGTCGA
356418 GATTATGTTGGGTCGA
1 GATTATGTTGGGTCGA
356434 GAT
1 GAT
356437 CGAGTTTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.20, C:0.06, G:0.37, T:0.37
Consensus pattern (16 bp):
GATTATGTTGGGTCGA
Found at i:358029 original size:64 final size:64
Alignment explanation
Indices: 357921--358043 Score: 176
Period size: 64 Copynumber: 1.9 Consensus size: 64
357911 AATTGAAAAT
* * *
357921 AATATATTCGGGCTATTAATTAGTATCCGAATAAAATCAGAAATATTCAATTAATACCGCTTTA
1 AATATATTCGGGCTATTAATTAGTATCCGAATAAAATCAAAAATAATCAATTAACACCGCTTTA
* * *
357985 AATATATTTC-GGCTGTTAATTAGTATCTGAATAAAATTAAAAATAATCAATTAACACCG
1 AATATA-TTCGGGCTATTAATTAGTATCCGAATAAAATCAAAAATAATCAATTAACACCG
358044 TATTATATCA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
64 49 0.94
65 3 0.06
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (64 bp):
AATATATTCGGGCTATTAATTAGTATCCGAATAAAATCAAAAATAATCAATTAACACCGCTTTA
Found at i:360018 original size:23 final size:23
Alignment explanation
Indices: 359992--360068 Score: 68
Period size: 23 Copynumber: 3.3 Consensus size: 23
359982 GGAGAGAAAA
359992 AAACGTGCCACAAAGCTAAAGAT
1 AAACGTGCCACAAAGCTAAAGAT
*
360015 AAACATGCCACAAATGC-ATAA-AT
1 AAACGTGCCACAAA-GCTA-AAGAT
* * * *
360038 AAACGTGCAACACAGGTAGAGAT
1 AAACGTGCCACAAAGCTAAAGAT
*
360061 AAATGTGC
1 AAACGTGC
360069 AACACATGCA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
22 2 0.05
23 37 0.86
24 4 0.09
ACGTcount: A:0.47, C:0.19, G:0.18, T:0.16
Consensus pattern (23 bp):
AAACGTGCCACAAAGCTAAAGAT
Found at i:360078 original size:46 final size:45
Alignment explanation
Indices: 359988--360082 Score: 102
Period size: 46 Copynumber: 2.1 Consensus size: 45
359978 CGAGGGAGAG
* *
359988 AAAA-AAACGTGCCACAAAGCTAAAGATAAACATGCCACAAATGC
1 AAAATAAACGTGCAACAAAGCTAAAGATAAACATGCAACAAATGC
* * * ** *
360032 ATAAATAAACGTGCAACACAGGTAGAGATAAATGTGCAACACATGC
1 A-AAATAAACGTGCAACAAAGCTAAAGATAAACATGCAACAAATGC
360078 AAAAT
1 AAAAT
360083 TATTCTTATT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
44 1 0.02
45 7 0.17
46 33 0.80
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.15
Consensus pattern (45 bp):
AAAATAAACGTGCAACAAAGCTAAAGATAAACATGCAACAAATGC
Found at i:360110 original size:12 final size:13
Alignment explanation
Indices: 360093--360121 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
360083 TATTCTTATT
360093 AAAAAATAAA-AG
1 AAAAAATAAAGAG
360105 AAAAAATAAAGAG
1 AAAAAATAAAGAG
360118 AAAA
1 AAAA
360122 GAGAACTGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (13 bp):
AAAAAATAAAGAG
Found at i:360847 original size:21 final size:20
Alignment explanation
Indices: 360809--360848 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
360799 AATAATTTGA
*
360809 CCAAAAAAAATATCGGAAGG
1 CCAAAAAAAATATAGGAAGG
*
360829 CCAATAAAAAATGTAGGAAG
1 CCAA-AAAAAATATAGGAAG
360849 AGAAGTCAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.55, C:0.12, G:0.20, T:0.12
Consensus pattern (20 bp):
CCAAAAAAAATATAGGAAGG
Found at i:364004 original size:14 final size:14
Alignment explanation
Indices: 363981--364036 Score: 103
Period size: 14 Copynumber: 4.0 Consensus size: 14
363971 CGCTGGGCAT
*
363981 CCGAGACCATCCGA
1 CCGAGGCCATCCGA
363995 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
364009 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
364023 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
364037 ATGAACTATG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
14 41 1.00
ACGTcount: A:0.23, C:0.43, G:0.27, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:364150 original size:10 final size:10
Alignment explanation
Indices: 364131--364218 Score: 68
Period size: 10 Copynumber: 8.5 Consensus size: 10
364121 CCTACCCTCG
*
364131 CTCGGTTGCC
1 CTCGGATGCC
364141 CTCGGATGCC
1 CTCGGATGCC
*
364151 CTCGCATAGCTC
1 CTCGGAT-GC-C
* *
364163 GTTCGGATGGC
1 -CTCGGATGCC
*
364174 CTCGGATGCT
1 CTCGGATGCC
*
364184 CTCGGATGGC
1 CTCGGATGCC
*
364194 CTCGGATGCT
1 CTCGGATGCC
* *
364204 TTCGGATGGC
1 CTCGGATGCC
364214 CTCGG
1 CTCGG
364219 TCGAATGGCC
Statistics
Matches: 59, Mismatches: 16, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
10 49 0.83
11 3 0.05
12 2 0.03
13 5 0.08
ACGTcount: A:0.09, C:0.32, G:0.33, T:0.26
Consensus pattern (10 bp):
CTCGGATGCC
Found at i:364190 original size:20 final size:20
Alignment explanation
Indices: 364131--364218 Score: 104
Period size: 20 Copynumber: 4.2 Consensus size: 20
364121 CCTACCCTCG
* * *
364131 CTCGGTTGCCCTCGGATGCC
1 CTCGGATGCTCTCGGATGGC
*
364151 CTCGCATAGCTCGTTCGGATGGC
1 CTCGGAT-GCTC--TCGGATGGC
364174 CTCGGATGCTCTCGGATGGC
1 CTCGGATGCTCTCGGATGGC
*
364194 CTCGGATGCTTTCGGATGGC
1 CTCGGATGCTCTCGGATGGC
364214 CTCGG
1 CTCGG
364219 TCGAATGGCC
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
20 38 0.64
21 3 0.05
22 4 0.07
23 14 0.24
ACGTcount: A:0.09, C:0.32, G:0.33, T:0.26
Consensus pattern (20 bp):
CTCGGATGCTCTCGGATGGC
Found at i:366839 original size:56 final size:56
Alignment explanation
Indices: 366753--366896 Score: 202
Period size: 56 Copynumber: 2.6 Consensus size: 56
366743 GTACACCTGA
* ** * *
366753 CATGTGTTTTATCATCATTTTAAATATATGTCATGTCATC-ACTTATATACATGTGT
1 CATGTGTTATATCATCATTTTGGACATATGTCATGTCATCGA-TTATATACATGTGC
*
366809 CATGTGCTATATCATCATTTTGGACATATGTCATGTCATCGATTATATACATGTGC
1 CATGTGTTATATCATCATTTTGGACATATGTCATGTCATCGATTATATACATGTGC
366865 CATGTGTTATAGT-ATCATTTTGGACATATGTC
1 CATGTGTTATA-TCATCATTTTGGACATATGTC
366897 TTGCCACATT
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
56 77 0.97
57 2 0.03
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (56 bp):
CATGTGTTATATCATCATTTTGGACATATGTCATGTCATCGATTATATACATGTGC
Found at i:368486 original size:20 final size:19
Alignment explanation
Indices: 368461--368514 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
368451 GCGAAATAAA
368461 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATCT-CAG
** *
368481 AATCGCAAATCAGTTCTCAG
1 AATCGCAACGC-GATCTCAG
368501 AATCGCAACGCGAT
1 AATCGCAACGCGAT
368515 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 21 0.78
21 4 0.15
ACGTcount: A:0.33, C:0.30, G:0.19, T:0.19
Consensus pattern (19 bp):
AATCGCAACGCGATCTCAG
Found at i:368525 original size:21 final size:20
Alignment explanation
Indices: 368501--368596 Score: 70
Period size: 21 Copynumber: 4.7 Consensus size: 20
368491 CAGTTCTCAG
368501 AATCGCAACGCGATTATGAA
1 AATCGCAACGCGATTATGAA
*
368521 GAATCGCAATGCGA-TA-GTACA
1 -AATCGCAACGCGATTATG-A-A
** * * *
368542 AATTCGCATTGCGATTTTTCAT
1 AA-TCGCAACGCGA-TTATGAA
*
368564 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGATTATGAA
368584 AATCGCAACGCGA
1 AATCGCAACGCGA
368597 ACATATAAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
19 1 0.02
20 21 0.36
21 32 0.55
22 2 0.03
23 2 0.03
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (20 bp):
AATCGCAACGCGATTATGAA
Found at i:368589 original size:20 final size:20
Alignment explanation
Indices: 368564--368778 Score: 209
Period size: 20 Copynumber: 10.7 Consensus size: 20
368554 GATTTTTCAT
* *
368564 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGTA
* **
368584 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAATACGTA
** * *
368604 AATCGCAACTAGTATCCGTAA
1 AATCGCAACGCGAATACGT-A
* *
368625 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
368645 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
*
368665 AATCGCAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
*
368685 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* * *
368705 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
368725 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACGT-A
* *
368746 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
368766 AATCGCAACGCGA
1 AATCGCAACGCGA
368779 CTTTTAAAGC
Statistics
Matches: 160, Mismatches: 29, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
19 1 0.01
20 123 0.77
21 36 0.22
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGAATACGTA
Found at i:368611 original size:40 final size:40
Alignment explanation
Indices: 368564--368775 Score: 273
Period size: 40 Copynumber: 5.2 Consensus size: 40
368554 GATTTTTCAT
* * * **
368564 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACATATA
1 AATCGCAACGAGAATACGAAAATCGCAACGCGTATC-CGTA
* * *
368604 AATCGCAACTAGTATCCGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGAGAATACG-AAAATCGCAACGCGTATCCGTA
* *
368645 AATCGCAACGAGAATACGTAAATCGCAACGCGTATCTGTA
1 AATCGCAACGAGAATACGAAAATCGCAACGCGTATCCGTA
* *
368685 AATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGAGAATACGAAAATCGCAACGCGTATCCGTA
*
368725 AATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGAGAATACG-AAAATCGCAACGCGTATCCGTA
368766 AATCGCAACG
1 AATCGCAACG
368776 CGACTTTTAA
Statistics
Matches: 151, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
40 88 0.58
41 61 0.40
42 2 0.01
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (40 bp):
AATCGCAACGAGAATACGAAAATCGCAACGCGTATCCGTA
Found at i:368694 original size:101 final size:101
Alignment explanation
Indices: 368564--368778 Score: 265
Period size: 101 Copynumber: 2.1 Consensus size: 101
368554 GATTTTTCAT
* *
368564 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATAAATCGCAACT-AGTATCCGTAAAAT
1 AATCGCAACGCGAATATGAAAATCGCAACGAGAACACATAAATCGCAA-TGAGTATCCGT-AAAT
* *
368628 CGCAACG-CGTATCCGT-AAATCGCAACGAGAATACGTA
64 CGCAACGAC-AATACGTAAAATCGCAACGAGAATACGTA
* * * * * *
368665 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAAATCG
1 AATCGCAACGCGAATATGAAAATCGCAACGAGAACACATAAATCGCAATGAGTATCCGTAAATCG
* * *
368730 CAACGACAATACGTAAAATCGCAACGCGTATCCGTA
66 CAACGACAATACGTAAAATCGCAACGAGAATACGTA
368766 AATCGCAACGCGA
1 AATCGCAACGCGA
368779 CTTTTAAAGC
Statistics
Matches: 97, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
100 17 0.18
101 80 0.82
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.18
Consensus pattern (101 bp):
AATCGCAACGCGAATATGAAAATCGCAACGAGAACACATAAATCGCAATGAGTATCCGTAAATCG
CAACGACAATACGTAAAATCGCAACGAGAATACGTA
Found at i:369370 original size:20 final size:20
Alignment explanation
Indices: 369347--369410 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
369337 TTAAAATTGT
*
369347 AACATGAAAATGAAAATCGC
1 AACACGAAAATGAAAATCGC
* **
369367 AACACAAAAATGACTATCGC
1 AACACGAAAATGAAAATCGC
*
369387 AACGCGAGAAATGAAAATCGC
1 AACACGA-AAATGAAAATCGC
369408 AAC
1 AAC
369411 GAGAAACCAA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
20 21 0.60
21 14 0.40
ACGTcount: A:0.52, C:0.20, G:0.16, T:0.12
Consensus pattern (20 bp):
AACACGAAAATGAAAATCGC
Found at i:369493 original size:20 final size:20
Alignment explanation
Indices: 369428--369516 Score: 77
Period size: 20 Copynumber: 4.8 Consensus size: 20
369418 CAAAATCGCA
369428 TTGCGATTTTCATTT-CGCG
1 TTGCGATTTTCATTTCCGCG
*
369447 TTGCGA--TTC---T-CTCG
1 TTGCGATTTTCATTTCCGCG
**
369461 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTTCCGCG
*
369481 TTGCGATTTTCA-TTCTCTCG
1 TTGCGATTTTCATTTC-CGCG
369501 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
369517 AACCAAAAGA
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
14 10 0.18
16 2 0.04
17 3 0.05
19 10 0.18
20 28 0.50
21 3 0.05
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (20 bp):
TTGCGATTTTCATTTCCGCG
Found at i:372082 original size:296 final size:296
Alignment explanation
Indices: 371548--372144 Score: 1140
Period size: 296 Copynumber: 2.0 Consensus size: 296
371538 AATGAACACC
*
371548 ACAAAGTCCATGAAAAGCATCTGGGAAACACCTTCTAACAACGTTGTCAATTGAGTTTGCCCTAT
1 ACAAAGTCCATGAAAAGCATATGGGAAACACCTTCTAACAACGTTGTCAATTGAGTTTGCCCTAT
371613 CGGATATGATTGTCAGATTGCTAATAGGACCTATGCAATCCCTAAGATGCCCCATAAACCATGTC
66 CGGATATGATTGTCAGATTGCTAATAGGACCTATGCAATCCCTAAGATGCCCCATAAACCATGTC
* *
371678 CATGAATCAGAGGTTTCATATTTGCCAACCCCGTAAGCTATTGGCAGTATCCCATTGTTAGCATC
131 CATGAATCAGAGGTTTCAGATTTGCCAACCCCGTAAGCTATTGACAGTATCCCATTGTTAGCATC
*
371743 CATGGCTACTGCTAATAAGTTTACTCCAAGGTATCGACCTTTTAAATGTGCTTCTTCAACTATAA
196 CATGGCTACTGCTAATAAGTTTACTCCAAGGTATCGACCTTTTAAATGTGCTCCTTCAACTATAA
371808 TAACTGGGCGCATGCAATTAATAAACGAACGAATCT
261 TAACTGGGCGCATGCAATTAATAAACGAACGAATCT
*
371844 ACAAAGTCCATGAAAAGCATATGGGAAACACCTTCTAACAGCGTTGTCAATTGAGTTTGCCCTAT
1 ACAAAGTCCATGAAAAGCATATGGGAAACACCTTCTAACAACGTTGTCAATTGAGTTTGCCCTAT
371909 CGGATATGATTGTCAGATTGCTAATAGGACCTATGCAATCCCTAAGATGCCCCATAAACCATGTC
66 CGGATATGATTGTCAGATTGCTAATAGGACCTATGCAATCCCTAAGATGCCCCATAAACCATGTC
*
371974 CATGAATTAGAGGTTTCAGATTTGCCAACCCCGTAAGCTATTGACAGTATCCCATTGTTAGCATC
131 CATGAATCAGAGGTTTCAGATTTGCCAACCCCGTAAGCTATTGACAGTATCCCATTGTTAGCATC
372039 CATGGCTACTGCTAATAAGTTTACTCCAAGGTATCGACCTTTTAAATGTGCTCCTTCAACTATAA
196 CATGGCTACTGCTAATAAGTTTACTCCAAGGTATCGACCTTTTAAATGTGCTCCTTCAACTATAA
372104 TAACTGGGCGCATGCAATTAATAAACGAACGAATCT
261 TAACTGGGCGCATGCAATTAATAAACGAACGAATCT
372140 ACAAA
1 ACAAA
372145 ATCATATACA
Statistics
Matches: 295, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
296 295 1.00
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (296 bp):
ACAAAGTCCATGAAAAGCATATGGGAAACACCTTCTAACAACGTTGTCAATTGAGTTTGCCCTAT
CGGATATGATTGTCAGATTGCTAATAGGACCTATGCAATCCCTAAGATGCCCCATAAACCATGTC
CATGAATCAGAGGTTTCAGATTTGCCAACCCCGTAAGCTATTGACAGTATCCCATTGTTAGCATC
CATGGCTACTGCTAATAAGTTTACTCCAAGGTATCGACCTTTTAAATGTGCTCCTTCAACTATAA
TAACTGGGCGCATGCAATTAATAAACGAACGAATCT
Found at i:373149 original size:24 final size:24
Alignment explanation
Indices: 373115--373168 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
373105 CTGAAAAATC
*
373115 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACAAAG
* *
373139 ATCAAAGTCCGGGTATTGACAAAG
1 ATCAAAATCCGAGTATTGACAAAG
373163 ATCAAA
1 ATCAAA
373169 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:0.43, C:0.19, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACAAAG
Found at i:374035 original size:20 final size:19
Alignment explanation
Indices: 374014--374273 Score: 141
Period size: 20 Copynumber: 12.9 Consensus size: 19
374004 GCGATAGTCA
374014 GAATCTCGTTGCGATTTAC
1 GAATCTCGTTGCGATTTAC
* * *
374033 AGATTCGCATTGCGATTTAC
1 -GAATCTCGTTGCGATTTAC
*
374053 GTAT-TCGCATTGCGATTTAC
1 GAATCTCG--TTGCGATTTAC
* *
374073 GTAT-TCGCATTGCGATTTAT
1 GAATCTCG--TTGCGATTTAC
* * *
374093 GGATACGCATTGCGATTTAC
1 GAAT-CTCGTTGCGATTTAC
*
374113 GTATTCTCGTTGCGATTTAC
1 G-AATCTCGTTGCGATTTAC
*
374133 AGATAT-GCGTTGCGATTTAC
1 -GA-ATCTCGTTGCGATTTAC
*
374153 GTATTCTCGTTGCGATTTAC
1 G-AATCTCGTTGCGATTTAC
* *
374173 GGATACGCGTTGCGATTTTAC
1 GAAT-CTCGTTGCGA-TTTAC
* *
374194 GTATTGTCGTTGCGATTTAC
1 G-AATCTCGTTGCGATTTAC
* *
374214 GGATACGCGTTGCGATTTTAC
1 GAAT-CTCGTTGCGA-TTTAC
* *
374235 GGATACTCGTTGCGATAGT-C
1 GAAT-CTCGTTGCGAT-TTAC
*
374255 AGAATCGCGTTGCGATTTA
1 -GAATCTCGTTGCGATTTA
374274 TATGTTCGCG
Statistics
Matches: 187, Mismatches: 36, Indels: 34
0.73 0.14 0.13
Matches are distributed among these distances:
18 1 0.01
19 7 0.04
20 137 0.73
21 40 0.21
22 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (19 bp):
GAATCTCGTTGCGATTTAC
Found at i:374066 original size:40 final size:40
Alignment explanation
Indices: 374020--374311 Score: 295
Period size: 40 Copynumber: 7.2 Consensus size: 40
374010 GTCAGAATCT
* * *
374020 CGTTGCGATTTACAG-ATTCGCATTGCGATTTACGTATTCG
1 CGTTGCGATTTAC-GTATTCGCGTTGCGATTTACGGATACG
* * *
374060 CATTGCGATTTACGTATTCGCATTGCGATTTATGGATACG
1 CGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATACG
* * * *
374100 CATTGCGATTTACGTATTCTCGTTGCGATTTACAGATATG
1 CGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATACG
*
374140 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATACG
374180 CGTTGCGATTTTACGTATT-GTCGTTGCGATTTACGGATACG
1 CGTTGCGA-TTTACGTATTCG-CGTTGCGATTTACGGATACG
* * * * *
374221 CGTTGCGATTTTACGGATACTCGTTGCGATAGT-CAGA-ATCG
1 CGTTGCGA-TTTACGTATTCGCGTTGCGAT-TTACGGATA-CG
** * * ** *
374262 CGTTGCGATTTATATGTTCGCGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATACG
374302 CGTTGCGATT
1 CGTTGCGATT
374312 ATGGAAAATC
Statistics
Matches: 217, Mismatches: 27, Indels: 16
0.83 0.10 0.06
Matches are distributed among these distances:
39 2 0.01
40 145 0.67
41 69 0.32
42 1 0.00
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.38
Consensus pattern (40 bp):
CGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATACG
Found at i:374086 original size:60 final size:59
Alignment explanation
Indices: 374020--374311 Score: 257
Period size: 60 Copynumber: 4.8 Consensus size: 59
374010 GTCAGAATCT
* * *
374020 CGTTGCGATTTACAGATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCG
1 CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCGCGTTGCGATTTACGTATT-G
* * *
374080 CATTGCGATTTATGGATACGCATTGCGATTTACGTATTCTCGTTGCGATTTACAG-ATATG
1 CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCGCGTTGCGATTTAC-GTAT-TG
* * * * * *
374140 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTG
1 CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCGCGTTGCGA-TTTACGTATTG
* * * * * * *
374200 TCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGATAGT-CAGAATCG
1 -CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCGCGTTGCGAT-TTAC-GTATTG
** * * * *
374262 CGTTGCGATTTATATG-TTCGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGTTGCGATTTA-CGGATACGCATTGCGATTTACGTATTCGCGTTGCGATT
374312 ATGGAAAATC
Statistics
Matches: 192, Mismatches: 31, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
60 108 0.56
61 59 0.31
62 25 0.13
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.38
Consensus pattern (59 bp):
CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCGCGTTGCGATTTACGTATTG
Found at i:374282 original size:20 final size:20
Alignment explanation
Indices: 374259--374311 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
374249 ATAGTCAGAA
*
374259 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
374279 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
374299 TCGCGTTGCGATT
1 TCGCGTTGCGATT
374312 ATGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:374414 original size:20 final size:19
Alignment explanation
Indices: 374361--374414 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
374351 ATTCTTCATA
374361 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* ** *
374380 AACTGATTTGTGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
374401 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
374415 TTTATTTCGC
Statistics
Matches: 25, Mismatches: 8, Indels: 3
0.69 0.22 0.08
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.31, T:0.35
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:386399 original size:150 final size:151
Alignment explanation
Indices: 386229--386529 Score: 532
Period size: 150 Copynumber: 2.0 Consensus size: 151
386219 ATTTGTGTAC
* *
386229 TAAAGAAACCAACATCGTGCTTACATAATTTCTAATTGAAATTGTTTTCAAAAACATTGTAGTTG
1 TAAAGAAACCAACATCGTGCTTACATAATTTCTAATTGAAATTGTTGTCAAAAACAGTGTAGTTG
386294 CATTTAATTAATTTATTTTTATTATACCCTAAATTAATGGGGGTCATAACTCCCACCTAAACCCA
66 CATTTAATTAATTTATTTTTATTATACCCTAAATTAATGGGGGTCATAACTCCCACCTAAACCCA
386359 ATTTCAATTAGAAATT-TGTG
131 ATTTCAATTAGAAATTATGTG
* * *
386379 TAAAGAAACCAACATTGTGCTTACATAATTTCTGATTGAAATTGTTGTCCAAAACAGTGTAGTTG
1 TAAAGAAACCAACATCGTGCTTACATAATTTCTAATTGAAATTGTTGTCAAAAACAGTGTAGTTG
* *
386444 CATTTAATTAATTTATTTTTATTATACCCTAAATTAGTGGGGGTCATAACTCTCACCTAAACCCA
66 CATTTAATTAATTTATTTTTATTATACCCTAAATTAATGGGGGTCATAACTCCCACCTAAACCCA
386509 ATTTCAATTAGAAATTATGTG
131 ATTTCAATTAGAAATTATGTG
386530 AGCACGATGT
Statistics
Matches: 143, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
150 139 0.97
151 4 0.03
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (151 bp):
TAAAGAAACCAACATCGTGCTTACATAATTTCTAATTGAAATTGTTGTCAAAAACAGTGTAGTTG
CATTTAATTAATTTATTTTTATTATACCCTAAATTAATGGGGGTCATAACTCCCACCTAAACCCA
ATTTCAATTAGAAATTATGTG
Found at i:387888 original size:26 final size:26
Alignment explanation
Indices: 387852--387904 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
387842 CGTAAAGCAG
387852 CAACTAGGATGGTGAGCCCCACTCTA
1 CAACTAGGATGGTGAGCCCCACTCTA
387878 CAACTAGGATGGTGAGCCCCACTCTA
1 CAACTAGGATGGTGAGCCCCACTCTA
387904 C
1 C
387905 CACGGAGGTC
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:0.26, C:0.32, G:0.23, T:0.19
Consensus pattern (26 bp):
CAACTAGGATGGTGAGCCCCACTCTA
Found at i:388051 original size:2 final size:2
Alignment explanation
Indices: 388044--388116 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
388034 TTTGAAAATA
388044 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
388086 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
388117 CCCGAATATG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:388243 original size:16 final size:16
Alignment explanation
Indices: 388194--388244 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
388184 CATTATAATT
*
388194 GAACCGAAATCAACCC
1 GAACCGAAATCAAACC
* *
388210 GAACCAAAAAT-AATCC
1 GAACC-GAAATCAAACC
388226 GAACCGAAATCAAACC
1 GAACCGAAATCAAACC
388242 GAA
1 GAA
388245 TTTAATTTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 4 0.14
16 21 0.72
17 4 0.14
ACGTcount: A:0.51, C:0.29, G:0.12, T:0.08
Consensus pattern (16 bp):
GAACCGAAATCAAACC
Found at i:391540 original size:29 final size:29
Alignment explanation
Indices: 391506--391593 Score: 176
Period size: 29 Copynumber: 3.0 Consensus size: 29
391496 CCTAAATTAA
391506 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
391535 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
391564 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
391593 T
1 T
391594 AGGTGAAAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:396250 original size:29 final size:29
Alignment explanation
Indices: 396216--396274 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
396206 CCTGAATTAA
396216 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
396245 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
396274 T
1 T
396275 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:398190 original size:21 final size:21
Alignment explanation
Indices: 398164--398205 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
398154 CCATAATGGG
*
398164 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
398185 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
398206 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:398369 original size:20 final size:21
Alignment explanation
Indices: 398333--398394 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
398323 ATCTGTACCC
398333 GGGGAATC-GATACCCCCTGGG
1 GGGGAATCTG-TACCCCCTGGG
*
398354 GGGGAATCTGTTCCCCCTGGG
1 GGGGAATCTGTACCCCCTGGG
398375 GGGGAATCTGTACCCCCTGG
1 GGGGAATCTGTACCCCCTGG
398395 ATAATCTGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 37 0.97
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.37, T:0.19
Consensus pattern (21 bp):
GGGGAATCTGTACCCCCTGGG
Found at i:411412 original size:30 final size:30
Alignment explanation
Indices: 411349--411413 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
411339 TTTTTTAAAA
** *
411349 TTATACTTTGGTCACTGAACTTTTCAAAGT
1 TTATACTTTGGTCACCAAACTTTCCAAAGT
411379 TTATACTTTGGTCACCAAACTTTACCAAA-T
1 TTATACTTTGGTCACCAAACTTT-CCAAAGT
411409 TTATA
1 TTATA
411414 ATTTAGCCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 27 0.87
31 4 0.13
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42
Consensus pattern (30 bp):
TTATACTTTGGTCACCAAACTTTCCAAAGT
Found at i:417752 original size:30 final size:30
Alignment explanation
Indices: 417718--417783 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
417708 TTAAAATTAC
*
417718 ACTTTGATC-CCTAAACTTT-TCAAAGTTTAT
1 ACTTTGATCACC-AAACTTTACCAAA-TTTAT
*
417748 ACTTTGGTCACCAAACTTTACCAAATTTAT
1 ACTTTGATCACCAAACTTTACCAAATTTAT
*
417778 AATTTG
1 ACTTTG
417784 GTCATTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 25 0.81
31 6 0.19
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.41
Consensus pattern (30 bp):
ACTTTGATCACCAAACTTTACCAAATTTAT
Found at i:417784 original size:30 final size:30
Alignment explanation
Indices: 417730--417787 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
417720 TTTGATCCCT
* *
417730 AAACTTTTCAAAGTTTATACTTTGGTCACC
1 AAACTTTCCAAAGTTTATAATTTGGTCACC
417760 AAACTTTACCAAA-TTTATAATTTGGTCA
1 AAACTTT-CCAAAGTTTATAATTTGGTCA
417788 TTAAATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (30 bp):
AAACTTTCCAAAGTTTATAATTTGGTCACC
Found at i:424760 original size:58 final size:60
Alignment explanation
Indices: 424689--424833 Score: 145
Period size: 58 Copynumber: 2.5 Consensus size: 60
424679 AAAATAGGGT
** * *
424689 AAAA-TACACAAATGGTCCCTCGACTATAGGGTATTATTTTATTAAGTCTCTC-A-TATTA
1 AAAATTACA-AAATGGTCCCTCGACTATAGAATATTACTTTATTAAGTCTCTCGACCATTA
* * *
424747 AAAATTACAAAATGGT-CCTCTAACTATAGAATGTTGCTTTATTAAGTCTCTCGACCATTA
1 AAAATTACAAAATGGTCCCTC-GACTATAGAATATTACTTTATTAAGTCTCTCGACCATTA
* * * *
424807 GAAGTTACAAAATGATCACTCGACTAT
1 AAAATTACAAAATGGTCCCTCGACTAT
424834 TCATTATGTT
Statistics
Matches: 70, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
57 4 0.06
58 36 0.51
59 5 0.07
60 22 0.31
61 3 0.04
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (60 bp):
AAAATTACAAAATGGTCCCTCGACTATAGAATATTACTTTATTAAGTCTCTCGACCATTA
Found at i:425876 original size:22 final size:22
Alignment explanation
Indices: 425849--425921 Score: 119
Period size: 22 Copynumber: 3.3 Consensus size: 22
425839 TTTTTTCAAG
425849 TCAAGTCGAAAAAATGGGATTT
1 TCAAGTCGAAAAAATGGGATTT
425871 TCAAGTCGAAAAAATGGGATTT
1 TCAAGTCGAAAAAATGGGATTT
* *
425893 CCAAGTCGAAAAAATTGGATTT
1 TCAAGTCGAAAAAATGGGATTT
*
425915 TCGAGTC
1 TCAAGTC
425922 AAATCGAGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.27
Consensus pattern (22 bp):
TCAAGTCGAAAAAATGGGATTT
Found at i:430171 original size:20 final size:20
Alignment explanation
Indices: 430146--430184 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
430136 CTTGTTGCAA
430146 GGTCTTCTTAAATTCGATCT
1 GGTCTTCTTAAATTCGATCT
430166 GGTCTTCTTAAATTCGATC
1 GGTCTTCTTAAATTCGATC
430185 CTTGCAGTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.44
Consensus pattern (20 bp):
GGTCTTCTTAAATTCGATCT
Found at i:437446 original size:24 final size:23
Alignment explanation
Indices: 437419--437488 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
437409 AAAAATTCAG
437419 GAGCTCGATTGAAGCTCGAGACTC
1 GAGCTCGATTGAAGCTCGA-ACTC
* *
437443 GAGCTCGATTGAAGCTC-AATTTT
1 GAGCTCGATTGAAGCTCGAA-CTC
*
437466 GAGCTCGATTCAAGCTCGAACTC
1 GAGCTCGATTGAAGCTCGAACTC
437489 AAACTCGAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
22 1 0.03
23 19 0.49
24 19 0.49
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (23 bp):
GAGCTCGATTGAAGCTCGAACTC
Found at i:439931 original size:14 final size:14
Alignment explanation
Indices: 439912--439966 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
439902 CATATAATCG
*
439912 GGTTTAGGGGTTAA
1 GGTTTAGGGTTTAA
*
439926 GGTTTAGTGTTTAA
1 GGTTTAGGGTTTAA
**
439940 GGTTTATAGTTTAA
1 GGTTTAGGGTTTAA
*
439954 GGTTTAGGATTTA
1 GGTTTAGGGTTTA
439967 TGGAATAGAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (14 bp):
GGTTTAGGGTTTAA
Found at i:440052 original size:7 final size:7
Alignment explanation
Indices: 440040--440110 Score: 63
Period size: 7 Copynumber: 10.3 Consensus size: 7
440030 GTAAATATAA
440040 TTTAGGG
1 TTTAGGG
440047 TTTAGGG
1 TTTAGGG
**
440054 TTTAGAC
1 TTTAGGG
* *
440061 TTTATGA
1 TTTAGGG
* *
440068 TTTATGT
1 TTTAGGG
440075 TTTAGGG
1 TTTAGGG
*
440082 TTTATGG
1 TTTAGGG
440089 -TTAGGG
1 TTTAGGG
*
440095 TTTAAGG
1 TTTAGGG
440102 TTTAGGG
1 TTTAGGG
440109 TT
1 TT
440111 CATTATAAAA
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
6 5 0.10
7 46 0.90
ACGTcount: A:0.18, C:0.01, G:0.31, T:0.49
Consensus pattern (7 bp):
TTTAGGG
Found at i:440094 original size:13 final size:14
Alignment explanation
Indices: 440075--440110 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
440065 TGATTTATGT
*
440075 TTTAGGGTTTATGG
1 TTTAGGGTTTAAGG
440089 -TTAGGGTTTAAGG
1 TTTAGGGTTTAAGG
440102 TTTAGGGTT
1 TTTAGGGTT
440111 CATTATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.47
Consensus pattern (14 bp):
TTTAGGGTTTAAGG
Found at i:441556 original size:45 final size:45
Alignment explanation
Indices: 441488--442022 Score: 777
Period size: 45 Copynumber: 11.9 Consensus size: 45
441478 GGGTTTTGCG
* *
441488 GACTCTGGACCAGAGCCTGATAGATGGTCCCGAGGTGGTGTTCGC
1 GACTCTGGACCGGAGCCTGATAGATGGTCCCGAGGTGGTGTTCGT
* * * * *
441533 GACCCTGGACCGGAACCTGATAGATGGTCCCGAGCTGGTGCTCGC
1 GACTCTGGACCGGAGCCTGATAGATGGTCCCGAGGTGGTGTTCGT
* * * *
441578 GACCCTGGACCGGAACCTGATAGATGGTCCCGAGCTGGTGTTCGC
1 GACTCTGGACCGGAGCCTGATAGATGGTCCCGAGGTGGTGTTCGT
* * * *
441623 GACCCTGGACCGGTGCCTGATAGATGGTCCCGAGGTGGTGTTTGC
1 GACTCTGGACCGGAGCCTGATAGATGGTCCCGAGGTGGTGTTCGT
* * *
441668 GACCCTGGACCGGAGCCTGATAGATGGTCCCGAAGTGGTGTTAGT
1 GACTCTGGACCGGAGCCTGATAGATGGTCCCGAGGTGGTGTTCGT
* * *
441713 GA-TACTGGACCGGAGCCTGATAGATGGTCTCGAGCTGGTGTACGT
1 GACT-CTGGACCGGAGCCTGATAGATGGTCCCGAGGTGGTGTTCGT
* * *
441758 GACTCTGGACTGGAGCCTGATAGATGGTCTCGAGGTGGTGTTCAT
1 GACTCTGGACCGGAGCCTGATAGATGGTCCCGAGGTGGTGTTCGT
* *
441803 GACTCTGGACCGGAGTCTGATAGATGGTCTCGAGGTGGTGTTCGT
1 GACTCTGGACCGGAGCCTGATAGATGGTCCCGAGGTGGTGTTCGT
* *
441848 GAATCTGGACCGGAGCCTGATAGATGGTCTCGAGGTGGTGTTCGT
1 GACTCTGGACCGGAGCCTGATAGATGGTCCCGAGGTGGTGTTCGT
441893 GACTCTGGACCGGAGCCTGATAGATGGTCCCGAGGTGGTGTTCGT
1 GACTCTGGACCGGAGCCTGATAGATGGTCCCGAGGTGGTGTTCGT
*
441938 GACTCTGGACCGGAGCCTGATAGATGGTCCCGAGGCGGTGTTCGT
1 GACTCTGGACCGGAGCCTGATAGATGGTCCCGAGGTGGTGTTCGT
441983 GACTCTGGACCGGAGCCTGATAGATGGTCTCC-AGGTGGTG
1 GACTCTGGACCGGAGCCTGATAGATGGTC-CCGAGGTGGTG
442023 GGGGCGGAAT
Statistics
Matches: 454, Mismatches: 33, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
45 451 0.99
46 3 0.01
ACGTcount: A:0.17, C:0.23, G:0.36, T:0.24
Consensus pattern (45 bp):
GACTCTGGACCGGAGCCTGATAGATGGTCCCGAGGTGGTGTTCGT
Found at i:443778 original size:128 final size:126
Alignment explanation
Indices: 443534--443779 Score: 366
Period size: 126 Copynumber: 1.9 Consensus size: 126
443524 TTTCGACTAT
* * ** *
443534 GAGTTCCGAACAGATGTTTGGCTTCTGAGTCAAGCTTTTACATTTTTTTCATGCATTAAATTCAC
1 GAGTTCAGAACAGAGGTTTGGCTTCTGAGTCAAGCTTTTACAGCTCTTTCATGCATTAAATTCAC
* * *
443599 GTACTGTTGTATTATAAAATTTATTTTATTTATGAAAACACAGCCAACTGAATTTTTGGTC
66 GCACTGTTGTATTACAAAATTTATTTCATTTATGAAAACACAGCCAACTGAATTTTTGGTC
*
443660 GAGTTCAGAACAGAGGTTTGGCTTCTGAGTCAAGCTTTTGCAGCTCTTTCATGCATTAAATTAAC
1 GAGTTCAGAACAGAGGTTTGGCTTCTGAGTCAAGCTTTTACAGCTCTTTCATGCATTAAATT--C
* * *
443725 ATGCACTGTTGTATTCCAAAATTTATTTCATTTATGAATACACAGCCAACTGAAT
64 ACGCACTGTTGTATTACAAAATTTATTTCATTTATGAAAACACAGCCAACTGAAT
443780 CGTGACTTAA
Statistics
Matches: 106, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
126 56 0.53
128 50 0.47
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (126 bp):
GAGTTCAGAACAGAGGTTTGGCTTCTGAGTCAAGCTTTTACAGCTCTTTCATGCATTAAATTCAC
GCACTGTTGTATTACAAAATTTATTTCATTTATGAAAACACAGCCAACTGAATTTTTGGTC
Found at i:444732 original size:18 final size:20
Alignment explanation
Indices: 444706--444752 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 20
444696 CCAGAAACCG
444706 AAGAGGAAA-AGAT-ATTGA
1 AAGAGGAAATAGATCATTGA
* *
444724 AAGATGAAATAGATCATTTA
1 AAGAGGAAATAGATCATTGA
444744 AAGAAGGAA
1 AAG-AGGAA
444753 GTTGAGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 8 0.35
19 4 0.17
20 7 0.30
21 4 0.17
ACGTcount: A:0.55, C:0.02, G:0.23, T:0.19
Consensus pattern (20 bp):
AAGAGGAAATAGATCATTGA
Found at i:445034 original size:36 final size:36
Alignment explanation
Indices: 444987--445064 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
444977 GTTCACGAAT
*
444987 AGGCCTAGATCTCAG-GGTACTGCAGATGCACGGACA
1 AGGCCTAGATCTC-GTGGTACCGCAGATGCACGGACA
*
445023 AGGCCTAGATCTCGTGGTACCGCAGATGCATGGACA
1 AGGCCTAGATCTCGTGGTACCGCAGATGCACGGACA
445059 AGGCCT
1 AGGCCT
445065 GGTGATGAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
35 1 0.03
36 38 0.97
ACGTcount: A:0.26, C:0.26, G:0.31, T:0.18
Consensus pattern (36 bp):
AGGCCTAGATCTCGTGGTACCGCAGATGCACGGACA
Found at i:446694 original size:13 final size:13
Alignment explanation
Indices: 446665--446693 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
446655 ACTAATTCTC
446665 TTTTCTTTCTGTT
1 TTTTCTTTCTGTT
446678 TTTTCTTT-TGTT
1 TTTTCTTTCTGTT
446690 TTTT
1 TTTT
446694 TAATAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (13 bp):
TTTTCTTTCTGTT
Found at i:457695 original size:86 final size:86
Alignment explanation
Indices: 457594--457764 Score: 333
Period size: 86 Copynumber: 2.0 Consensus size: 86
457584 ATTATAAAAC
*
457594 AATTATTACAAAATAATCATTAAAATTTATCATTATTATATAACGGACAATTACAATTTTGTAAT
1 AATTAGTACAAAATAATCATTAAAATTTATCATTATTATATAACGGACAATTACAATTTTGTAAT
457659 AACTTGATAAATTTAATGATA
66 AACTTGATAAATTTAATGATA
457680 AATTAGTACAAAATAATCATTAAAATTTATCATTATTATATAACGGACAATTACAATTTTGTAAT
1 AATTAGTACAAAATAATCATTAAAATTTATCATTATTATATAACGGACAATTACAATTTTGTAAT
457745 AACTTGATAAATTTAATGAT
66 AACTTGATAAATTTAATGAT
457765 TATTTTATAA
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 84 1.00
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.39
Consensus pattern (86 bp):
AATTAGTACAAAATAATCATTAAAATTTATCATTATTATATAACGGACAATTACAATTTTGTAAT
AACTTGATAAATTTAATGATA
Found at i:462629 original size:35 final size:36
Alignment explanation
Indices: 462558--462629 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
462548 AATTATTAAA
* *
462558 TATGAATGTTTGTATTTGTTTGTCTCCCGTATGAAC
1 TATGAATGCTTGTATTTGTTTGTCCCCCGTATGAAC
462594 TATGAATGCTTGTATTTGTTTG-CCCCCGTATGAAC
1 TATGAATGCTTGTATTTGTTTGTCCCCCGTATGAAC
462629 T
1 T
462630 GTCCTTGAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 13 0.38
36 21 0.62
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.44
Consensus pattern (36 bp):
TATGAATGCTTGTATTTGTTTGTCCCCCGTATGAAC
Found at i:465402 original size:21 final size:20
Alignment explanation
Indices: 465368--465406 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
465358 GTCCTCGGCG
*
465368 TTAGAAGAATCTGCCTTTGTT
1 TTAGAAGAAGCTG-CTTTGTT
*
465389 TTAGAATAAGCTGCTTTG
1 TTAGAAGAAGCTGCTTTG
465407 AGTTTAGAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.41
Consensus pattern (20 bp):
TTAGAAGAAGCTGCTTTGTT
Found at i:466200 original size:39 final size:39
Alignment explanation
Indices: 466121--466228 Score: 112
Period size: 39 Copynumber: 2.8 Consensus size: 39
466111 GGGTTTTTTA
* *
466121 TTACTCTGAAGATGTCATATAGTC-TAGG-GTCTTCTCCAT
1 TTAC-CTGAAGACGTCATACAGTCGT-GGAGTCTTCTCCAT
** * * * *
466160 TTGTCTGAAGATGTCGTGCAGTCGTGGAGTCTTCTTCAT
1 TTACCTGAAGACGTCATACAGTCGTGGAGTCTTCTCCAT
466199 TTACCTGAAGACGTCATACAGTCGTGGAGT
1 TTACCTGAAGACGTCATACAGTCGTGGAGT
466229 GGATTGTTTG
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
38 18 0.32
39 38 0.68
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.35
Consensus pattern (39 bp):
TTACCTGAAGACGTCATACAGTCGTGGAGTCTTCTCCAT
Found at i:467632 original size:36 final size:37
Alignment explanation
Indices: 467589--467671 Score: 116
Period size: 36 Copynumber: 2.3 Consensus size: 37
467579 AATCGAATTA
*
467589 AACGGGGACGGAA-AAAAATCGTTTATGTTAAACAGG
1 AACGGGGACGGAAGAAAAATCATTTATGTTAAACAGG
* *
467625 AACGGGGAC-GAAGAAAAATTATTTATGTTAAACGGG
1 AACGGGGACGGAAGAAAAATCATTTATGTTAAACAGG
*
467661 GACGGGGACGG
1 AACGGGGACGG
467672 GAACGAGTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
35 3 0.07
36 37 0.90
37 1 0.02
ACGTcount: A:0.39, C:0.11, G:0.33, T:0.18
Consensus pattern (37 bp):
AACGGGGACGGAAGAAAAATCATTTATGTTAAACAGG
Found at i:470504 original size:2 final size:2
Alignment explanation
Indices: 470497--470521 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
470487 TCATCAAGTA
470497 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
470522 ACAAGAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:473982 original size:13 final size:13
Alignment explanation
Indices: 473966--473999 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
473956 TATCTTTTTT
473966 ATTTTAATTTAGA
1 ATTTTAATTTAGA
473979 ATTTTAA-TTAGA
1 ATTTTAATTTAGA
*
473991 AATTTAATT
1 ATTTTAATT
474000 CTGACAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (13 bp):
ATTTTAATTTAGA
Found at i:474451 original size:16 final size:16
Alignment explanation
Indices: 474440--474497 Score: 75
Period size: 16 Copynumber: 3.6 Consensus size: 16
474430 ATAATTTTTT
474440 TTTATAAAAATTATTA
1 TTTATAAAAATTATTA
474456 TTTATAAAAATTATTA
1 TTTATAAAAATTATTA
*
474472 TTCTAT-CAAATTAATT-
1 TT-TATAAAAATT-ATTA
474488 TTTATAAAAA
1 TTTATAAAAA
474498 ATCTTACTCG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
15 3 0.08
16 28 0.76
17 6 0.16
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTATAAAAATTATTA
Done.