Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009576.1 Hibiscus syriacus cultivar Beakdansim tig00116944_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: 1684752
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 10
Found at i:235893 original size:33 final size:33
Alignment explanation
Indices: 235840--235938 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
235830 TTTGTTTCAA
235840 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
235872 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
235905 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
235938 T
1 T
235939 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:235967 original size:13 final size:13
Alignment explanation
Indices: 235924--235978 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
235914 TTGGAAGTAT
235924 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
235937 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
235951 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
235964 TTAAGTATTTGAA
1 TTAAGTATTTCAA
235977 TT
1 TT
235979 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:236200 original size:21 final size:21
Alignment explanation
Indices: 236174--236222 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
236164 TGGAGCATGG
236174 GGGAATCAGTACCCTCTCATA
1 GGGAATCAGTACCCTCTCATA
* **
236195 GGGAATCGGTTTCCTCTCATA
1 GGGAATCAGTACCCTCTCATA
236216 GGGAATC
1 GGGAATC
236223 GGTTCCCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (21 bp):
GGGAATCAGTACCCTCTCATA
Found at i:236223 original size:21 final size:21
Alignment explanation
Indices: 236186--236226 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
236176 GAATCAGTAC
236186 CCTCTCATAGGGAATCGGTTT
1 CCTCTCATAGGGAATCGGTTT
236207 CCTCTCATAGGGAATCGGTT
1 CCTCTCATAGGGAATCGGTT
236227 CCCTAAGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (21 bp):
CCTCTCATAGGGAATCGGTTT
Found at i:236425 original size:15 final size:15
Alignment explanation
Indices: 236373--236425 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
236363 ATCTGGAATA
236373 TTAAAATCGGTTTTT
1 TTAAAATCGGTTTTT
* *
236388 TTATAACCGGTTTTT
1 TTAAAATCGGTTTTT
* *
236403 TAAAAAAATCGATTTTT
1 T--TAAAATCGGTTTTT
236420 TTAAAA
1 TTAAAA
236426 CCGAAACCGG
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
15 18 0.62
17 11 0.38
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (15 bp):
TTAAAATCGGTTTTT
Found at i:236545 original size:15 final size:17
Alignment explanation
Indices: 236519--236550 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
236509 TTCTATGGGA
236519 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
236535 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
236551 TGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:237197 original size:36 final size:36
Alignment explanation
Indices: 237147--237222 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
237137 TTATAGCAAA
*
237147 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
237183 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
237219 AAAA
1 AAAA
237223 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:241717 original size:15 final size:15
Alignment explanation
Indices: 241699--241728 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
241689 CCACGGTGCT
241699 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
241714 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
241729 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:242201 original size:36 final size:36
Alignment explanation
Indices: 242151--242226 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
242141 TTATAGCAAA
*
242151 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
242187 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
242223 AAAA
1 AAAA
242227 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:246470 original size:23 final size:23
Alignment explanation
Indices: 246434--246484 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
246424 ATCGTTAATA
*
246434 ATTAAAAAATATTCTGAATATAT
1 ATTAAAAAAGATTCTGAATATAT
* *
246457 ATTAAGAAAGATTCTGAGTATAT
1 ATTAAAAAAGATTCTGAATATAT
246480 ATTAA
1 ATTAA
246485 TTATAATCAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.49, C:0.04, G:0.10, T:0.37
Consensus pattern (23 bp):
ATTAAAAAAGATTCTGAATATAT
Found at i:258831 original size:16 final size:17
Alignment explanation
Indices: 258810--258844 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
258800 TTACTATTCA
258810 CGTGAATAGTG-AATTT
1 CGTGAATAGTGAAATTT
258826 CGTGAATAGTGAAATTT
1 CGTGAATAGTGAAATTT
258843 CG
1 CG
258845 GTCGGCGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:264388 original size:107 final size:107
Alignment explanation
Indices: 264261--264475 Score: 430
Period size: 107 Copynumber: 2.0 Consensus size: 107
264251 TTAAATTTAA
264261 ATTTTTAAAACTTTAGTGATCAAAATAGGTGCGTGAATATAGTTGAGTGATGACCTGTGTAGTTT
1 ATTTTTAAAACTTTAGTGATCAAAATAGGTGCGTGAATATAGTTGAGTGATGACCTGTGTAGTTT
264326 AACCAAATAAAAAATATCAGTAAGATGTACAATTAACTTTTT
66 AACCAAATAAAAAATATCAGTAAGATGTACAATTAACTTTTT
264368 ATTTTTAAAACTTTAGTGATCAAAATAGGTGCGTGAATATAGTTGAGTGATGACCTGTGTAGTTT
1 ATTTTTAAAACTTTAGTGATCAAAATAGGTGCGTGAATATAGTTGAGTGATGACCTGTGTAGTTT
264433 AACCAAATAAAAAATATCAGTAAGATGTACAATTAACTTTTT
66 AACCAAATAAAAAATATCAGTAAGATGTACAATTAACTTTTT
264475 A
1 A
264476 ACGGCGGGTT
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
107 108 1.00
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (107 bp):
ATTTTTAAAACTTTAGTGATCAAAATAGGTGCGTGAATATAGTTGAGTGATGACCTGTGTAGTTT
AACCAAATAAAAAATATCAGTAAGATGTACAATTAACTTTTT
Found at i:265821 original size:2 final size:2
Alignment explanation
Indices: 265805--265854 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
265795 AAGAAACATC
*
265805 AT AT GT AT A- AT AT AT AT AT AT AT A- 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
265845 AT AT AT AT AT
1 AT AT AT AT AT
265855 TATTTGACTA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 42 0.95
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:268794 original size:82 final size:80
Alignment explanation
Indices: 268617--268857 Score: 206
Period size: 82 Copynumber: 3.0 Consensus size: 80
268607 AAAATGATAC
* *
268617 TTTAGTGGCGTTTT-AAATAAACGCCGCGATAGAGTAGTATGTTAGCGGCGTTTTGATACAAACG
1 TTTAGTGGCGTTTTCCAATAAACGCCGCGATAGAGTAGTATGTTAGCGACGTTTTGATACAAACG
*
268681 TCGTAATAGGGTTAGT
66 -CGCAATAGGGTTAGT
* * *
268697 TTATAGTGGCGTTTTCCAATAAACGTCGCGATAGAGTAGTAAT-TTAGCTACGTTTT-CTACAAA
1 TT-TAGTGGCGTTTTCCAATAAACGCCGCGATAGAGTAGT-ATGTTAGCGACGTTTTGATAC-AA
* *
268760 TACG-GCAATAGTGTTCGT
63 -ACGCGCAATAGGGTTAGT
* * * * * * * *
268778 TCTTAGTGGCGTTTTTCCAACAGATGTCGTGATA-AATAGTACT-TTAGCGACATTTTTATACAA
1 T-TTAGTGGCG-TTTTCCAATAAACGCCGCGATAGAGTAGTA-TGTTAGCGACGTTTTGATACAA
*
268841 ACGCCGCAATAGAGTTA
63 ACG-CGCAATAGGGTTA
268858 ATCTATAGCT
Statistics
Matches: 132, Mismatches: 18, Indels: 20
0.78 0.11 0.12
Matches are distributed among these distances:
80 6 0.05
81 54 0.41
82 67 0.51
83 5 0.04
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (80 bp):
TTTAGTGGCGTTTTCCAATAAACGCCGCGATAGAGTAGTATGTTAGCGACGTTTTGATACAAACG
CGCAATAGGGTTAGT
Found at i:271774 original size:22 final size:23
Alignment explanation
Indices: 271742--271785 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
271732 TCGTCAAATA
*
271742 AATATATTACTAGTATTGTTGTC
1 AATATATTACTAATATTGTTGTC
271765 AATAT-TTACTAATATTGTTGT
1 AATATATTACTAATATTGTTGT
271786 TTGTTTATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (23 bp):
AATATATTACTAATATTGTTGTC
Found at i:274152 original size:22 final size:23
Alignment explanation
Indices: 274120--274163 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
274110 TCGTCAAATA
*
274120 AATATATTACTAGTATTGTTGTC
1 AATATATTACTAATATTGTTGTC
274143 AATAT-TTACTAATATTGTTGT
1 AATATATTACTAATATTGTTGT
274164 TTGTTTATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (23 bp):
AATATATTACTAATATTGTTGTC
Found at i:275752 original size:21 final size:21
Alignment explanation
Indices: 275726--275769 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
275716 AAGCGAAAGA
*
275726 AGCAACGAGAGAATCAGAGAG
1 AGCAACAAGAGAATCAGAGAG
275747 AGCAACAAGAGAATCAGAGAG
1 AGCAACAAGAGAATCAGAGAG
275768 AG
1 AG
275770 AAGCAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.50, C:0.14, G:0.32, T:0.05
Consensus pattern (21 bp):
AGCAACAAGAGAATCAGAGAG
Found at i:277405 original size:32 final size:34
Alignment explanation
Indices: 277369--277438 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
277359 ACCTTACAAC
* * *
277369 TCCCTAG-TTTTTC-CGGGCTAAACTAGAACTTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACATT
*
277401 TCCCTAGCTTTTACACGGGATAAGCTAGAACATT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACATT
277435 TCCC
1 TCCC
277439 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGATAAACTAGAACATT
Found at i:277824 original size:20 final size:20
Alignment explanation
Indices: 277795--277868 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
277785 GCAGCCTTCG
*
277795 TGCATGGATGCACAACAGGA
1 TGCATCGATGCACAACAGGA
** *
277815 TGCATCGATGCACAACCTTGT
1 TGCATCGATGCACAA-CAGGA
277836 TGCATCGATGCACAGA-AGGA
1 TGCATCGATGCACA-ACAGGA
*
277856 TGCATTGATGCAC
1 TGCATCGATGCAC
277869 TAATTGCATT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 27 0.61
21 16 0.36
22 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.22
Consensus pattern (20 bp):
TGCATCGATGCACAACAGGA
Found at i:277935 original size:22 final size:23
Alignment explanation
Indices: 277903--277945 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
277893 ATGGATGCAT
277903 TGCATGGTGCATCGATGCACTAG
1 TGCATGGTGCATCGATGCACTAG
*
277926 TGCA-GGTGCATGGATGCACT
1 TGCATGGTGCATCGATGCACT
277946 GCAGGGATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.26
Consensus pattern (23 bp):
TGCATGGTGCATCGATGCACTAG
Found at i:278114 original size:34 final size:29
Alignment explanation
Indices: 278046--278104 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
278036 AAACTTTGAA
*
278046 TAAATTCAATTAAGTCCAAAAGCATTTTG
1 TAAATTCAATTAAGTCCAAAACCATTTTG
278075 TAAATTCAATTCAAGTCCAAAAACCATTTT
1 TAAATTCAATT-AAGTCC-AAAACCATTTT
278105 ACCTTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.41
30 6 0.22
31 10 0.37
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.34
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAACCATTTTG
Found at i:279002 original size:2 final size:2
Alignment explanation
Indices: 278995--279037 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
278985 TATAAATTAA
278995 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
279037 A
1 A
279038 CACATTTTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:286184 original size:50 final size:51
Alignment explanation
Indices: 286103--286202 Score: 148
Period size: 50 Copynumber: 2.0 Consensus size: 51
286093 CACGGATAAT
* *
286103 TTTTGTTTTATTTTTTATTTGTCATGGGTTTAAGCT-TTAAAAAAGAAGAG
1 TTTTGTTTTATTTTTTAATTGTCATGAGTTTAAGCTCTTAAAAAAGAAGAG
* * *
286153 TTTTGTTTTATTTTTTAATTGTTATGAGTTTAAGCTCTTGAAGAAGAAGA
1 TTTTGTTTTATTTTTTAATTGTCATGAGTTTAAGCTCTTAAAAAAGAAGA
286203 ATAGTTAACG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
50 33 0.75
51 11 0.25
ACGTcount: A:0.28, C:0.04, G:0.18, T:0.50
Consensus pattern (51 bp):
TTTTGTTTTATTTTTTAATTGTCATGAGTTTAAGCTCTTAAAAAAGAAGAG
Found at i:287336 original size:22 final size:22
Alignment explanation
Indices: 287311--287356 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
287301 CAGGGAAGAT
287311 CATCATGTTAATAGATAAGTGC
1 CATCATGTTAATAGATAAGTGC
287333 CATCATGTTAATAGATAAGTGC
1 CATCATGTTAATAGATAAGTGC
287355 CA
1 CA
287357 CTTAAAATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.30
Consensus pattern (22 bp):
CATCATGTTAATAGATAAGTGC
Found at i:287898 original size:2 final size:2
Alignment explanation
Indices: 287891--287919 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
287881 ATAGATCATA
287891 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 A
287920 CTAATAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:288282 original size:20 final size:19
Alignment explanation
Indices: 288235--288273 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
288225 ATGACCAATA
*
288235 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
*
288254 AAATCGCAACGTGATCTCT
1 AAATCGCAACGCGATCTCT
288273 A
1 A
288274 GTATCGCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:288401 original size:20 final size:19
Alignment explanation
Indices: 288378--288529 Score: 133
Period size: 20 Copynumber: 7.5 Consensus size: 19
288368 GAATATGTAA
288378 ATCGCAACGCGATTCTAACT
1 ATCGCAACGCGATTCT-ACT
**
288398 ATCGCAACGCGATAATACAT
1 ATCGCAACGCGATTCTAC-T
288418 AATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATTCT-ACT
**
288439 ATCGCAACGCGATAATACAT
1 ATCGCAACGCGATTCTAC-T
**
288459 AATCGCAACGCGATAATACAT
1 -ATCGCAACGCGATTCTAC-T
* *
288480 AATCGCAACTCGATTCCGACT
1 -ATCGCAACGCGATT-CTACT
288501 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCT-ACT
*
288521 GTCGCAACG
1 ATCGCAACG
288530 TTGAATTTCA
Statistics
Matches: 112, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
19 5 0.04
20 54 0.48
21 49 0.44
22 4 0.04
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (19 bp):
ATCGCAACGCGATTCTACT
Found at i:288422 original size:41 final size:41
Alignment explanation
Indices: 288377--288472 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
288367 CGAATATGTA
288377 AATCGCAACGCGATTCTAACTATCGCAACGCGATAATACAT
1 AATCGCAACGCGATTCTAACTATCGCAACGCGATAATACAT
*
288418 AATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAT
1 AATCGCAACGCGATTCTAACTATCGCAACGCGATAATACAT
288459 AATCGCAACGCGAT
1 AATCGCAACGCGAT
288473 AATACATAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (41 bp):
AATCGCAACGCGATTCTAACTATCGCAACGCGATAATACAT
Found at i:288424 original size:21 final size:21
Alignment explanation
Indices: 288377--288493 Score: 143
Period size: 21 Copynumber: 5.7 Consensus size: 21
288367 CGAATATGTA
**
288377 AATCGCAACGCGATTCTA-ACT
1 AATCGCAACGCGATAATACA-T
288398 -ATCGCAACGCGATAATACAT
1 AATCGCAACGCGATAATACAT
**
288418 AATCGCAACGCGATTCTGAC-T
1 AATCGCAACGCGATAAT-ACAT
288439 -ATCGCAACGCGATAATACAT
1 AATCGCAACGCGATAATACAT
288459 AATCGCAACGCGATAATACAT
1 AATCGCAACGCGATAATACAT
*
288480 AATCGCAACTCGAT
1 AATCGCAACGCGAT
288494 TCCGACTATC
Statistics
Matches: 84, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.02
20 31 0.37
21 49 0.58
22 2 0.02
ACGTcount: A:0.37, C:0.26, G:0.15, T:0.21
Consensus pattern (21 bp):
AATCGCAACGCGATAATACAT
Found at i:291122 original size:20 final size:20
Alignment explanation
Indices: 291099--291139 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
291089 TCTGAAACTT
291099 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
291119 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
291139 A
1 A
291140 CTACCGCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.20, G:0.15, T:0.10
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:291147 original size:20 final size:20
Alignment explanation
Indices: 291099--291154 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
291089 TCTGAAACTT
*
291099 AAAATCGCAACACGAAAATG
1 AAAACCGCAACACGAAAATG
*
291119 AAAATCGCAACACGAAAATG
1 AAAACCGCAACACGAAAATG
** *
291139 ACTACCGCAACGCGAA
1 AAAACCGCAACACGAA
291155 TTTGACTATC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.50, C:0.25, G:0.16, T:0.09
Consensus pattern (20 bp):
AAAACCGCAACACGAAAATG
Found at i:291786 original size:21 final size:21
Alignment explanation
Indices: 291762--291838 Score: 59
Period size: 21 Copynumber: 3.7 Consensus size: 21
291752 CGCTTTGAAA
291762 ATCGCATTGCGATTTTGTATT
1 ATCGCATTGCGATTTTGTATT
** * **
291783 ATCGCAACGCGA--TAGTCAGA
1 ATCGCATTGCGATTTTGT-ATT
* *
291803 ATCGCGTTGCGATTATGTATT
1 ATCGCATTGCGATTTTGTATT
*
291824 ATCGCGTTGCGATTT
1 ATCGCATTGCGATTT
291839 ACATATTCGC
Statistics
Matches: 40, Mismatches: 13, Indels: 6
0.68 0.22 0.10
Matches are distributed among these distances:
19 3 0.08
20 10 0.25
21 25 0.62
22 2 0.05
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.36
Consensus pattern (21 bp):
ATCGCATTGCGATTTTGTATT
Found at i:291814 original size:20 final size:20
Alignment explanation
Indices: 291791--291875 Score: 75
Period size: 20 Copynumber: 4.2 Consensus size: 20
291781 TTATCGCAAC
*
291791 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCATAATCGCGTT
*
291811 GCGATTATGT-ATTATCGCGTT
1 GCGA-TA-GTCATAATCGCGTT
* * *
291832 GCGAT-TTACATATTCGCATT
1 GCGATAGT-CATAATCGCGTT
*
291852 GCGATAGTCAAAATCGCGTT
1 GCGATAGTCATAATCGCGTT
291872 GCGA
1 GCGA
291876 ATCTGGAAAC
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
18 1 0.02
20 31 0.62
21 16 0.32
22 2 0.04
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (20 bp):
GCGATAGTCATAATCGCGTT
Found at i:292171 original size:27 final size:27
Alignment explanation
Indices: 292119--292171 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
292109 TGTCTTAATT
* **
292119 TTATTATTTAATATTTGATACTTTTTA
1 TTATTATTTAATATTTAATAAATTTTA
292146 TTATTATTTGAA-ATTTAATAAATTTT
1 TTATTATTT-AATATTTAATAAATTTT
292172 TAAATGTGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (27 bp):
TTATTATTTAATATTTAATAAATTTTA
Found at i:294501 original size:21 final size:21
Alignment explanation
Indices: 294477--294576 Score: 148
Period size: 21 Copynumber: 4.8 Consensus size: 21
294467 CAACATAGTT
*
294477 TCCAAAATCGCAACGCGATTC
1 TCCAAAATCGCAACGCGGTTC
*
294498 TCCAAAATCGTAACGCGGTT-
1 TCCAAAATCGCAACGCGGTTC
* * *
294518 TTCAAATTCGCAACACGGTTC
1 TCCAAAATCGCAACGCGGTTC
294539 TCCAAAATCGCAACGCGGTTC
1 TCCAAAATCGCAACGCGGTTC
294560 TCCAAAATCGCAACGCG
1 TCCAAAATCGCAACGCG
294577 TTTTGCGAAT
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 16 0.23
21 53 0.77
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (21 bp):
TCCAAAATCGCAACGCGGTTC
Found at i:294529 original size:41 final size:41
Alignment explanation
Indices: 294474--294576 Score: 152
Period size: 41 Copynumber: 2.5 Consensus size: 41
294464 TCACAACATA
*
294474 GTTTCCAAAATCGCAACGCGATTCTCCAAAATCGTAACGCG
1 GTTTCCAAAATCGCAACGCGATTCTCCAAAATCGCAACGCG
* * * *
294515 GTTTTCAAATTCGCAACACGGTTCTCCAAAATCGCAACGCG
1 GTTTCCAAAATCGCAACGCGATTCTCCAAAATCGCAACGCG
294556 GTTCTCCAAAATCGCAACGCG
1 GTT-TCCAAAATCGCAACGCG
294577 TTTTGCGAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 39 0.74
42 14 0.26
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.22
Consensus pattern (41 bp):
GTTTCCAAAATCGCAACGCGATTCTCCAAAATCGCAACGCG
Found at i:296657 original size:42 final size:43
Alignment explanation
Indices: 296611--296700 Score: 112
Period size: 42 Copynumber: 2.1 Consensus size: 43
296601 GTAAAAAACA
* *
296611 CCACTAAAGTAT-AACTCTGTCGCGACATTTGTTAAAAAAATG
1 CCACTAAAGAATGAACACTGTCGCGACATTTGTTAAAAAAATG
* * * *
296653 CCACT-ATGAATGAACACTGTTGCGACATTTGTTGAAAAAATT
1 CCACTAAAGAATGAACACTGTCGCGACATTTGTTAAAAAAATG
296695 CCACTA
1 CCACTA
296701 TAAACGAACC
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
41 4 0.10
42 36 0.90
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (43 bp):
CCACTAAAGAATGAACACTGTCGCGACATTTGTTAAAAAAATG
Found at i:296726 original size:42 final size:42
Alignment explanation
Indices: 296635--296733 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 42
296625 CTCTGTCGCG
* * * *
296635 ACATTTGTTAAAAAAATGCCACTATGAATGAACACTGTTGCG
1 ACATTTGTTAAAAAAATGCCACTATAAACGAACACTATTGCA
* * *
296677 ACATTTGTTGAAAAAATTCCACTATAAACGAACCCTATTGCA
1 ACATTTGTTAAAAAAATGCCACTATAAACGAACACTATTGCA
*
296719 ACCTTTGTATAAAAA
1 ACATTTGT-TAAAAA
296734 CACCGCTAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 42 0.89
43 5 0.11
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.29
Consensus pattern (42 bp):
ACATTTGTTAAAAAAATGCCACTATAAACGAACACTATTGCA
Found at i:296793 original size:82 final size:82
Alignment explanation
Indices: 296687--296872 Score: 216
Period size: 82 Copynumber: 2.3 Consensus size: 82
296677 ACATTTGTTG
* * * * *
296687 AAAAAATTCCACTATAAACGAACCCTATTGCAACCTTTGTATAAAAACACCGCTAAAGTAGAACT
1 AAAAAATGCCACTATAAACGAACCCTATTGCAACATTTAT-TAAAAACACCCCTAAAGTACAACT
296752 CTGTCACTG-CGTTTA-TT
65 CTGTCAC-GACGTTTATTT
* *** * *
296769 AAAAAATGCCACTATGAATC-AACCCTATTGTGGCATTTATTTAAAACACCCCTAAAGTACTACT
1 AAAAAATGCCACTAT-AAACGAACCCTATTGCAACATTTATTAAAAACACCCCTAAAGTACAACT
296833 CTGTCACGACGTTTATTT
65 CTGTCACGACGTTTATTT
*
296851 AAAAAAGGCCACTATAAACGAA
1 AAAAAATGCCACTATAAACGAA
296873 TCTTATTACG
Statistics
Matches: 87, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
80 1 0.01
81 36 0.41
82 47 0.54
83 3 0.03
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (82 bp):
AAAAAATGCCACTATAAACGAACCCTATTGCAACATTTATTAAAAACACCCCTAAAGTACAACTC
TGTCACGACGTTTATTT
Found at i:299444 original size:22 final size:24
Alignment explanation
Indices: 299409--299453 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
299399 GTTTTAATTC
299409 AATCTTAATTCCTAATAA-ATAATA
1 AATCTTAATTCCTAA-AAGATAATA
299433 AATC-TAA-TCCTAAAAGATAAT
1 AATCTTAATTCCTAAAAGATAAT
299454 GCATCATCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 2 0.10
22 11 0.55
23 3 0.15
24 4 0.20
ACGTcount: A:0.51, C:0.13, G:0.02, T:0.33
Consensus pattern (24 bp):
AATCTTAATTCCTAAAAGATAATA
Found at i:302686 original size:46 final size:44
Alignment explanation
Indices: 302620--302727 Score: 110
Period size: 46 Copynumber: 2.3 Consensus size: 44
302610 AAAACAAATT
* * * *
302620 AAATAAAAGATAAGATAAAGAAAGCA-AAGATAAAATAGTAAGTAAAAT
1 AAATAAAA-A-AA-ATAAAGAAA-AAGAAGAAAAAATA-TAAATAAAAC
302668 AAATATAAAAAAATAAAGAAAAAGAAGAAAAAATATAAATAAAAC
1 AAATA-AAAAAAATAAAGAAAAAGAAGAAAAAATATAAATAAAAC
*
302713 AAATAAATAAAATAA
1 AAATAAAAAAAATAA
302728 TAATAAAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
44 9 0.17
45 14 0.26
46 19 0.36
47 2 0.04
48 6 0.11
49 3 0.06
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.16
Consensus pattern (44 bp):
AAATAAAAAAAATAAAGAAAAAGAAGAAAAAATATAAATAAAAC
Found at i:302720 original size:4 final size:4
Alignment explanation
Indices: 302702--302835 Score: 50
Period size: 4 Copynumber: 33.8 Consensus size: 4
302692 AAGAAAAAAT
*
302702 ATAA ATAAA ACAA ATAA ATAA A-ATA AT-A ATAA A-AA AGT-A A-AA ATAA
1 ATAA AT-AA ATAA ATAA ATAA ATA-A ATAA ATAA ATAA A-TAA ATAA ATAA
* * * * * * *
302748 TATAT ATAT ATAT ATAT ATAA A-AA AGTAA AAAA ATAA TATAT ATAT ATATA
1 -ATAA ATAA ATAA ATAA ATAA ATAA A-TAA ATAA ATAA -ATAA ATAA ATA-A
* * *
302799 ATAA A-AA ATAA A-AA ATAA ATAT ATAT ATAA ATTA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
302836 TGATAATAAA
Statistics
Matches: 103, Mismatches: 12, Indels: 30
0.71 0.08 0.21
Matches are distributed among these distances:
3 18 0.17
4 70 0.68
5 15 0.15
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (4 bp):
ATAA
Found at i:302775 original size:35 final size:35
Alignment explanation
Indices: 302727--302870 Score: 172
Period size: 35 Copynumber: 4.1 Consensus size: 35
302717 AAATAAAATA
302727 ATAATAAAAAAGTAAAAATAATATATATATATATAT
1 ATAATAAAAAA-TAAAAATAATATATATATATATAT
302763 AT-ATAAAAAAGTAAAAA-AATA-ATATATATATAT
1 ATAATAAAAAA-TAAAAATAATATATATATATATAT
*
302796 ATAATAAAAAATAAAAAATAA-ATATATATATAAAT
1 ATAATAAAAAAT-AAAAATAATATATATATATATAT
* *
302831 -TAATATGATAATAAAAAATATATATATATATATATAT
1 ATAATA-AAAAAT-AAAAATA-ATATATATATATATAT
302868 ATA
1 ATA
302871 TATATATATA
Statistics
Matches: 96, Mismatches: 4, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
33 15 0.16
34 23 0.24
35 40 0.42
36 3 0.03
37 13 0.14
38 2 0.02
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (35 bp):
ATAATAAAAAATAAAAATAATATATATATATATAT
Found at i:302793 original size:33 final size:33
Alignment explanation
Indices: 302730--302864 Score: 161
Period size: 33 Copynumber: 4.1 Consensus size: 33
302720 TAAAATAATA
302730 ATAAAAAAGTAAAAATAATATATATATATATATAT
1 ATAAAAAAGTAAAAA-AATA-ATATATATATATAT
302765 ATAAAAAAGTAAAAAAATAATATATATATATAT
1 ATAAAAAAGTAAAAAAATAATATATATATATAT
*
302798 AATAAAAAA-T-AAAAAATAA-ATATATATATAA
1 -ATAAAAAAGTAAAAAAATAATATATATATATAT
* * * *
302829 ATTAATATGATAATAAAA-AATATATATATATAT
1 ATAAAAAAG-TAAAAAAATAATATATATATATAT
302862 ATA
1 ATA
302865 TATATATATA
Statistics
Matches: 88, Mismatches: 7, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
30 5 0.06
31 11 0.12
32 12 0.14
33 33 0.38
34 12 0.14
35 15 0.17
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (33 bp):
ATAAAAAAGTAAAAAAATAATATATATATATAT
Found at i:302907 original size:2 final size:2
Alignment explanation
Indices: 302747--302887 Score: 84
Period size: 2 Copynumber: 74.0 Consensus size: 2
302737 AGTAAAAATA
* * * * *
302747 AT AT AT AT AT AT AT AT AT AT A- AA AA AGT AA AA AA AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* * * * *
302788 AT AT AT AT AT A- AT A- AA AA AT A- AA AA AT AA 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
* * *
302827 AA AT -T A- AT AT GAT A- AT A- AA AA 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
302866 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
302888 CTAAAAAAAA
Statistics
Matches: 118, Mismatches: 10, Indels: 22
0.79 0.07 0.15
Matches are distributed among these distances:
1 9 0.08
2 106 0.90
3 3 0.03
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (2 bp):
AT
Found at i:304099 original size:41 final size:38
Alignment explanation
Indices: 304038--304134 Score: 119
Period size: 41 Copynumber: 2.6 Consensus size: 38
304028 AACTCGAGGG
*
304038 TTTG-GTGTTTCAAGAGAAACATTTTCAAAGGTTTTTT
1 TTTGTGTGTTTCAAGAGAAACAATTTCAAAGGTTTTTT
* *
304075 GTGTGTGTGTGTTTCAAGAGAAACAATTTCGAGGGTTTTTT
1 -T-T-TGTGTGTTTCAAGAGAAACAATTTCAAAGGTTTTTT
304116 TTTGTGT-TTT-AAGAGAAAC
1 TTTGTGTGTTTCAAGAGAAAC
304135 TGTCTCAAGA
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
36 9 0.17
37 3 0.06
38 6 0.11
39 2 0.04
40 3 0.06
41 30 0.57
ACGTcount: A:0.26, C:0.07, G:0.24, T:0.43
Consensus pattern (38 bp):
TTTGTGTGTTTCAAGAGAAACAATTTCAAAGGTTTTTT
Found at i:304160 original size:36 final size:37
Alignment explanation
Indices: 304120--304222 Score: 138
Period size: 36 Copynumber: 2.8 Consensus size: 37
304110 TTTTTTTTTG
*
304120 TGTTTTAAGAGAAACTGTCTCAAGAG-GTACAAAA-TT
1 TGTTTTAAAAGAAACTGTCTCAAGAGAG-ACAAAACTT
*
304156 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTTAAAAGAAACTGTCTCAAGAGAGACAAAACTT
* * *
304193 AGTTCTAAAAGAAACTGTCTCAAGGGAGAC
1 TGTTTTAAAAGAAACTGTCTCAAGAGAGAC
304223 GAAATATTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
36 30 0.51
37 29 0.49
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (37 bp):
TGTTTTAAAAGAAACTGTCTCAAGAGAGACAAAACTT
Found at i:304212 original size:37 final size:36
Alignment explanation
Indices: 304129--304227 Score: 130
Period size: 37 Copynumber: 2.7 Consensus size: 36
304119 GTGTTTTAAG
*
304129 AGAAACTGTCTCAAGAG-GTACAAAATTTGTTTCAAA
1 AGAAACTGTCTCAAGAGAG-ACAAAATTAGTTTCAAA
304165 AGAAACTGTCTCAAGAGAGACAAAACTTAG-TTCTAAA
1 AGAAACTGTCTCAAGAGAGACAAAA-TTAGTTTC-AAA
* *
304202 AGAAACTGTCTCAAGGGAGACGAAAT
1 AGAAACTGTCTCAAGAGAGACAAAAT
304228 ATTTTTCAAG
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
36 27 0.47
37 30 0.53
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.22
Consensus pattern (36 bp):
AGAAACTGTCTCAAGAGAGACAAAATTAGTTTCAAA
Found at i:304431 original size:36 final size:36
Alignment explanation
Indices: 304381--304567 Score: 149
Period size: 36 Copynumber: 5.4 Consensus size: 36
304371 TCAAGGTTTA
*
304381 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAATTT
1 TGTTTCAAGGGAAACTATCTCAAGGGAGACAAATTT
* *
304417 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGGGAGACAAATTT
** * * * *
304453 AATTTCAAAGGAAA-TGTTTTCAA---TG-----TTT
1 TGTTTCAAGGGAAACT-ATCTCAAGGGAGACAAATTT
* *
304481 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAATTT
1 -TGTTTCAAGGGAAACTATCTCAAGGGAGACAAATTT
* * * *
304518 TGTTTCAAGGGAAACTATCCCAAGCGAGATAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGGGAGACAAATTT
*
304554 TATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
304568 TGTTTTCAAT
Statistics
Matches: 116, Mismatches: 24, Indels: 22
0.72 0.15 0.14
Matches are distributed among these distances:
28 2 0.02
29 15 0.13
30 1 0.01
32 1 0.01
33 1 0.01
35 1 0.01
36 92 0.79
37 3 0.03
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTATCTCAAGGGAGACAAATTT
Found at i:304474 original size:101 final size:101
Alignment explanation
Indices: 304354--304591 Score: 404
Period size: 101 Copynumber: 2.4 Consensus size: 101
304344 ATATTTTGTG
* *
304354 TTTCAAGGGAAACGTTTTCAAGGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAATTTTG
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAATTTTG
*
304419 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAA
66 TTTCAAGGGAAACTATCCCAAGAGAGACAAAATTAA
* *
304455 TTTCAAAGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAATTTTG
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAATTTTG
* * *
304520 TTTCAAGGGAAACTATCCCAAGCGAGATAAAATTTA
66 TTTCAAGGGAAACTATCCCAAGAGAGACAAAATTAA
304556 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAG
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAG
304592 GGAGACAAAA
Statistics
Matches: 128, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 128 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.32
Consensus pattern (101 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAATTTTG
TTTCAAGGGAAACTATCCCAAGAGAGACAAAATTAA
Found at i:304591 original size:86 final size:87
Alignment explanation
Indices: 304501--304678 Score: 322
Period size: 87 Copynumber: 2.1 Consensus size: 87
304491 AGAAACTGTC
*
304501 TCAAGGGAGAC-AAATTTTGTTTCAAGGGAAACTATCCCAAGCGAGATAAAATTTATTTCAAGGG
1 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCCCAAGCGAGATAAAATTCATTTCAAGGG
304565 AAATGTTTTCAATGTTTATGTT
66 AAATGTTTTCAATGTTTATGTT
* *
304587 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTCAAGGG
1 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCCCAAGCGAGATAAAATTCATTTCAAGGG
304652 AAATGTTTTCAATGTTTATGTT
66 AAATGTTTTCAATGTTTATGTT
304674 TCAAG
1 TCAAG
304679 AGAAACTGTC
Statistics
Matches: 88, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
86 11 0.12
87 77 0.88
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (87 bp):
TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCCCAAGCGAGATAAAATTCATTTCAAGGG
AAATGTTTTCAATGTTTATGTT
Found at i:305121 original size:106 final size:106
Alignment explanation
Indices: 304936--305257 Score: 439
Period size: 106 Copynumber: 3.0 Consensus size: 106
304926 GTATTGTTCT
* * * * * * * *
304936 GAGTCCAATATCCTCCGCCGTGAAGTTAAAATTGGCTCTGGAACTAAGAAATTATTTGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* * * *
305001 CCAG-TCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTC
66 CCAGCT-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
* * *
305042 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
305107 CCAGCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
* * * *
305148 AAGTCCAATATCCTTCGCTGTGAAATTGAAATTAGCTTTGAAATTGAGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* *
305213 CCAGCTGTCCCTTCGTTGTGGAGTTGAACTTATGTTGTCTC
66 CCAGCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
305254 GAGT
1 GAGT
305258 GGCACGATAT
Statistics
Matches: 190, Mismatches: 25, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
106 189 0.99
107 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
CCAGCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
Found at i:305909 original size:31 final size:32
Alignment explanation
Indices: 305853--305941 Score: 135
Period size: 31 Copynumber: 2.8 Consensus size: 32
305843 GTTCCCAAAG
* * *
305853 ATGCCCCAATATTCGATGTTGAATCTAAAAAA
1 ATGCCCCAACATTTGATGTTAAATCTAAAAAA
*
305885 ATG-CCCAGCATTTGATGTTAAATCTAAAAAA
1 ATGCCCCAACATTTGATGTTAAATCTAAAAAA
305916 ATGCCCCAACATTTGATGTTAAATCT
1 ATGCCCCAACATTTGATGTTAAATCT
305942 TCAAAGATGT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 27 0.53
32 24 0.47
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.30
Consensus pattern (32 bp):
ATGCCCCAACATTTGATGTTAAATCTAAAAAA
Found at i:306933 original size:69 final size:69
Alignment explanation
Indices: 306850--306987 Score: 177
Period size: 69 Copynumber: 2.0 Consensus size: 69
306840 TGTCTCTCTC
* * *
306850 TTGATGCTCCATGATCTTCGAGTGGACTGATTCAGTAATTCATAAATGATTGTGCTTGATCAATC
1 TTGATGCTCCATGATCTTCAAGTGAACTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAATC
306915 TCAT
66 TCAT
* * * * * * * *
306919 TTGATGCTCTATGATCTTTAAGTGAAGTGGTTCAGTGATTCGGAAATGATTGTTCTTGATCAATT
1 TTGATGCTCCATGATCTTCAAGTGAACTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAATC
306984 TCAT
66 TCAT
306988 AGTTTGAATC
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
69 58 1.00
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.40
Consensus pattern (69 bp):
TTGATGCTCCATGATCTTCAAGTGAACTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAATC
TCAT
Found at i:307088 original size:14 final size:14
Alignment explanation
Indices: 307059--307108 Score: 68
Period size: 13 Copynumber: 3.7 Consensus size: 14
307049 TTTTCTTCAA
307059 TTTTC-CTTTGTTT
1 TTTTCTCTTTGTTT
*
307072 TTTTCTCTTT-TTA
1 TTTTCTCTTTGTTT
*
307085 TTTTCTCTTTGCTT
1 TTTTCTCTTTGTTT
307099 TTTTCTCTTT
1 TTTTCTCTTT
307109 TTGCTTTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 17 0.53
14 15 0.47
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (14 bp):
TTTTCTCTTTGTTT
Found at i:307094 original size:27 final size:26
Alignment explanation
Indices: 307058--307110 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
307048 TTTTTCTTCA
*
307058 ATTTTCCTTTGTTTTTTTCTCTTTTT
1 ATTTTCCTTTGCTTTTTTCTCTTTTT
307084 ATTTTCTCTTTGCTTTTTTCTCTTTTT
1 ATTTTC-CTTTGCTTTTTTCTCTTTTT
307111 GCTTTGATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.75
Consensus pattern (26 bp):
ATTTTCCTTTGCTTTTTTCTCTTTTT
Found at i:307113 original size:16 final size:15
Alignment explanation
Indices: 307065--307115 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 15
307055 TCAATTTTCC
*
307065 TTTGTTTTTTTCTCT
1 TTTGCTTTTTTCTCT
*
307080 TTT--TATTTTCTC-
1 TTTGCTTTTTTCTCT
307092 TTTGCTTTTTTCTCTT
1 TTTGCTTTTTTCTC-T
307108 TTTGCTTT
1 TTTGCTTT
307116 GATTAAATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
12 3 0.10
13 8 0.27
14 8 0.27
15 3 0.10
16 8 0.27
ACGTcount: A:0.02, C:0.16, G:0.06, T:0.76
Consensus pattern (15 bp):
TTTGCTTTTTTCTCT
Found at i:310231 original size:13 final size:12
Alignment explanation
Indices: 310213--310292 Score: 69
Period size: 13 Copynumber: 6.7 Consensus size: 12
310203 AATAGTAAGT
310213 AAAATAAATATAA
1 AAAATAAATA-AA
*
310226 AAAAT-AA-AGA
1 AAAATAAATAAA
310236 AAAATAAGA-AAA
1 AAAATAA-ATAAA
310248 AAATATAAATAAA
1 AAA-ATAAATAAA
310261 ACAAATAAATAAA
1 A-AAATAAATAAA
*
310274 ATAAT-AATAAA
1 AAAATAAATAAA
*
310285 AAAGTAAA
1 AAAATAAA
310293 AATAATATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 13
0.76 0.07 0.18
Matches are distributed among these distances:
10 6 0.11
11 11 0.20
12 14 0.25
13 23 0.41
14 2 0.04
ACGTcount: A:0.78, C:0.01, G:0.04, T:0.17
Consensus pattern (12 bp):
AAAATAAATAAA
Found at i:310250 original size:23 final size:23
Alignment explanation
Indices: 310180--310261 Score: 60
Period size: 23 Copynumber: 3.4 Consensus size: 23
310170 AAAAGATAAG
*
310180 ATAAAGAAAGA-AAGAAAAGATAAA
1 ATAAAGAAAAATAAGAAAA-A-AAA
* *
310204 ATAGTAAGTAAAATAA-ATATAAAAA
1 ATA--AAGAAAAATAAGA-AAAAAAA
*
310229 ATAAAGAAAAATAAGAAAAAAAT
1 ATAAAGAAAAATAAGAAAAAAAA
*
310252 ATAAATAAAA
1 ATAAAGAAAA
310262 CAAATAAATA
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
23 24 0.52
24 4 0.09
25 6 0.13
26 8 0.17
27 4 0.09
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (23 bp):
ATAAAGAAAAATAAGAAAAAAAA
Found at i:310261 original size:45 final size:44
Alignment explanation
Indices: 310201--310338 Score: 120
Period size: 45 Copynumber: 3.0 Consensus size: 44
310191 AAGAAAAGAT
*
310201 AAAATAGTAAGTAAAATAAATATAAAAAATAAAGAAAAATAAGAAA
1 AAAATA-TAAATAAAATAAATATAAAAAATAAA-AAAAATAAGAAA
*
310247 AAAATATAAATAAAACAAATA-AATAAAATAATAATAAAA-AAGTAAA
1 AAAATATAAATAAAATAAATATAA-AAAATAA-AA-AAAATAAG-AAA
* * * * *
310293 AATAATATATATATATATATATATAATAAATAAATAAAATAA-AAA
1 AA-AATATAAATA-AAATAAATATAAAAAATAAAAAAAATAAGAAA
310338 A
1 A
310339 TAGCAAATAT
Statistics
Matches: 76, Mismatches: 8, Indels: 17
0.75 0.08 0.17
Matches are distributed among these distances:
44 2 0.03
45 28 0.37
46 20 0.26
47 12 0.16
48 12 0.16
49 2 0.03
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.23
Consensus pattern (44 bp):
AAAATATAAATAAAATAAATATAAAAAATAAAAAAAATAAGAAA
Found at i:310321 original size:44 final size:44
Alignment explanation
Indices: 310274--310362 Score: 121
Period size: 44 Copynumber: 2.1 Consensus size: 44
310264 AATAAATAAA
* * *
310274 ATAAT-AATAAA-AAAGT-AAAAATAATATATATATATATATAT
1 ATAATAAATAAATAAAATAAAAAATAACAAATATATATATATAT
*
310315 ATAATAAATAAATAAAATAAAAAATAGCAAATATATATATATAT
1 ATAATAAATAAATAAAATAAAAAATAACAAATATATATATATAT
310359 ATAA
1 ATAA
310363 ATTAACAATC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
41 5 0.12
42 6 0.15
43 4 0.10
44 26 0.63
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.31
Consensus pattern (44 bp):
ATAATAAATAAATAAAATAAAAAATAACAAATATATATATATAT
Found at i:310334 original size:9 final size:9
Alignment explanation
Indices: 310212--310335 Score: 51
Period size: 9 Copynumber: 13.0 Consensus size: 9
310202 AAATAGTAAG
310212 TAAAATAAA
1 TAAAATAAA
310221 TATAAA-AAA
1 TA-AAATAAA
*
310230 TAAAGAAAAA
1 TAAA-ATAAA
*
310240 TAAGAAAAAAA
1 T-A-AAATAAA
310251 TATAAATAAA
1 TA-AAATAAA
310261 -ACAAATAAA
1 TA-AAATAAA
310270 TAAAATAATAA
1 TAAAAT-A-AA
*
310281 TAAAA-AAG
1 TAAAATAAA
310289 TAAAA-ATAA
1 TAAAATA-AA
* *
310298 TATATATATA
1 TA-AAATAAA
*
310308 TATATATATAA
1 TA-AAATA-AA
310319 T-AAATAAA
1 TAAAATAAA
310327 TAAAATAAA
1 TAAAATAAA
310336 AAATAGCAAA
Statistics
Matches: 93, Mismatches: 9, Indels: 26
0.73 0.07 0.20
Matches are distributed among these distances:
8 12 0.13
9 35 0.38
10 27 0.29
11 17 0.18
12 2 0.02
ACGTcount: A:0.73, C:0.01, G:0.02, T:0.24
Consensus pattern (9 bp):
TAAAATAAA
Found at i:310335 original size:13 final size:13
Alignment explanation
Indices: 310214--310340 Score: 66
Period size: 13 Copynumber: 9.4 Consensus size: 13
310204 ATAGTAAGTA
310214 AAATAAATATAAA-
1 AAATAAA-ATAAAT
*
310227 AAATAAAGAAAAAT
1 AAATAAA-ATAAAT
310241 AAGA-AAAA-AATAT
1 AA-ATAAAATAA-AT
*
310254 AAATAAAACAAAT
1 AAATAAAATAAAT
310267 AAATAAAATAATAAT
1 AAATAAAAT-A-AAT
*
310282 AAA-AAAGTAAAAAT
1 AAATAAA--ATAAAT
* *
310296 AATATATATATATAT
1 AA-ATA-AAATAAAT
* *
310311 ATATATAATAAAT
1 AAATAAAATAAAT
310324 AAATAAAATAAA-
1 AAATAAAATAAAT
310336 AAATA
1 AAATA
310341 GCAAATATAT
Statistics
Matches: 89, Mismatches: 13, Indels: 25
0.70 0.10 0.20
Matches are distributed among these distances:
12 8 0.09
13 45 0.51
14 19 0.21
15 14 0.16
16 2 0.02
17 1 0.01
ACGTcount: A:0.73, C:0.01, G:0.02, T:0.24
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:315390 original size:30 final size:29
Alignment explanation
Indices: 315295--315388 Score: 109
Period size: 29 Copynumber: 3.2 Consensus size: 29
315285 ATTATGATCT
315295 TTTAAATTTCTAATTTTTCTATTTTAGTCC
1 TTTAAATTTCT-ATTTTTCTATTTTAGTCC
* *
315325 TTTAAATTTTTATTTTTTTATTTTAGTGCC
1 TTTAAATTTCTATTTTTCTATTTTAGT-CC
* * *
315355 -TTAAGTCTCTATTTTTGCTATTTTGGTCC
1 TTTAAATTTCTATTTTT-CTATTTTAGTCC
315384 TTTAA
1 TTTAA
315389 GTTTATGTAA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
29 30 0.56
30 24 0.44
ACGTcount: A:0.20, C:0.12, G:0.07, T:0.61
Consensus pattern (29 bp):
TTTAAATTTCTATTTTTCTATTTTAGTCC
Found at i:315448 original size:29 final size:29
Alignment explanation
Indices: 315366--315466 Score: 89
Period size: 29 Copynumber: 3.4 Consensus size: 29
315356 TAAGTCTCTA
* *
315366 TTTTTGCTATTTTGGTCCTTTAAGTTTATG
1 TTTTTGCTA-TTTAGTACTTTAAGTTTATG
*
315396 TAATTATTG-T-TTTAGGACTTTAAGTTTATG
1 T--TT-TTGCTATTTAGTACTTTAAGTTTATG
* *
315426 TTTTTGCTATTTAGTTCTTTAAGTTTCTG
1 TTTTTGCTATTTAGTACTTTAAGTTTATG
* *
315455 TTGTTGCCATTT
1 TTTTTGCTATTT
315467 TAATCCTTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
27 3 0.05
28 3 0.05
29 27 0.47
30 19 0.33
32 3 0.05
33 3 0.05
ACGTcount: A:0.17, C:0.09, G:0.16, T:0.58
Consensus pattern (29 bp):
TTTTTGCTATTTAGTACTTTAAGTTTATG
Found at i:321354 original size:17 final size:15
Alignment explanation
Indices: 321332--321404 Score: 69
Period size: 15 Copynumber: 4.7 Consensus size: 15
321322 TGCAAAGATC
321332 AAATCAAAGAAGAGAGA
1 AAATCAAAGAAGA-A-A
*
321349 AAATCAAAGAACAAA
1 AAATCAAAGAAGAAA
321364 AAATCAAA-AAGAAA
1 AAATCAAAGAAGAAA
*
321378 AGAAGCAAAG-AGAAA
1 A-AATCAAAGAAGAAA
*
321393 ATAAACAAAGAA
1 A-AATCAAAGAA
321405 AAAGGAAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
14 6 0.12
15 28 0.58
16 2 0.04
17 12 0.25
ACGTcount: A:0.71, C:0.08, G:0.15, T:0.05
Consensus pattern (15 bp):
AAATCAAAGAAGAAA
Found at i:321368 original size:15 final size:17
Alignment explanation
Indices: 321332--321371 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
321322 TGCAAAGATC
*
321332 AAATCAAAGAAGAGAGA
1 AAATCAAAGAACAGAGA
321349 AAATCAAAGAACA-A-A
1 AAATCAAAGAACAGAGA
321364 AAATCAAA
1 AAATCAAA
321372 AAGAAAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 1 0.05
17 12 0.55
ACGTcount: A:0.70, C:0.10, G:0.12, T:0.07
Consensus pattern (17 bp):
AAATCAAAGAACAGAGA
Found at i:322492 original size:30 final size:31
Alignment explanation
Indices: 322456--322574 Score: 134
Period size: 30 Copynumber: 3.8 Consensus size: 31
322446 GGAACAATGG
322456 GGGCATCTTTGAAGATTCAACATCAAA-TGA
1 GGGCATCTTTGAAGATTCAACATCAAATTGA
*
322486 GGGCATCTTTGAAGATTCAACATCAAATGTTGG
1 GGGCATCTTTGAAGATTCAACATCAAA--TTGA
* *
322519 GGGCATCTTTGGAGATTCAGCATCGAATATTGA
1 GGGCATCTTTGAAGATTCAACATC-AA-ATTGA
* **
322552 -GGTATCTTTGGGGATTCAACATC
1 GGGCATCTTTGAAGATTCAACATC
322575 CTGATGCGAA
Statistics
Matches: 77, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
30 27 0.35
32 20 0.26
33 27 0.35
34 2 0.03
35 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (31 bp):
GGGCATCTTTGAAGATTCAACATCAAATTGA
Found at i:323058 original size:123 final size:123
Alignment explanation
Indices: 322837--323249 Score: 585
Period size: 123 Copynumber: 3.4 Consensus size: 123
322827 AAATTCACTA
* * * *
322837 ACCAAGACTCATTGCACATGAGCAGTGTCAACCCTTGATAACCAACC-ATCCTCATCATGTAGGA
1 ACCAAGACTCATCGCATATGAGCAGTGTCAACCCTTGATAACCAGCCGA-CCTCATCACGTAGGA
* * * *
322901 ACCGTGTTATCACCTTTATATGGTCAAGAATCATCACATATGAGAAGTACCATCCTCTG
65 ACCATGTTATCACCTTTATATGGTCAAGACTCATCGCATATGAGCAGTACCATCCTCTG
* *
322960 ACCAAGACTCATTGCATATGAGTAGTGTCAACCCTTGATAACCAGCCGACCTCATCACGTAGGAA
1 ACCAAGACTCATCGCATATGAGCAGTGTCAACCCTTGATAACCAGCCGACCTCATCACGTAGGAA
* *
323025 CCATGTTATCATCTTTATATGGTCAAGACTCATCGCATATAAGCAGTACCATCCTCTG
66 CCATGTTATCACCTTTATATGGTCAAGACTCATCGCATATGAGCAGTACCATCCTCTG
* * * *
323083 ACCAAGACTCATCGCATATGAGCAGTGTCAATCCTTGATAACTAGCCGTCCTCATCACGTAGAAA
1 ACCAAGACTCATCGCATATGAGCAGTGTCAACCCTTGATAACCAGCCGACCTCATCACGTAGGAA
* * * *
323148 CCATGTTATCACCTTTATATGGTCAAGACTCATTGCATATGAGCAGTATCTTCCCCTG
66 CCATGTTATCACCTTTATATGGTCAAGACTCATCGCATATGAGCAGTACCATCCTCTG
* * * * *
323206 GCCAAGACTCATCACATATGAGCAGTGCCAATCCTAGATAACCA
1 ACCAAGACTCATCGCATATGAGCAGTGTCAACCCTTGATAACCA
323250 AGACTTATCA
Statistics
Matches: 262, Mismatches: 27, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
123 261 1.00
124 1 0.00
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (123 bp):
ACCAAGACTCATCGCATATGAGCAGTGTCAACCCTTGATAACCAGCCGACCTCATCACGTAGGAA
CCATGTTATCACCTTTATATGGTCAAGACTCATCGCATATGAGCAGTACCATCCTCTG
Found at i:323702 original size:3 final size:3
Alignment explanation
Indices: 323687--323749 Score: 110
Period size: 3 Copynumber: 21.3 Consensus size: 3
323677 GGGTCAAAAA
*
323687 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
323734 TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
323750 TTTAATTTTA
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 1 0.02
3 56 0.98
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:325188 original size:30 final size:30
Alignment explanation
Indices: 325148--325240 Score: 134
Period size: 30 Copynumber: 3.1 Consensus size: 30
325138 TTCTGGTCTT
*
325148 TTAAAATTCTATTTTTTCTATTTTAGTCCC
1 TTAAATTTCTATTTTTTCTATTTTAGTCCC
325178 TTAAATTTCTATTTTTT-TATTTTAGTCCC
1 TTAAATTTCTATTTTTTCTATTTTAGTCCC
* * * *
325207 TTAAGTCTCTATTTTTTCTATTTTGGTCCT
1 TTAAATTTCTATTTTTTCTATTTTAGTCCC
325237 TTAA
1 TTAA
325241 GTTTATGTAA
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 27 0.47
30 30 0.53
ACGTcount: A:0.20, C:0.15, G:0.05, T:0.59
Consensus pattern (30 bp):
TTAAATTTCTATTTTTTCTATTTTAGTCCC
Found at i:325241 original size:30 final size:30
Alignment explanation
Indices: 325155--325242 Score: 133
Period size: 29 Copynumber: 3.0 Consensus size: 30
325145 CTTTTAAAAT
* *
325155 TCTATTTTTTCTATTTTAGTCCCTTAAATT
1 TCTATTTTTTCTATTTTAGTCCCTTAAGTC
325185 TCTATTTTTT-TATTTTAGTCCCTTAAGTC
1 TCTATTTTTTCTATTTTAGTCCCTTAAGTC
* *
325214 TCTATTTTTTCTATTTTGGTCCTTTAAGT
1 TCTATTTTTTCTATTTTAGTCCCTTAAGT
325243 TTATGTAATT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
29 27 0.51
30 26 0.49
ACGTcount: A:0.17, C:0.16, G:0.07, T:0.60
Consensus pattern (30 bp):
TCTATTTTTTCTATTTTAGTCCCTTAAGTC
Found at i:327206 original size:14 final size:14
Alignment explanation
Indices: 327187--327217 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
327177 TCGGTAATAT
327187 GTTCATTTATATTC
1 GTTCATTTATATTC
*
327201 GTTCATTTATGTTC
1 GTTCATTTATATTC
327215 GTT
1 GTT
327218 TATGTGCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.13, G:0.13, T:0.58
Consensus pattern (14 bp):
GTTCATTTATATTC
Found at i:327212 original size:24 final size:24
Alignment explanation
Indices: 327184--327237 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
327174 CGTTCGGTAA
* *
327184 TATGTTCATTTATATTCGTTCATT
1 TATGTTCATTTATATGCATTCATT
* *
327208 TATGTTCGTTTATGTGCATTCATT
1 TATGTTCATTTATATGCATTCATT
327232 TATGTT
1 TATGTT
327238 TAACCCAATC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.19, C:0.11, G:0.13, T:0.57
Consensus pattern (24 bp):
TATGTTCATTTATATGCATTCATT
Found at i:327425 original size:10 final size:10
Alignment explanation
Indices: 327403--327508 Score: 95
Period size: 10 Copynumber: 9.9 Consensus size: 10
327393 AAAATATAAT
327403 TTCATTTATG
1 TTCATTTATG
* *
327413 TTCGTTTACG
1 TTCATTTATG
327423 TTCATTTATG
1 TTCATTTATG
327433 TTCATTTATG
1 TTCATTTATG
327443 TTCATTTATTGTG
1 TTCATTTA---TG
*
327456 TTCGTTTATGTTTG
1 TTCATTTA----TG
*
327470 TTCATTTGTG
1 TTCATTTATG
* *
327480 TTCGTTTACG
1 TTCATTTATG
327490 TTCATTTATG
1 TTCATTTATG
327500 TTCATTTAT
1 TTCATTTAT
327509 TGTGTTCGTT
Statistics
Matches: 78, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
10 60 0.77
13 9 0.12
14 9 0.12
ACGTcount: A:0.15, C:0.11, G:0.14, T:0.59
Consensus pattern (10 bp):
TTCATTTATG
Found at i:327524 original size:10 final size:10
Alignment explanation
Indices: 327407--327591 Score: 73
Period size: 10 Copynumber: 16.5 Consensus size: 10
327397 TATAATTTCA
327407 TTTATGTTCG
1 TTTATGTTCG
* *
327417 TTTACGTTCA
1 TTTATGTTCG
*
327427 TTTATGTTCA
1 TTTATGTTCG
*
327437 TTTATGTTCA
1 TTTATGTTCG
327447 TTTATTGTGTTCG
1 TTTA---TGTTCG
*
327460 TTTATGTTTGTTCA
1 TTTA----TGTTCG
*
327474 TTTGTGTTCG
1 TTTATGTTCG
* *
327484 TTTACGTTCA
1 TTTATGTTCG
*
327494 TTTATGTTCA
1 TTTATGTTCG
327504 TTTATTGTGTTCG
1 TTTA---TGTTCG
*
327517 TTTATGTTTGTTCA
1 TTTA----TGTTCG
*
327531 TTTGTGTTCG
1 TTTATGTTCG
*
327541 TTTACGTTCG
1 TTTATGTTCG
327551 TTATTATGTTCG
1 -T-TTATGTTCG
*
327563 TGTACATCCGTTCG
1 T-T-TAT--GTTCG
327577 TTTATGTTCG
1 TTTATGTTCG
327587 TTTAT
1 TTTAT
327592 CATTTAAATG
Statistics
Matches: 137, Mismatches: 25, Indels: 26
0.73 0.13 0.14
Matches are distributed among these distances:
10 79 0.58
11 3 0.02
12 12 0.09
13 19 0.14
14 24 0.18
ACGTcount: A:0.13, C:0.12, G:0.17, T:0.58
Consensus pattern (10 bp):
TTTATGTTCG
Found at i:328203 original size:6 final size:7
Alignment explanation
Indices: 328188--328224 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
328178 CCTATAACCG
328188 AAAAGAA
1 AAAAGAA
328195 AAAAGAA
1 AAAAGAA
328202 AAAAGAA
1 AAAAGAA
328209 AAAAG-A
1 AAAAGAA
328215 AAAAGAA
1 AAAAGAA
328222 AAA
1 AAA
328225 CAGAGAGCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:330903 original size:64 final size:64
Alignment explanation
Indices: 330835--330959 Score: 189
Period size: 64 Copynumber: 1.9 Consensus size: 64
330825 GTGCACTAAG
* * * *
330835 TGTGCATCGATGCATCAAATGCATTCGATGTTTTGA-AAAAGCCTGAGTTCATCGATGCATGGTA
1 TGTGCATCGATGCATCAAATGAATTCGATGTTTTCATAAAA-CCCGAGTGCATCGATGCATGGTA
330899 TGTGCATCGATGCATCAAATGAATTCGATGTTTTCATTAAAACCCGAGTGCATCGATGCAT
1 TGTGCATCGATGCATCAAATGAATTCGATGTTTTCA-TAAAACCCGAGTGCATCGATGCAT
330960 AAACTGCATT
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
64 34 0.62
65 17 0.31
66 4 0.07
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (64 bp):
TGTGCATCGATGCATCAAATGAATTCGATGTTTTCATAAAACCCGAGTGCATCGATGCATGGTA
Found at i:330973 original size:64 final size:63
Alignment explanation
Indices: 330837--330974 Score: 163
Period size: 64 Copynumber: 2.2 Consensus size: 63
330827 GCACTAAGTG
* * * * * **
330837 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAAGCCTGAGTTCATCGATGCATGGTATG
1 TGCATCGATGCATCAAATGAATTCGATGTTTTCAAAAAGCCCGAGTGCATCGATGCAT-GAAAC
330901 TGCATCGATGCATCAAATGAATTCGATGTTTTCATTAAAA-CCCGAGTGCATCGATGCAT-AAAC
1 TGCATCGATGCATCAAATGAATTCGATGTTTTCA--AAAAGCCCGAGTGCATCGATGCATGAAAC
330964 TGCATTCGATG
1 TGCA-TCGATG
330975 TTCAATTTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
63 5 0.08
64 38 0.59
65 17 0.27
66 4 0.06
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (63 bp):
TGCATCGATGCATCAAATGAATTCGATGTTTTCAAAAAGCCCGAGTGCATCGATGCATGAAAC
Found at i:340394 original size:64 final size:62
Alignment explanation
Indices: 340324--340503 Score: 175
Period size: 64 Copynumber: 2.8 Consensus size: 62
340314 TGAGACACTT
* * *
340324 AGTGCATCGGTGCACTAAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGA-AAAAGCCTG
1 AGTGCATCGATGCA-T-AGTGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAA-CCCG
* * * *
340388 AGTGCATCGATACATGGTATGTGCATCGATGCATCAAGTGTATTCGATGTTTTCATTAAAACCCG
1 AGTGCATCGATGCATAG--TGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-TAAAACCCG
* * *
340453 AGTGCATCGATGCATGGAGAGTGCATCGATGCAT-AAACTACATTCAATGTT
1 AGTGCATCGATGCAT--AGTGTGCATCGATGCATCAAA-TGCATTCGATGTT
340504 CAATTTATTT
Statistics
Matches: 95, Mismatches: 14, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 47 0.49
65 41 0.43
66 4 0.04
67 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.29
Consensus pattern (62 bp):
AGTGCATCGATGCATAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACCCG
Found at i:340485 original size:65 final size:64
Alignment explanation
Indices: 340344--340503 Score: 191
Period size: 65 Copynumber: 2.5 Consensus size: 64
340334 TGCACTAAGT
* * *
340344 GTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAAGCCTGAGTGCATCGATACATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAAGCCCGAGTGCATCGATACATGGTAA
* * *
340408 GTGCATCGATGCATCAAGTGTATTCGATGTTTTCATTAAAA-CCCGAGTGCATCGATGCATGG-A
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA--AAAAGCCCGAGTGCATCGATACATGGTA
340471 GA
64 -A
* *
340473 GTGCATCGATGCAT-AAACTACATTCAATGTT
1 GTGCATCGATGCATCAAA-TGCATTCGATGTT
340504 CAATTTATTT
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
64 35 0.43
65 43 0.52
66 4 0.05
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAAGCCCGAGTGCATCGATACATGGTAA
Found at i:345947 original size:27 final size:27
Alignment explanation
Indices: 345916--345967 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
345906 ATCCAGGCGG
345916 ATTTCTCGGTCATGATCAGAGATCCGA
1 ATTTCTCGGTCATGATCAGAGATCCGA
*
345943 ATTTCTCGGTCATGGTCAGAGATCC
1 ATTTCTCGGTCATGATCAGAGATCC
345968 CATGAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (27 bp):
ATTTCTCGGTCATGATCAGAGATCCGA
Found at i:346234 original size:20 final size:20
Alignment explanation
Indices: 346197--346239 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
346187 ATTCCACCAC
*
346197 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
346217 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
346237 ATG
1 ATG
346240 TGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:348844 original size:13 final size:13
Alignment explanation
Indices: 348828--348862 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
348818 AGGAAACTAG
348828 AAAGTGAAAGTAA
1 AAAGTGAAAGTAA
* *
348841 AAAGAGAAAGTGA
1 AAAGTGAAAGTAA
348854 AAAGTGAAA
1 AAAGTGAAA
348863 AATAAGTGGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.11
Consensus pattern (13 bp):
AAAGTGAAAGTAA
Found at i:356206 original size:27 final size:27
Alignment explanation
Indices: 356175--356229 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
356165 CTGATCCAGG
356175 CGGATTTCTCGGTCATGATCAGAGATC
1 CGGATTTCTCGGTCATGATCAGAGATC
*
356202 CGGATTTCTCGGTCATGGTCAGAGATC
1 CGGATTTCTCGGTCATGATCAGAGATC
356229 C
1 C
356230 CGTGAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (27 bp):
CGGATTTCTCGGTCATGATCAGAGATC
Found at i:356496 original size:20 final size:20
Alignment explanation
Indices: 356459--356501 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
356449 ATTCCACCAC
*
356459 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
356479 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
356499 ATG
1 ATG
356502 TGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:356611 original size:19 final size:20
Alignment explanation
Indices: 356568--356619 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
356558 GGAGTTATCA
**
356568 GGTATCGATACCATGGTTGG
1 GGTATCGATACCATGGTAAG
356588 GGTATC-ATACCATGGTAAG
1 GGTATCGATACCATGGTAAG
*
356607 TGTATCGATACCA
1 GGTATCGATACCA
356620 GTAAACATCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (20 bp):
GGTATCGATACCATGGTAAG
Found at i:356758 original size:95 final size:94
Alignment explanation
Indices: 356586--356761 Score: 237
Period size: 95 Copynumber: 1.9 Consensus size: 94
356576 TACCATGGTT
* * *
356586 GGGGTATCATACCATGGTAAGTGTATCGATACCAGTAAACATCGAATCTAATTTGGGTATCGATA
1 GGGGTATCATACCATGGTAAGGGTATCGATACCAGGAAACATCGAAGCTAATTTGGGTATCGATA
* *
356651 CCTAGAGGGGGTATCGGTATCATAGCATA
66 CATAGAGAGGGTATCGGTATCATAGCATA
* ** * *
356680 GGGGTATCGATACCATGGTGAGGGTATCGATACCAGGCTACATCGAAGCTAATTTTGGTATTGAT
1 GGGGTATC-ATACCATGGTAAGGGTATCGATACCAGGAAACATCGAAGCTAATTTGGGTATCGAT
356745 ACAT-GAAGAGGGTATCG
65 ACATAG-AGAGGGTATCG
356762 ATACCCTAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
94 9 0.13
95 61 0.87
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (94 bp):
GGGGTATCATACCATGGTAAGGGTATCGATACCAGGAAACATCGAAGCTAATTTGGGTATCGATA
CATAGAGAGGGTATCGGTATCATAGCATA
Found at i:356782 original size:95 final size:94
Alignment explanation
Indices: 356589--356809 Score: 214
Period size: 95 Copynumber: 2.3 Consensus size: 94
356579 CATGGTTGGG
* * * *
356589 GTATC-ATACCATGGTAAGTGTATCGATACCAGTAAACATCGAATCTAATTTGGGTATCGATACC
1 GTATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCGAAGCTAATTTGGGTATCGATACA
* * * *
356653 TAGAGGGGGTATCGGTATCATAGCATAGGG
66 TAGAGAGGGTATCGATACCATA-CATAGGA
* ** * *
356683 GTATCGATACCATGGTGAGGGTATCGATACCAGGCTACATCGAAGCTAATTTTGGTATTGATACA
1 GTATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCGAAGCTAATTTGGGTATCGATACA
*
356748 T-GAAGAGGGTATCGATACCCTA-ATAGAGTA
66 TAG-AGAGGGTATCGATACCATACATAG-G-A
* * * *
356778 GTATCGATATCATAAGCAGGGGTATCGATACC
1 GTATCGATACCAT-GGTAAGGGTATCGATACC
356810 TAAGGGCCAG
Statistics
Matches: 103, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
93 4 0.04
94 7 0.07
95 78 0.76
96 14 0.14
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.27
Consensus pattern (94 bp):
GTATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCGAAGCTAATTTGGGTATCGATACA
TAGAGAGGGTATCGATACCATACATAGGA
Found at i:357214 original size:57 final size:57
Alignment explanation
Indices: 357153--357285 Score: 248
Period size: 57 Copynumber: 2.3 Consensus size: 57
357143 AAAATATAAC
* *
357153 AAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTATGCTAAAATGTTAAG
1 AAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCCTACGCTAAAATGTTAAG
357210 AAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCCTACGCTAAAATGTTAAG
1 AAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCCTACGCTAAAATGTTAAG
357267 AAATCATACTAAGTGTATG
1 AAATCATACTAAGTGTATG
357286 TGTTGTAACC
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 74 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (57 bp):
AAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCCTACGCTAAAATGTTAAG
Found at i:357837 original size:10 final size:10
Alignment explanation
Indices: 357824--357849 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
357814 CTCTAAAAAT
357824 AATTAAATAA
1 AATTAAATAA
357834 AATTAAATAA
1 AATTAAATAA
357844 AATTAA
1 AATTAA
357850 TTAATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AATTAAATAA
Found at i:359352 original size:3 final size:3
Alignment explanation
Indices: 359344--359385 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
359334 TTTGGGCATG
*
359344 TAA TAA TAA TAA TAT TAA TAA TAA TAA TAA -ATA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
359386 AAACAAATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 1 0.03
3 33 0.94
4 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:359385 original size:15 final size:18
Alignment explanation
Indices: 359344--359385 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
359334 TTTGGGCATG
359344 TAATAATAATAATATTAA
1 TAATAATAATAATATTAA
359362 TAATAATAATAA-ATATAA
1 TAATAATAATAATAT-TAA
359380 TAATAA
1 TAATAA
359386 AAACAAATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TAATAATAATAATATTAA
Found at i:359900 original size:139 final size:138
Alignment explanation
Indices: 359598--359910 Score: 364
Period size: 139 Copynumber: 2.3 Consensus size: 138
359588 GTTGAACAAG
*
359598 TTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAAC-TCCTTCTGGAAATACTGATCCTCAAAAG
1 TTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTTCTGAAAATACTGATCCTCAAAAG
* * * * * * *
359662 AGGTGTCATTGATTCAATTTCATATGTGATGAATTAAGGCAAGACTGAACATGTTCTTCTCATTA
66 AGGTGTCATTCATTCAACTCCATAGGTGATGAATCAAGGCAAGACTAAACAAGTTCTTCTCATTA
359727 TGAACTTC
131 TGAACTTC
* * * ** **
359735 TTCATCCTCTTCAGATGAGTTATTCTCATTATGAACTTTC-TCTGAAAATGTTGATCCTCAAGTG
1 TTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTTCTGAAAATACTGATCCTCAAAAG
* * * *
359799 AGGTTCTTCTTTCATTCAACTCCATAGGTGATGAATCAA-GCTAAG-GTCAAACAAGTTCTTCTT
66 AGG-T-GTCATTCATTCAACTCCATAGGTGATGAATCAAGGC-AAGACT-AAACAAGTTCTTCTC
*
359862 ATTATGAACTTT
127 ATTATGAACTTC
* *
359874 TTCTTCCCCTTCAGATGAATTCTTCTCATTATGAACT
1 TTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACT
359911 CTATTTAGAA
Statistics
Matches: 147, Mismatches: 24, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
137 56 0.38
138 6 0.04
139 85 0.58
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (138 bp):
TTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTTCTGAAAATACTGATCCTCAAAAG
AGGTGTCATTCATTCAACTCCATAGGTGATGAATCAAGGCAAGACTAAACAAGTTCTTCTCATTA
TGAACTTC
Found at i:360009 original size:123 final size:122
Alignment explanation
Indices: 359848--360513 Score: 648
Period size: 123 Copynumber: 5.6 Consensus size: 122
359838 GCTAAGGTCA
* * * *
359848 AACAAGTTCTTCTTATTATGAACTTTTTCTTCCCCTTCAGATGAATTCTTCTCATTATGAACTCT
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCT
* * * *
359913 ATTTAGAAACATTAATGCTGATTTATCTCCTTTTGTGATAGAGTCGAGAAAAAGGTTG
66 ATTTGGAAATATTAATGCTGATCTATCTCCTTCTGTGATAGAGTC-AGAAAAAGGTTG
* * *
359971 AACAAGTTCTTCTCATTATGAACTTCTTATTCCTCTTCAGATGATTTCTTCTTATTATGAACTC-
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCT
* * *
360035 ATTCTGGAAATGTTAATGCTGATCTATCTCATTCTGTGATAGAGTCATGCAAAAGGTTG
66 ATT-TGGAAATATTAATGCTGATCTATCTCCTTCTGTGATAGAGTCA-GAAAAAGGTTG
* *
360094 AACAAGTTCTTCTCATTATAAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATAAACTCC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACT-C
* * * *
360159 T-TCTGGAAATATTGATGATGATCTATCTCCTTCTGTGATAGAGTCACACAAAAGGTTG
65 TATTTGGAAATATTAATGCTGATCTATCTCCTTCTGTGATAGAGTCAGA-AAAAGGTTG
360217 AACAAGTTCTTCTCATTATGAAC-TCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCT
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCT
** * * * *** * * *
360281 ACCTGG------CAATGTTGATCCA--T-C--GAATGAT-GAATTCGAGCAAAATGTTG
66 ATTTGGAAATATTAATGCTGATCTATCTCCTTCTGTGATAG-AGTC-AGAAAAAGGTTG
* * *
360328 AAAAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCATATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTATGAACTC
** * * * ** * * * *
360393 TACCTGG------CAATGTTGATCCA--T-C--GGGTGATGGATTTGAGCAAAAGGTTG
65 TATTTGGAAATATTAATGCTGATCTATCTCCTTCTGTGATAGA-GTCAGAAAAAGGTTG
360441 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCT
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCT
*
360506 -TCTGGAAA
66 ATTTGGAAA
360514 AGTTTTAAGA
Statistics
Matches: 478, Mismatches: 50, Indels: 39
0.84 0.09 0.07
Matches are distributed among these distances:
110 1 0.00
111 41 0.09
112 40 0.08
113 101 0.21
114 4 0.01
116 9 0.02
121 2 0.00
122 46 0.10
123 232 0.49
124 2 0.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (122 bp):
AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCT
ATTTGGAAATATTAATGCTGATCTATCTCCTTCTGTGATAGAGTCAGAAAAAGGTTG
Found at i:360403 original size:113 final size:112
Alignment explanation
Indices: 360207--360505 Score: 510
Period size: 113 Copynumber: 2.7 Consensus size: 112
360197 TAGAGTCACA
360207 CAAAAGGTTGAACAAGTTCTTCTCATTATGAAC-TCTTCTTCCTCTTCAGATGAGTTCTTCTCAT
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCAT
360271 TATGAACTCTACCTGGCAATGTTGATCCATCGAATGATGAATTCGAG
66 TATGAACTCTACCTGGCAATGTTGATCCATCGAATGATGAATTCGAG
* * * *
360318 CAAAATGTTGAAAAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCATATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCA
** * *
360383 TTATGAACTCTACCTGGCAATGTTGATCCATCGGGTGATGGATTTGAG
65 TTATGAACTCTACCTGGCAATGTTGATCCATCGAATGATGAATTCGAG
360431 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCAT
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCAT
360496 TATGAACTCT
66 TATGAACTCT
360506 TCTGGAAAAG
Statistics
Matches: 174, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
111 31 0.18
112 39 0.22
113 104 0.60
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (112 bp):
CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCAT
TATGAACTCTACCTGGCAATGTTGATCCATCGAATGATGAATTCGAG
Found at i:360602 original size:73 final size:73
Alignment explanation
Indices: 360515--360774 Score: 358
Period size: 73 Copynumber: 3.6 Consensus size: 73
360505 TTCTGGAAAA
* ** * *
360515 GTTTTAAGAAAAACAATCTCAAGTGAGATAAATGGATATTTTGAGTGAAACTTTCTCAAGAAAGA
1 GTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGATATTTCAAGTGAAACTTTCTCTAGCAAGA
* ***
360580 CACGGTTT
66 AATAATTT
* * * *
360588 GTTTTAAGAGAAACAAACTCAAGTGAGAGAAATTGTTATTTCAAGTGAAACTTTCTCTAGCAAGA
1 GTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGATATTTCAAGTGAAACTTTCTCTAGCAAGA
360653 AATAATTT
66 AATAATTT
* * * *
360661 GTTTTAAGAAAAATAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTATCTAGCGAGA
1 GTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGATATTTCAAGTGAAACTTTCTCTAGCAAGA
360726 AATAATTT
66 AATAATTT
*
360734 GTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTT
1 GTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGATATTT
360775 GAAAACATCA
Statistics
Matches: 166, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 166 1.00
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.32
Consensus pattern (73 bp):
GTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGATATTTCAAGTGAAACTTTCTCTAGCAAGA
AATAATTT
Found at i:361516 original size:22 final size:22
Alignment explanation
Indices: 361491--361545 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
361481 AATAAAGCTT
*
361491 TCATCTTTGAAAAGAGAATATA
1 TCATCTTTGAAAAGAAAATATA
* *
361513 TCATCTTTGTAAAGAAAATCTA
1 TCATCTTTGAAAAGAAAATATA
361535 TCATCTTTGAA
1 TCATCTTTGAA
361546 GAATGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAAAATATA
Found at i:362040 original size:54 final size:55
Alignment explanation
Indices: 361912--362065 Score: 206
Period size: 54 Copynumber: 2.9 Consensus size: 55
361902 TAATCACTGG
* * ** *
361912 TTCATAAAACTTTTAACAACACATTCATCC--AGTTGTGGCTTCTGCACAGATGT
1 TTCATAAAACATTTGACAACACATTCATCCTTTCTTGTGGCTTCTGCACAAATGT
* *
361965 TTCATAAAACATTTGACAACACATTCATTCTTTCTTGTGGCTTCTGCTCAAATG-
1 TTCATAAAACATTTGACAACACATTCATCCTTTCTTGTGGCTTCTGCACAAATGT
* *
362019 TTCGTAAAACATTTGACAACACATTCATCCTTTCATGTGGCTTCTGC
1 TTCATAAAACATTTGACAACACATTCATCCTTTCTTGTGGCTTCTGC
362066 CCAGATTTCT
Statistics
Matches: 89, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
53 27 0.30
54 44 0.49
55 18 0.20
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.36
Consensus pattern (55 bp):
TTCATAAAACATTTGACAACACATTCATCCTTTCTTGTGGCTTCTGCACAAATGT
Found at i:363084 original size:75 final size:75
Alignment explanation
Indices: 362958--363126 Score: 266
Period size: 75 Copynumber: 2.3 Consensus size: 75
362948 GCCTTCAGTG
* * * * * * *
362958 TGCCCTAACATTTGCTGATACGAACGTTCAAAATATATCAACATTCTTGATTCTGATTGAAATGG
1 TGCCCCAACATTTGTTGATACAAACATTCAAAACACATCAACATTCCTGATTCTGATTGAAATGG
*
363023 GCTTTTAGCA
66 GCTTTCAGCA
363033 TGCCCCAACATTTGTTGATACAAACATTCAAAACACATCAACATTCCTGATTCTGATTGAAATGG
1 TGCCCCAACATTTGTTGATACAAACATTCAAAACACATCAACATTCCTGATTCTGATTGAAATGG
363098 GCTTTCAGCA
66 GCTTTCAGCA
363108 TGCCCCAACATTTGTTGAT
1 TGCCCCAACATTTGTTGAT
363127 TGCTAATATG
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 86 1.00
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.33
Consensus pattern (75 bp):
TGCCCCAACATTTGTTGATACAAACATTCAAAACACATCAACATTCCTGATTCTGATTGAAATGG
GCTTTCAGCA
Found at i:365233 original size:17 final size:17
Alignment explanation
Indices: 365190--365241 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
365180 TTTACAGTAG
*
365190 AAACTCTTTAAATTAAT
1 AAACTCTATAAATTAAT
*
365207 --ACTCGATAAATTAAT
1 AAACTCTATAAATTAAT
* *
365222 AAACTCTCTAAAATAAT
1 AAACTCTATAAATTAAT
365239 AAA
1 AAA
365242 TTTTTCCGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (17 bp):
AAACTCTATAAATTAAT
Found at i:368851 original size:43 final size:42
Alignment explanation
Indices: 368778--368859 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 42
368768 TACATCAAAT
* *
368778 AAAACTTTACATATAGGGATAGCTTTCACTCCTAACTTCAAC
1 AAAACTTTACATATAGGGATAACCTTCACTCCTAACTTCAAC
*
368820 AAAACTTTACATGTAGAGGATAACCTTCACTCCTAACTTC
1 AAAACTTTACATATAG-GGATAACCTTCACTCCTAACTTC
368860 TCTAAAGCCA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 15 0.42
43 21 0.58
ACGTcount: A:0.35, C:0.24, G:0.10, T:0.30
Consensus pattern (42 bp):
AAAACTTTACATATAGGGATAACCTTCACTCCTAACTTCAAC
Found at i:369375 original size:36 final size:36
Alignment explanation
Indices: 369324--369426 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 36
369314 CCATAAACTG
*
369324 CTTTTGGTACCAATCTAACAGGATCTTTGTGGAATA
1 CTTTTGGTATCAATCTAACAGGATCTTTGTGGAATA
* *
369360 CTTTTGGTATTAATCTAACGGGATCTTTGTGGAATA
1 CTTTTGGTATCAATCTAACAGGATCTTTGTGGAATA
* *
369396 CTTTTGGTATCAATATAATAGGATCTTTGTG
1 CTTTTGGTATCAATCTAACAGGATCTTTGTG
369427 TGCATATCTC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (36 bp):
CTTTTGGTATCAATCTAACAGGATCTTTGTGGAATA
Found at i:370854 original size:2 final size:2
Alignment explanation
Indices: 370841--370881 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
370831 TTTTAAGAAA
*
370841 AT AT AT -T A- AT AT AT AT AT AT TT A- 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
370880 AT
1 AT
370882 TAAGTTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 3 0.09
2 31 0.91
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:370866 original size:15 final size:15
Alignment explanation
Indices: 370841--370875 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
370831 TTTTAAGAAA
370841 ATATA-TTAATATAT
1 ATATATTTAATATAT
370855 ATATATTTAATATAT
1 ATATATTTAATATAT
370870 ATATAT
1 ATATAT
370876 ATATATTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATATTTAATATAT
Found at i:370893 original size:21 final size:21
Alignment explanation
Indices: 370840--370882 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
370830 ATTTTAAGAA
370840 AATATATTAATATATATATATTT
1 AATATA-T-ATATATATATATTT
370863 AATATATATATATATATATT
1 AATATATATATATATATATT
370883 AAGTTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 13 0.65
22 1 0.05
23 6 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATATATATATATATATTT
Found at i:371115 original size:20 final size:20
Alignment explanation
Indices: 371090--371185 Score: 124
Period size: 20 Copynumber: 4.8 Consensus size: 20
371080 TGCGATTTTC
* *
371090 CAAATTCGCAACGTGATAGT
1 CAAATTCGCAACGCGAAAGT
*
371110 CAAATTCTCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
371130 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* *
371150 CAAATTCGCAA--CTAAATTT
1 CAAATTCGCAACGCGAAA-GT
371169 CAAATTCGCAACGCGAA
1 CAAATTCGCAACGCGAA
371186 TTTAATTTCG
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
18 4 0.06
19 12 0.18
20 47 0.71
21 3 0.05
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.21
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:372129 original size:24 final size:24
Alignment explanation
Indices: 372102--372155 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
372092 GTATTCAAAA
*
372102 TTTGATATTGGTCAATACTCGGAC
1 TTTGATATTGGTCAATACTCAGAC
* *
372126 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATATTGGTCAATACTCAGAC
372150 TTTGAT
1 TTTGAT
372156 GATGTGATGG
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:0.24, C:0.15, G:0.19, T:0.43
Consensus pattern (24 bp):
TTTGATATTGGTCAATACTCAGAC
Found at i:373488 original size:20 final size:20
Alignment explanation
Indices: 373472--373526 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
373462 TATGAAACTT
373472 AAATTCGCAACGCGAAAATG
1 AAATTCGCAACGCGAAAATG
373492 AAATTCGCAACGCGAAAATG
1 AAATTCGCAACGCGAAAATG
*
373512 AAAATCGCAACGCGA
1 AAATTCGCAACGCGA
373527 TTTTAGTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.45, C:0.22, G:0.20, T:0.13
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAATG
Found at i:373558 original size:20 final size:19
Alignment explanation
Indices: 373523--373585 Score: 81
Period size: 20 Copynumber: 3.2 Consensus size: 19
373513 AAATCGCAAC
*
373523 GCGATTTTAGTTTCGCGTT
1 GCGATTTTATTTTCGCGTT
373542 GCGATTTTAATTTTCGCGTT
1 GCGATTTT-ATTTTCGCGTT
* *
373562 GCGATTTTCATTTTTGTGTT
1 GCGATTTT-ATTTTCGCGTT
373582 GCGA
1 GCGA
373586 ATTTGGTGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 8 0.21
20 31 0.79
ACGTcount: A:0.13, C:0.14, G:0.24, T:0.49
Consensus pattern (19 bp):
GCGATTTTATTTTCGCGTT
Found at i:375404 original size:29 final size:29
Alignment explanation
Indices: 375358--375433 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 29
375348 GTTTTTATTA
*
375358 GGCTGGTCTAGGTTGGGCTCTTGTAACTG
1 GGCTGGTCTGGGTTGGGCTCTTGTAACTG
*
375387 GG-TCGGTCTGGGTTGGGCTCTTTTAACTG
1 GGCT-GGTCTGGGTTGGGCTCTTGTAACTG
*
375416 GGCTGGTCTGGTTTGGGC
1 GGCTGGTCTGGGTTGGGC
375434 CTGTAATAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 1 0.02
29 40 0.95
30 1 0.02
ACGTcount: A:0.07, C:0.17, G:0.41, T:0.36
Consensus pattern (29 bp):
GGCTGGTCTGGGTTGGGCTCTTGTAACTG
Found at i:375445 original size:3 final size:3
Alignment explanation
Indices: 375437--375478 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
375427 TTTGGGCCTG
*
375437 TAA TAA TAA TAA TAT TAA TAA TAA TAA -ATA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
375479 CAAATGTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 1 0.03
3 33 0.94
4 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:375457 original size:15 final size:15
Alignment explanation
Indices: 375437--375478 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
375427 TTTGGGCCTG
375437 TAATAATAAT-AATA
1 TAATAATAATAAATA
375451 TTAATAATAATAAATA
1 -TAATAATAATAAATA
375467 TAATAATAATAA
1 TAATAATAATAA
375479 CAAATGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 22 0.85
16 4 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TAATAATAATAAATA
Found at i:375586 original size:57 final size:57
Alignment explanation
Indices: 375504--376197 Score: 1093
Period size: 57 Copynumber: 12.2 Consensus size: 57
375494 AGTGTCTACA
* * * *
375504 GTATGAATTCCATATAGGGCATTTCGTTCGCTAAAATGTTAAGAAATCATACTAAGT
1 GTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACTAAGT
* *
375561 GTATGAATTTCAGATAAGGCGTTTCGTATGCTAAAATGTTAAGAAATCATACTAAGT
1 GTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACTAAGT
*
375618 GTATGAATTTCAGATAGGGCGTTTCGTGCGCTAAAATGTTAAGAAATCATACTAAGT
1 GTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACTAAGT
* * *
375675 GTATGAATTTTAGATAGGGCGTTTCATACGCTAAAATATTAAGAAATCATACTAAGT
1 GTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACTAAGT
**
375732 GTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAAAATTAAGAAATCATACTAAGT
1 GTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACTAAGT
*
375789 GTATGAATTTCAGATATGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACTAAGT
1 GTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACTAAGT
* * *
375846 GTATTAATTTCATATAAGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACTAAGT
1 GTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACTAAGT
* *
375903 GTATGAATTTCAGATAGGGCATTTCATACGCT-AAATGTTAAGAAATCATACTAAGT
1 GTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACTAAGT
* *** *
375959 GTATGAATTTCAGAGAGGGTACTTCGTGCGCTAAAATGTTAAGAAATCATACTAAGT
1 GTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACTAAGT
376016 GTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACTAAGT
1 GTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACTAAGT
* * *
376073 GTATGAATTTCAGAGAAGGTGTTTCGTACGCTAAAATGTTAAGAAATCATACTAAGT
1 GTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACTAAGT
** * * * *
376130 GTATGAATTTCAGATAGGGCACTCCGTATGCTAAAATGTTAACAAATCATACTAATT
1 GTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACTAAGT
376187 GTATGAATTTC
1 GTATGAATTTC
376198 TGTATTGGAC
Statistics
Matches: 587, Mismatches: 49, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
56 51 0.09
57 536 0.91
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.32
Consensus pattern (57 bp):
GTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGTTAAGAAATCATACTAAGT
Found at i:376834 original size:45 final size:45
Alignment explanation
Indices: 376775--376982 Score: 317
Period size: 45 Copynumber: 4.6 Consensus size: 45
376765 AATGCATAAT
*
376775 TGTATCAAAGGCATGAAAGGATGCCATAAATGAAAGGTATAATAG
1 TGTATTAAAGGCATGAAAGGATGCCATAAATGAAAGGTATAATAG
* * *
376820 TGTATTAAAAGCATGAAAGGATGTCATAAATGAAAGGTATAAAAG
1 TGTATTAAAGGCATGAAAGGATGCCATAAATGAAAGGTATAATAG
* *
376865 TGTATCAAAGGCATGAAATGATGCCATAAATGAAAGGTATAATAG
1 TGTATTAAAGGCATGAAAGGATGCCATAAATGAAAGGTATAATAG
*
376910 TGTATTAAAGGCATGAAAGAATGCCATAAATGAAAGGTATAATAG
1 TGTATTAAAGGCATGAAAGGATGCCATAAATGAAAGGTATAATAG
* * * *
376955 TGTATAAAAGACATGTAAGGATGACATA
1 TGTATTAAAGGCATGAAAGGATGCCATA
376983 GTTCAAATGC
Statistics
Matches: 146, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 146 1.00
ACGTcount: A:0.46, C:0.07, G:0.23, T:0.24
Consensus pattern (45 bp):
TGTATTAAAGGCATGAAAGGATGCCATAAATGAAAGGTATAATAG
Found at i:385707 original size:24 final size:26
Alignment explanation
Indices: 385646--385707 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 26
385636 AATGCTTTTC
*
385646 TTATTTTATTTTAAATAATAGCAATG
1 TTATGTTATTTTAAATAATAGCAATG
* *
385672 -CATGTT-TCTTTAAA-AATAG-TATG
1 TTATGTTAT-TTTAAATAATAGCAATG
385695 TTATGTTATTTTA
1 TTATGTTATTTTA
385708 TTTATTTATC
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
23 3 0.10
24 15 0.52
25 11 0.38
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.52
Consensus pattern (26 bp):
TTATGTTATTTTAAATAATAGCAATG
Found at i:388037 original size:37 final size:36
Alignment explanation
Indices: 387994--388106 Score: 163
Period size: 37 Copynumber: 3.1 Consensus size: 36
387984 TATTTAGGTC
387994 AGTTTTGGAGGGTACCGTAAATGGAACTAATTAATTG
1 AGTTTTGGAGGGTACC-TAAATGGAACTAATTAATTG
* * *
388031 AGTTTTGTAGGGTATACTAAATGTAACTAATTAATTG
1 AGTTTTGGAGGGTA-CCTAAATGGAACTAATTAATTG
*
388068 AGTTTTGGAGGGTACCCTAAATTGAACTAATTAATTG
1 AGTTTTGGAGGGTA-CCTAAATGGAACTAATTAATTG
388105 AG
1 AG
388107 GAAAAGCAAC
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
37 66 0.99
38 1 0.01
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.35
Consensus pattern (36 bp):
AGTTTTGGAGGGTACCTAAATGGAACTAATTAATTG
Found at i:395776 original size:39 final size:39
Alignment explanation
Indices: 395732--395811 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
395722 ATAAGATTAT
395732 TGTAAAACAAAACCATTAGTATTGATCAATAAATAATGA
1 TGTAAAACAAAACCATTAGTATTGATCAATAAATAATGA
395771 TGTAAAACAAAACCATTAGTATTGATCAATAAATAATGA
1 TGTAAAACAAAACCATTAGTATTGATCAATAAATAATGA
395810 TG
1 TG
395812 AAATAATATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.50, C:0.10, G:0.11, T:0.29
Consensus pattern (39 bp):
TGTAAAACAAAACCATTAGTATTGATCAATAAATAATGA
Found at i:396796 original size:22 final size:23
Alignment explanation
Indices: 396770--396812 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
396760 TTTAACCAAT
396770 AAATATTATTATTA-TTATTATA
1 AAATATTATTATTATTTATTATA
396792 AAATATTATTATTATTTATTA
1 AAATATTATTATTATTTATTA
396813 CAAACCTAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
AAATATTATTATTATTTATTATA
Found at i:398787 original size:17 final size:16
Alignment explanation
Indices: 398767--398798 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
398757 AAATGTTTAA
398767 ATTTTTCTTTAGTTTTC
1 ATTTTTCTTTA-TTTTC
398784 ATTTTTCTTTATTTT
1 ATTTTTCTTTATTTT
398799 GGTCCCTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.12, C:0.09, G:0.03, T:0.75
Consensus pattern (16 bp):
ATTTTTCTTTATTTTC
Done.