Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005466.1 Hibiscus syriacus cultivar Beakdansim tig00012523_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: 1151987
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
File 2 of 4
Found at i:191769 original size:3 final size:3
Alignment explanation
Indices: 191761--191788 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
191751 TAGTATACTA
191761 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
191789 GATGGTGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:192068 original size:15 final size:15
Alignment explanation
Indices: 192044--192083 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
192034 GGCTCTCTTT
*
192044 AAGAACAAAAAGAAA
1 AAGAAAAAAAAGAAA
* *
192059 AAGAAAAAAAATAAT
1 AAGAAAAAAAAGAAA
192074 AAGAAAAAAA
1 AAGAAAAAAA
192084 GCAACCAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.82, C:0.03, G:0.10, T:0.05
Consensus pattern (15 bp):
AAGAAAAAAAAGAAA
Found at i:192515 original size:2 final size:2
Alignment explanation
Indices: 192470--192499 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
192460 ATAATTACAT
*
192470 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
192500 ACTAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:193259 original size:15 final size:15
Alignment explanation
Indices: 193231--193273 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
193221 TATTTTCAAT
193231 TATATTGAATTTTATAA
1 TATA-TGAA-TTTATAA
*
193248 TATATGAATTTATAT
1 TATATGAATTTATAA
*
193263 TATATAAATTT
1 TATATGAATTT
193274 GTGTTTTGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 16 0.67
16 4 0.17
17 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (15 bp):
TATATGAATTTATAA
Found at i:193268 original size:17 final size:16
Alignment explanation
Indices: 193229--193268 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
193219 AATATTTTCA
193229 ATTATAT-TGAATTTT
1 ATTATATATGAATTTT
*
193244 ATAATATATGAATTTAT
1 ATTATATATGAATTT-T
193261 ATTATATA
1 ATTATATA
193269 AATTTGTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 6 0.29
16 7 0.33
17 8 0.38
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (16 bp):
ATTATATATGAATTTT
Found at i:196711 original size:19 final size:21
Alignment explanation
Indices: 196682--196721 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
196672 CAAATTTCGG
*
196682 TTTTTGTTTAC-TTTTAATTT
1 TTTTTGTTTACAATTTAATTT
196702 TTTTTG-TTACAATTTAATTT
1 TTTTTGTTTACAATTTAATTT
196722 AATATTACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (21 bp):
TTTTTGTTTACAATTTAATTT
Found at i:197203 original size:30 final size:30
Alignment explanation
Indices: 197146--197208 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
197136 AATATTGAGG
* * * *
197146 ATTAAAATTAAAATTATATTAATTTAATTA
1 ATTAAAATTAAAATAATAGTAAATTAATAA
197176 ATTAAAA-TAATAATAATAGTAAATTAATAA
1 ATTAAAATTAA-AATAATAGTAAATTAATAA
197206 ATT
1 ATT
197209 TATATACATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 3 0.11
30 25 0.89
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (30 bp):
ATTAAAATTAAAATAATAGTAAATTAATAA
Found at i:197383 original size:28 final size:29
Alignment explanation
Indices: 197336--197391 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
197326 AAATTTTATA
197336 TTAGGGGATGAACTTTAATTTATAAAATG
1 TTAGGGGATGAACTTTAATTTATAAAATG
197365 TTAGGGG-TGAA-TTTAAATTTATAAAAT
1 TTAGGGGATGAACTTT-AATTTATAAAAT
197392 TTCATAGGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 3 0.12
28 16 0.62
29 7 0.27
ACGTcount: A:0.39, C:0.02, G:0.20, T:0.39
Consensus pattern (29 bp):
TTAGGGGATGAACTTTAATTTATAAAATG
Found at i:198541 original size:13 final size:13
Alignment explanation
Indices: 198505--198543 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
198495 ACCGGCCCGT
*
198505 TGAGTCAACTTGT
1 TGAGTCAACTTGC
* *
198518 TGAATCTACTTGC
1 TGAGTCAACTTGC
198531 TGAGTCAACTTGC
1 TGAGTCAACTTGC
198544 ATTGGTTTGA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (13 bp):
TGAGTCAACTTGC
Found at i:199477 original size:16 final size:17
Alignment explanation
Indices: 199444--199483 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
199434 AGGATTATGG
*
199444 ATATTATTTTATTATTT
1 ATATTAATTTATTATTT
*
199461 ATTTTAATTTA-TATTT
1 ATATTAATTTATTATTT
199477 ATATTAA
1 ATATTAA
199484 ATAATAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATATTAATTTATTATTT
Found at i:201142 original size:60 final size:59
Alignment explanation
Indices: 200962--201145 Score: 201
Period size: 60 Copynumber: 3.1 Consensus size: 59
200952 CCTATGTCCT
** * * *
200962 CAAACTATGAACCTCATTTTAAATTAGTCCTTAAACTTTTAAATATTTCAGTTTCATCCC
1 CAAACTATGAATTTCATTTTAAATTAGTCCTTAAACTTTT-AATCTTCCAATTTCATCCC
* *
201022 AAAACTATGACTCTT-ATTTTAAATTAGTCCTTAAACTTTTGAA-CATTCCAATTTCATCCC
1 CAAACTATGAAT-TTCATTTTAAATTAGTCCTTAAACTTTT-AATC-TTCCAATTTCATCCC
* * * * *
201082 CAAACTATGAATTTCATTCTAAATTGGTCCCTAAACTTCTACATCTTCCAATTTTATCCC
1 CAAACTATGAATTTCATTTTAAATTAGTCCTTAAACTTTTA-ATCTTCCAATTTCATCCC
201142 CAAA
1 CAAA
201146 TTCATCCAAA
Statistics
Matches: 104, Mismatches: 15, Indels: 10
0.81 0.12 0.08
Matches are distributed among these distances:
59 3 0.03
60 99 0.95
61 2 0.02
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.39
Consensus pattern (59 bp):
CAAACTATGAATTTCATTTTAAATTAGTCCTTAAACTTTTAATCTTCCAATTTCATCCC
Found at i:201371 original size:58 final size:59
Alignment explanation
Indices: 201306--201417 Score: 156
Period size: 58 Copynumber: 1.9 Consensus size: 59
201296 TTTGGGGACC
* *
201306 AATTTAGAATGA-AGATCATAGTTTGGGGATGAAAATGAAATG-TTAAAAGTTTAAGACT
1 AATTTAGAATGATAG-TCATAGTTTAGGGATGAAAATGAAATGTTTAAAAATTTAAGACT
* * *
201364 AATTTAGAATGATAGTTATAGTTTAGGGATGAAATTTAAATGTTTAAAAATTTA
1 AATTTAGAATGATAGTCATAGTTTAGGGATGAAAATGAAATGTTTAAAAATTTA
201418 GGTATTGATT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
58 35 0.74
59 12 0.26
ACGTcount: A:0.43, C:0.02, G:0.20, T:0.36
Consensus pattern (59 bp):
AATTTAGAATGATAGTCATAGTTTAGGGATGAAAATGAAATGTTTAAAAATTTAAGACT
Found at i:203843 original size:24 final size:24
Alignment explanation
Indices: 203775--203849 Score: 82
Period size: 23 Copynumber: 3.2 Consensus size: 24
203765 GTGTTCGTTT
* *
203775 ATTTAT-TGCTCACGAACACGTTC
1 ATTTATATGTTCACGAACATGTTC
* *
203798 ATTTA-ATGTTCGCGACCATGTTC
1 ATTTATATGTTCACGAACATGTTC
*
203821 ATTTATATGTTCACGAACGTGTTC
1 ATTTATATGTTCACGAACATGTTC
*
203845 GTTTA
1 ATTTA
203850 GCTTTCGTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
23 23 0.55
24 19 0.45
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (24 bp):
ATTTATATGTTCACGAACATGTTC
Found at i:206171 original size:31 final size:32
Alignment explanation
Indices: 206121--206194 Score: 98
Period size: 31 Copynumber: 2.3 Consensus size: 32
206111 TCAACCAGAA
206121 CCGAAAGCAAACCGAACCAAA-ATAACCCGAT
1 CCGAAAGCAAACCGAACCAAATATAACCCGAT
* *
206152 CCGAAAG-AAACCCGGACCAAATTTTAACCCGAT
1 CCGAAAGCAAA-CCGAACCAAA-TATAACCCGAT
206185 CCGAAAGCAA
1 CCGAAAGCAA
206195 CTCAAATAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
30 3 0.08
31 16 0.43
33 16 0.43
34 2 0.05
ACGTcount: A:0.45, C:0.31, G:0.15, T:0.09
Consensus pattern (32 bp):
CCGAAAGCAAACCGAACCAAATATAACCCGAT
Found at i:211515 original size:38 final size:37
Alignment explanation
Indices: 211465--211538 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
211455 ATTTTTTATC
*
211465 GACCCGACTCGA-CTCGAAAATTATACATAC-TCCACCT
1 GACCCGACTCGACCT-GAAAAATATACAT-CTTCCACCT
211502 GACCCGAACTCGACCTGAAAAATATACATCTTCCACC
1 GACCCG-ACTCGACCTGAAAAATATACATCTTCCACC
211539 CGATCCGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
37 7 0.21
38 24 0.73
39 2 0.06
ACGTcount: A:0.34, C:0.35, G:0.11, T:0.20
Consensus pattern (37 bp):
GACCCGACTCGACCTGAAAAATATACATCTTCCACCT
Found at i:213661 original size:24 final size:26
Alignment explanation
Indices: 213597--213658 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
213587 AATTTCTATT
213597 AAATAATAAAAATAACACAACATAAA
1 AAATAATAAAAATAACACAACATAAA
213623 AAATAATAAAAATAACACAACATAAA
1 AAATAATAAAAATAACACAACATAAA
*
213649 AAATATTAAA
1 AAATAATAAA
213659 TAAAATAACC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.18
Consensus pattern (26 bp):
AAATAATAAAAATAACACAACATAAA
Found at i:216930 original size:3 final size:3
Alignment explanation
Indices: 216922--216957 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
216912 AAGGGAAGGG
216922 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
216958 GGGAACAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:221774 original size:16 final size:17
Alignment explanation
Indices: 221733--221774 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
221723 AATAAAAATA
221733 TAAAATTTA-ATACTTT
1 TAAAATTTATATACTTT
221749 T-AAATATTATATA-TTT
1 TAAAAT-TTATATACTTT
221765 TAAAATTTAT
1 TAAAATTTAT
221775 GAGTAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 4 0.17
16 12 0.52
17 7 0.30
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
TAAAATTTATATACTTT
Found at i:226157 original size:2 final size:2
Alignment explanation
Indices: 226150--226178 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
226140 ACAAATGCAC
226150 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
226179 AATAAATAAA
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:237150 original size:18 final size:15
Alignment explanation
Indices: 237106--237152 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 15
237096 TAGAGATTTG
237106 ACTGAATATAAACAA
1 ACTGAATATAAACAA
*
237121 AC-GAACATAAACATTGA
1 ACTGAATATAAACA---A
237138 ACTGAATATAAACAA
1 ACTGAATATAAACAA
237153 GTGAATTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
14 10 0.38
15 3 0.12
17 3 0.12
18 10 0.38
ACGTcount: A:0.57, C:0.15, G:0.09, T:0.19
Consensus pattern (15 bp):
ACTGAATATAAACAA
Found at i:246309 original size:20 final size:20
Alignment explanation
Indices: 246263--246413 Score: 158
Period size: 20 Copynumber: 7.5 Consensus size: 20
246253 CTTAGTTTCC
* * *
246263 AAAATCACAGCGTTAATAGT
1 AAAATCGCAACGTGAATAGT
246283 AAAAATCGCAACGTGAATAGT
1 -AAAATCGCAACGTGAATAGT
*
246304 AAAATCGTAACGTGAATAGT
1 AAAATCGCAACGTGAATAGT
246324 AAAATCGCAACGTGAATAGT
1 AAAATCGCAACGTGAATAGT
** * *
246344 AAAATCGCAACGCAAATTGG
1 AAAATCGCAACGTGAATAGT
* * *
246364 AAAATCGCAACGCGAATTGA
1 AAAATCGCAACGTGAATAGT
** * *
246384 AAAATCGCAACACGAATTGA
1 AAAATCGCAACGTGAATAGT
246404 AAAATCGCAA
1 AAAATCGCAA
246414 AATCGCGTTG
Statistics
Matches: 118, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
20 101 0.86
21 17 0.14
ACGTcount: A:0.47, C:0.17, G:0.18, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGTGAATAGT
Found at i:246788 original size:20 final size:21
Alignment explanation
Indices: 246763--246811 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
246753 TATATAGATT
*
246763 CGTTGCGA-TTTTATTATTCA
1 CGTTGCGATTTTTACTATTCA
*
246783 CGTTGCAATTTTTACTATTCA
1 CGTTGCGATTTTTACTATTCA
246804 CGTTGCGA
1 CGTTGCGA
246812 AATTGGAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.45
Consensus pattern (21 bp):
CGTTGCGATTTTTACTATTCA
Found at i:246871 original size:20 final size:20
Alignment explanation
Indices: 246846--246909 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
246836 GAAATTTCGC
246846 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
*
246866 GTTGCGAATTTGA-TTATTGC
1 GTTGCGAATTTGACTT-TTGT
*
246886 GTTGCGAATTTGACTTATGT
1 GTTGCGAATTTGACTTTTGT
246906 GTTG
1 GTTG
246910 TGATTTATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
19 2 0.05
20 35 0.90
21 2 0.05
ACGTcount: A:0.17, C:0.09, G:0.27, T:0.47
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:246928 original size:40 final size:41
Alignment explanation
Indices: 246830--246929 Score: 127
Period size: 40 Copynumber: 2.5 Consensus size: 41
246820 TTCGCATTGT
*
246830 GAATTTGA-AATTTCGCGTTGCGAATTTGACTTTTGTGTTGC
1 GAATTTGATAA-TTCGCGTTGCGAATTTGACTTATGTGTTGC
* *
246871 GAATTTGATTATT-GCGTTGCGAATTTGACTTATGTGTTGT
1 GAATTTGATAATTCGCGTTGCGAATTTGACTTATGTGTTGC
246911 G-ATTT-ATAAATTCGCGTTG
1 GAATTTGAT-AATTCGCGTTG
246930 TAATTTACAG
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
38 2 0.04
39 7 0.13
40 32 0.62
41 10 0.19
42 1 0.02
ACGTcount: A:0.21, C:0.10, G:0.24, T:0.45
Consensus pattern (41 bp):
GAATTTGATAATTCGCGTTGCGAATTTGACTTATGTGTTGC
Found at i:246935 original size:20 final size:20
Alignment explanation
Indices: 246906--246949 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
246896 TGACTTATGT
* *
246906 GTTGTGATTTATAAATTCGC
1 GTTGTAATTTACAAATTCGC
*
246926 GTTGTAATTTACAGATTCGC
1 GTTGTAATTTACAAATTCGC
246946 GTTG
1 GTTG
246950 CGAAATTAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.43
Consensus pattern (20 bp):
GTTGTAATTTACAAATTCGC
Found at i:247109 original size:2 final size:2
Alignment explanation
Indices: 247102--247126 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
247092 TATAAACGTG
247102 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 T
247127 GAATCTTACA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:247856 original size:385 final size:383
Alignment explanation
Indices: 247374--248150 Score: 1353
Period size: 382 Copynumber: 2.0 Consensus size: 383
247364 ATCGCATTGC
* *
247374 ATATACTATAAATTAATTAAATCCAAATATAATTAGGGATGATAATATGTCCGGTTTTTTTTTTA
1 ATATAATATAAATTAATTAAATCCAAATATAATTAGGGATGATAATATGTCCAG--TTTTTTTTA
* *
247439 AACCAATTAGACATGAAAATATGCATCATTCACTCGAGCCCGACC-CAAA-ATATATATATATAT
64 AACCAATCAGACATGAAAATATGCATCATTCACTCGAGCCCGACCTAAAATATATATATATATAT
*
247502 CCTTCACTCAATTTCAATCCAATTTTTTAGAGTATAAATTCGACTAAACCTAACTCGATATAAAT
129 CCTTCACTCAATTTCAACCCAATTTTTTAGAGTATAAATTCGACTAAACCTAACTCGATATAAAT
*
247567 TAAAGGATTTAGTTAAAAAAATAACATTTTTTTAAAAAAAATTACATTATTATTCTCAAATCGGA
194 TAAAGGATTTAGTTAAAAAAATAACATTTTTTT-----AAACTACATTATTATTCTCAAATCGGA
* *
247632 TTGAAATTTTTTCCATCCTCCACCCGAACCGATCTGACCCGATTTCACCCCTTAAAATATTTAAC
254 TCGAAATTTTTTCCATCCTCCACCCGAACCGATCTGACCCGACTTCACCCCTTAAAATATTTAAC
247697 CCGACCCATACCCGAATTTTTTCTAAAATAAATCCAACCTGATCGGATGAAATTGTCGTCCCAAA
319 CCGACCCATACCCGAATTTTTTCTAAAATAAATCCAACCTGATCGGATGAAATTGTCGTCCCAAA
247762 ATATAATATAAATTAATTAAATCCAAATATAATTAGGGATGATAATATGTCCAG-TTTTTTTAAA
1 ATATAATATAAATTAATTAAATCCAAATATAATTAGGGATGATAATATGTCCAGTTTTTTTTAAA
247826 CCAATCAGACATGAAAATATGCATCATTCACTCGAGCCCGACCTAAAATATATATATATATATCC
66 CCAATCAGACATGAAAATATGCATCATTCACTCGAGCCCGACCTAAAATATATATATATATATCC
* *
247891 TTTACTCAATTTCAACCCAATTTTTTAGAGTATAAATTCGACTAAACCTGACTCGATATAAATTA
131 TTCACTCAATTTCAACCCAATTTTTTAGAGTATAAATTCGACTAAACCTAACTCGATATAAATTA
*
247956 AAGGATTTAGTTAAAAAAATAACATTTTTTTAAACTATATTATTATTCTCAAATCGGATCGAAAT
196 AAGGATTTAGTTAAAAAAATAACATTTTTTTAAACTACATTATTATTCTCAAATCGGATCGAAAT
*
248021 TTTTTCTATCCTCCACCCGAACCGATCTGACCCGACTTCACCCCTTAAAATATTTAACCCGACCC
261 TTTTTCCATCCTCCACCCGAACCGATCTGACCCGACTTCACCCCTTAAAATATTTAACCCGACCC
*
248086 ATACCTGAATTTTTTCTAAAATAAATCCAACCTGATCGGATGAAATTGTCGTCCCAAA
326 ATACCCGAATTTTTTCTAAAATAAATCCAACCTGATCGGATGAAATTGTCGTCCCAAA
248144 ATATAAT
1 ATATAAT
248151 CCTACTTGCT
Statistics
Matches: 374, Mismatches: 13, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
382 158 0.42
385 52 0.14
386 3 0.01
387 109 0.29
388 52 0.14
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (383 bp):
ATATAATATAAATTAATTAAATCCAAATATAATTAGGGATGATAATATGTCCAGTTTTTTTTAAA
CCAATCAGACATGAAAATATGCATCATTCACTCGAGCCCGACCTAAAATATATATATATATATCC
TTCACTCAATTTCAACCCAATTTTTTAGAGTATAAATTCGACTAAACCTAACTCGATATAAATTA
AAGGATTTAGTTAAAAAAATAACATTTTTTTAAACTACATTATTATTCTCAAATCGGATCGAAAT
TTTTTCCATCCTCCACCCGAACCGATCTGACCCGACTTCACCCCTTAAAATATTTAACCCGACCC
ATACCCGAATTTTTTCTAAAATAAATCCAACCTGATCGGATGAAATTGTCGTCCCAAA
Found at i:248917 original size:185 final size:184
Alignment explanation
Indices: 248585--249018 Score: 464
Period size: 185 Copynumber: 2.3 Consensus size: 184
248575 CAACTTAATT
* * * * * * *
248585 ATTTTTTATGCTTTGTTAATGTAATATTAGATTAATTATTTAAAATAATATAATTTTTTTCGTTT
1 ATTTTTTACGGTTTATTAATGTAATATTAAATT-ATTTTTTAAAATAATAGAATTTATTTCGTTT
* * * * *
248650 TATAGGGCTTATTTTTGAGTTTCTGTTCAAGATTAATAGCTAAGAGTCCCTAATTGTTTTTCAAT
65 TATAGGGCCTATTTTTGAGTTTCTGATCAAGATTAATAACTAAGAGCCCCTAACTGTTTTTCAAT
*
248715 ATTATAAAAAAGTCCATACTTTCTACTTTTATAACT-AATGGCCTACAATTTAACC
130 ATTATAAAAAAGTCCATACTTTCTACCTTTATAA-TGAATGGCCTACAATTTAACC
* *
248770 ATTTTTATACGGTTTATTAATGTAATATTAAATTATTTTTTTAAATTATAGAATATATATTT-GT
1 ATTTTT-TACGGTTTATTAATGTAATATTAAATTATTTTTTAAAATAATAGAAT-T-TATTTCGT
* * *
248834 TTTATAGGGCCTATTTTTTAGTTT-TCGATCAA-AGTTTATAACTAAGGGCCCCTAACT-TTTTT
63 TTTATAGGGCCTATTTTTGAGTTTCT-GATCAAGA-TTAATAACTAAGAGCCCCTAACTGTTTTT
* * * * * * **
248896 CAATTTTATAAAATAGTCCATATTTTCTACCTTTATAATGGATGGCTTATAATTTAATT
126 CAATATTATAAAAAAGTCCATACTTTCTACCTTTATAATGAATGGCCTACAATTTAACC
* * * * * *
248955 ATTTTTTATGGTTTATTAATATAATGTTAAATTAGTTTTTCAAAATAATATAATATAATTTCGT
1 ATTTTTTACGGTTTATTAATGTAATATTAAATTA-TTTTTTAAAATAATAGAAT-TTATTTCGT
249019 CTATGTGATA
Statistics
Matches: 207, Mismatches: 34, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
184 30 0.14
185 102 0.49
186 71 0.34
187 4 0.02
ACGTcount: A:0.32, C:0.09, G:0.10, T:0.48
Consensus pattern (184 bp):
ATTTTTTACGGTTTATTAATGTAATATTAAATTATTTTTTAAAATAATAGAATTTATTTCGTTTT
ATAGGGCCTATTTTTGAGTTTCTGATCAAGATTAATAACTAAGAGCCCCTAACTGTTTTTCAATA
TTATAAAAAAGTCCATACTTTCTACCTTTATAATGAATGGCCTACAATTTAACC
Found at i:251169 original size:30 final size:30
Alignment explanation
Indices: 251135--251201 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 30
251125 ATATATATAT
251135 ATATATAATAAATTTA-A-ATTAAATTAAAAA
1 ATATATAAT--ATTTATATATTAAATTAAAAA
* *
251165 ATATATAATATTTATATATTAAATTTAAAT
1 ATATATAATATTTATATATTAAATTAAAAA
251195 ATATATA
1 ATATATA
251202 CCCGGCTCGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 5 0.15
29 1 0.03
30 27 0.82
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
ATATATAATATTTATATATTAAATTAAAAA
Found at i:257571 original size:23 final size:23
Alignment explanation
Indices: 257540--257583 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
257530 ATCTAAATTA
*
257540 TTAATTTTTATCTATTTTAATAT
1 TTAACTTTTATCTATTTTAATAT
* *
257563 TTAACTTTTATTTTTTTTAAT
1 TTAACTTTTATCTATTTTAAT
257584 TTAATGTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (23 bp):
TTAACTTTTATCTATTTTAATAT
Found at i:266258 original size:32 final size:31
Alignment explanation
Indices: 266202--266262 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
266192 TATGATTTTT
*
266202 AAAAAAATTAAAAGTTTAGGTACTATAACAGA
1 AAAAAAATTAAAAGTTTAGATACTA-AACAGA
* * *
266234 AAAAAAATTGATAGTTTATATACTAAACA
1 AAAAAAATTAAAAGTTTAGATACTAAACA
266263 TATAATTTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 4 0.16
32 21 0.84
ACGTcount: A:0.56, C:0.07, G:0.10, T:0.28
Consensus pattern (31 bp):
AAAAAAATTAAAAGTTTAGATACTAAACAGA
Found at i:268341 original size:5 final size:5
Alignment explanation
Indices: 268331--268356 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
268321 CTCTCAACAA
268331 AAAAC AAAAC AAAAC AAAAC AAAAC A
1 AAAAC AAAAC AAAAC AAAAC AAAAC A
268357 GATACTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:268508 original size:2 final size:2
Alignment explanation
Indices: 268501--268527 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
268491 AAATAAATTA
268501 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 A
268528 AGAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:273506 original size:25 final size:25
Alignment explanation
Indices: 273458--273506 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
273448 ACGAGACCAC
* *
273458 TAGTATAATTCCTTTATTACGAGGT
1 TAGTACAATTCCTTTATCACGAGGT
* *
273483 TAGTACAATTCTTTTATCATGAGG
1 TAGTACAATTCCTTTATCACGAGG
273507 CCATAAACCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (25 bp):
TAGTACAATTCCTTTATCACGAGGT
Found at i:276826 original size:144 final size:144
Alignment explanation
Indices: 276566--276853 Score: 576
Period size: 144 Copynumber: 2.0 Consensus size: 144
276556 GGAAGCTATA
276566 ACCTTCATGGTTAGTTCTGTTTGCATTTTTTCGCAGCTGGTGGATGTGCTTCTCGTACTTGCATT
1 ACCTTCATGGTTAGTTCTGTTTGCATTTTTTCGCAGCTGGTGGATGTGCTTCTCGTACTTGCATT
276631 TTTCAGTCATATTACATGGGCTGTCAGTGGCAGCTCACCTTGCAAACAGACCGATGTCGGGGTGA
66 TTTCAGTCATATTACATGGGCTGTCAGTGGCAGCTCACCTTGCAAACAGACCGATGTCGGGGTGA
276696 TTCGGCCTCATAGT
131 TTCGGCCTCATAGT
276710 ACCTTCATGGTTAGTTCTGTTTGCATTTTTTCGCAGCTGGTGGATGTGCTTCTCGTACTTGCATT
1 ACCTTCATGGTTAGTTCTGTTTGCATTTTTTCGCAGCTGGTGGATGTGCTTCTCGTACTTGCATT
276775 TTTCAGTCATATTACATGGGCTGTCAGTGGCAGCTCACCTTGCAAACAGACCGATGTCGGGGTGA
66 TTTCAGTCATATTACATGGGCTGTCAGTGGCAGCTCACCTTGCAAACAGACCGATGTCGGGGTGA
276840 TTCGGCCTCATAGT
131 TTCGGCCTCATAGT
276854 GTCACCATTA
Statistics
Matches: 144, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
144 144 1.00
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.35
Consensus pattern (144 bp):
ACCTTCATGGTTAGTTCTGTTTGCATTTTTTCGCAGCTGGTGGATGTGCTTCTCGTACTTGCATT
TTTCAGTCATATTACATGGGCTGTCAGTGGCAGCTCACCTTGCAAACAGACCGATGTCGGGGTGA
TTCGGCCTCATAGT
Found at i:283984 original size:13 final size:13
Alignment explanation
Indices: 283968--283992 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
283958 TTCAGTTTTA
283968 ATCGAATTAACCG
1 ATCGAATTAACCG
283981 ATCGAATTAACC
1 ATCGAATTAACC
283993 AAATTACTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (13 bp):
ATCGAATTAACCG
Found at i:297002 original size:31 final size:31
Alignment explanation
Indices: 296907--297003 Score: 115
Period size: 32 Copynumber: 3.1 Consensus size: 31
296897 TGTCAATATT
* * *
296907 GGGTCAGGTCAATACCGAATCGATTGATTTTT
1 GGGTC-GGTCAATATCGGATCGATTGATTTTC
* *
296939 GGGTCGGATTAATATCGGATCAATTAGA-TTTC
1 GGGTCGG-TCAATATCGGATCGATT-GATTTTC
296971 GGGTCGGTCAATATCGGATCGATTGATTTTC
1 GGGTCGGTCAATATCGGATCGATTGATTTTC
297002 GG
1 GG
297004 TTTAGGTCAA
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
30 2 0.04
31 23 0.42
32 28 0.51
33 2 0.04
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (31 bp):
GGGTCGGTCAATATCGGATCGATTGATTTTC
Found at i:297786 original size:32 final size:32
Alignment explanation
Indices: 297744--297806 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
297734 TTTCTTTCAG
297744 TTCGGATTGCTTTCGA-TTCAGGTTAATTTCGA
1 TTCGGATTGCTTT-GAGTTCAGGTTAATTTCGA
* * *
297776 TTCGGGTTGCTTTTAGTTCGGGTTAATTTCG
1 TTCGGATTGCTTTGAGTTCAGGTTAATTTCG
297807 GTTCTAGTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 1 0.04
32 26 0.96
ACGTcount: A:0.14, C:0.14, G:0.25, T:0.46
Consensus pattern (32 bp):
TTCGGATTGCTTTGAGTTCAGGTTAATTTCGA
Found at i:297810 original size:16 final size:16
Alignment explanation
Indices: 297754--297806 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
297744 TTCGGATTGC
*
297754 TTTCGATTCAGGTTAA
1 TTTCGATTCGGGTTAA
**
297770 TTTCGATTCGGGTTGC
1 TTTCGATTCGGGTTAA
*
297786 TTT-TAGTTCGGGTTAA
1 TTTCGA-TTCGGGTTAA
297802 TTTCG
1 TTTCG
297807 GTTCTAGTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
15 1 0.04
16 27 0.96
ACGTcount: A:0.15, C:0.13, G:0.25, T:0.47
Consensus pattern (16 bp):
TTTCGATTCGGGTTAA
Found at i:317883 original size:28 final size:28
Alignment explanation
Indices: 317834--317896 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
317824 TAGAATTGAC
* *
317834 TTACAATTTTTATTATCTAATTAAATGT
1 TTACAATTTTTATTATCCAATTAAATAT
*
317862 TTACAATTTTTATTA-CACAATTTAATAT
1 TTACAATTTTTATTATC-CAATTAAATAT
317890 TTACAAT
1 TTACAAT
317897 ATTCTCTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 1 0.03
28 30 0.97
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.51
Consensus pattern (28 bp):
TTACAATTTTTATTATCCAATTAAATAT
Found at i:322641 original size:21 final size:20
Alignment explanation
Indices: 322617--322655 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
322607 ATTTTTTTAG
*
322617 TACCTAAAATTTTAATTTTGA
1 TACCT-AAAGTTTAATTTTGA
*
322638 TACCTGAAGTTTAATTTT
1 TACCTAAAGTTTAATTTT
322656 TGTTTCATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (20 bp):
TACCTAAAGTTTAATTTTGA
Found at i:330129 original size:42 final size:42
Alignment explanation
Indices: 330073--330156 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
330063 ACAATTTCAT
* * *
330073 CACTTTTTAATTGAAGAAGAAAAGGAATAATCCTTGAATGAC
1 CACTTATTAATTGAAGAACAAAAAGAATAATCCTTGAATGAC
*
330115 CACTTATTACTTGAAGAACAAAAAGAATAATCCTTGAATGAC
1 CACTTATTAATTGAAGAACAAAAAGAATAATCCTTGAATGAC
330157 TGAGGCGACT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.27
Consensus pattern (42 bp):
CACTTATTAATTGAAGAACAAAAAGAATAATCCTTGAATGAC
Found at i:332641 original size:3 final size:3
Alignment explanation
Indices: 332625--332670 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
332615 CTAATAACTA
* *
332625 ATT A-T ATT ATTT ATT ATT ATT ATT ATT TTT ATT ATT ATT ATG ATT
1 ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
332670 A
1 A
332671 AACTTAGAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:332655 original size:18 final size:19
Alignment explanation
Indices: 332625--332670 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
332615 CTAATAACTA
332625 ATTA-TATTATTTATTATT
1 ATTATTATTATTTATTATT
332643 ATTATTATT-TTTATTATT
1 ATTATTATTATTTATTATT
*
332661 ATTATGATTA
1 ATTATTATTA
332671 AACTTAGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
ATTATTATTATTTATTATT
Found at i:333989 original size:2 final size:2
Alignment explanation
Indices: 333982--334031 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
333972 CTAAAAGAAT
333982 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
334024 TA TA TA TA
1 TA TA TA TA
334032 CGTGCGCGTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:335186 original size:2 final size:2
Alignment explanation
Indices: 335179--335203 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
335169 GCAGCAAACC
335179 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
335204 AACCGAACAT
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:339107 original size:37 final size:39
Alignment explanation
Indices: 339029--339112 Score: 95
Period size: 39 Copynumber: 2.2 Consensus size: 39
339019 AATAAGTTGA
* * *
339029 AAAATATTTATATATTTTCTTTAAAAAAATTAAATTCAT
1 AAAATATATATAAATTTTCTTTAAAAAAATTAAAATCAT
*
339068 AAAATATATATAAATTTT-TTT-ACAAAATTAAAAAT-AT
1 AAAATATATATAAATTTTCTTTAAAAAAATT-AAAATCAT
339105 AAAA-ATAT
1 AAAATATAT
339113 TTAATGAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
36 4 0.10
37 13 0.32
38 7 0.17
39 16 0.40
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (39 bp):
AAAATATATATAAATTTTCTTTAAAAAAATTAAAATCAT
Found at i:342590 original size:12 final size:12
Alignment explanation
Indices: 342563--342599 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
342553 AAATTTCGGG
342563 ATTTTA-TTTT-
1 ATTTTATTTTTA
342573 ATTTTATTTTTA
1 ATTTTATTTTTA
*
342585 ATTTTATTATTA
1 ATTTTATTTTTA
342597 ATT
1 ATT
342600 ACATTTTACC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 6 0.25
11 4 0.17
12 14 0.58
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
ATTTTATTTTTA
Found at i:343045 original size:21 final size:21
Alignment explanation
Indices: 343009--343081 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
342999 CCGTAATTTC
**
343009 AAACCCTAAATTATAAATCCT
1 AAACCCTAAACCATAAATCCT
* *
343030 AAACCCTAAACCAT-AATACA
1 AAACCCTAAACCATAAATCCT
*
343050 ATAACCTCTAAACCATAAATCAT
1 A-AACC-CTAAACCATAAATCCT
*
343073 AAATCCTAA
1 AAACCCTAA
343082 TTTAGGTTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
20 5 0.12
21 20 0.49
22 12 0.29
23 4 0.10
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (21 bp):
AAACCCTAAACCATAAATCCT
Found at i:344455 original size:30 final size:30
Alignment explanation
Indices: 344428--344524 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 30
344418 CGTAAAATAG
*
344428 ATTACCTAAAAATTGTTGTACGCAAAATGA
1 ATTACATAAAAATTGTTGTACGCAAAATGA
* * * * *
344458 ATTACATGAAAATTGTTTTTGCGTAAATTGA
1 ATTACATAAAAATTG-TTGTACGCAAAATGA
* * * * *
344489 ATTGC-TTAAAATTGTTTTATGTAAAATGA
1 ATTACATAAAAATTGTTGTACGCAAAATGA
344518 ATTACAT
1 ATTACAT
344525 TTTCTGAAAA
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
29 16 0.30
30 22 0.42
31 15 0.28
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.39
Consensus pattern (30 bp):
ATTACATAAAAATTGTTGTACGCAAAATGA
Found at i:344775 original size:24 final size:27
Alignment explanation
Indices: 344748--344800 Score: 67
Period size: 24 Copynumber: 2.1 Consensus size: 27
344738 TTAATTTTAG
*
344748 TATTTTATCAATA-T-AATAC-TAAAT
1 TATTATATCAATATTAAATACATAAAT
*
344772 TATTATATTAATATTAAATACATAAAT
1 TATTATATCAATATTAAATACATAAAT
344799 TA
1 TA
344801 ATATTACTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 11 0.46
25 1 0.04
26 5 0.21
27 7 0.29
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (27 bp):
TATTATATCAATATTAAATACATAAAT
Found at i:344957 original size:14 final size:15
Alignment explanation
Indices: 344940--345011 Score: 69
Period size: 15 Copynumber: 4.7 Consensus size: 15
344930 AGTACATATT
344940 AATATAATATTA-AA
1 AATATAATATTATAA
344954 AATATAATATTATTAA
1 AATATAATATTA-TAA
*
344970 AATTATAATATAATAA
1 AA-TATAATATTATAA
*
344986 AAT-TAAATATTTTAA
1 AATAT-AATATTATAA
345001 TAAT-TAATATT
1 -AATATAATATT
345012 TTTATTAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
14 13 0.26
15 15 0.30
16 13 0.26
17 9 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATATAATATTATAA
Found at i:345059 original size:9 final size:10
Alignment explanation
Indices: 345031--345066 Score: 56
Period size: 9 Copynumber: 3.6 Consensus size: 10
345021 ATGATGTTAA
345031 AATATTAAATT
1 AATATTAAA-T
345042 AATATTAAAT
1 AATATTAAAT
345052 AA-ATTAAAT
1 AATATTAAAT
345061 AATATT
1 AATATT
345067 TTTTGAGTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.38
10 6 0.25
11 9 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
AATATTAAAT
Found at i:352259 original size:60 final size:60
Alignment explanation
Indices: 352195--352309 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
352185 AATCCTCAAG
* * * *
352195 CTATGA-CTCTCATTCTAAATTAATCCTTAAACTTTTAAACATTTTATTTTCATCCCTAAA
1 CTATGATC-CTCATTCTAAATTAACCCCTAAACTTTTAAACATTCTAATTTCATCCCTAAA
* * *
352255 CTATGATCCTCTTTCTAAATTAGCCCCTAAACTTTTAAATATTCTAATTTCATCC
1 CTATGATCCTCATTCTAAATTAACCCCTAAACTTTTAAACATTCTAATTTCATCC
352310 TCAAATTCAT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
60 46 0.98
61 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.03, T:0.43
Consensus pattern (60 bp):
CTATGATCCTCATTCTAAATTAACCCCTAAACTTTTAAACATTCTAATTTCATCCCTAAA
Found at i:352564 original size:60 final size:61
Alignment explanation
Indices: 352467--352629 Score: 163
Period size: 60 Copynumber: 2.7 Consensus size: 61
352457 TTGAATGCTA
* * ** * *
352467 AAAAATTTTGGGGATCAATTTAAAA-AGAGGGTCATAGTTTGA-AGATGAAATTAAAACGTT
1 AAAAAGTTTAGGGATCAATTTAAAACA-ATAGTTATAGTTTGAGAGATGAAATTAAAACATT
* * * ** * *
352527 CAAAAGTTT-GAGGATTAATTTAGAATGATAGTTATAGTTT-AGGGATGAAATTGAAACATT
1 AAAAAGTTTAG-GGATCAATTTAAAACAATAGTTATAGTTTGAGAGATGAAATTAAAACATT
352587 AAAAAGTTTAGGGATCAATTTAAAACAATAGTTATAGTTTGAG
1 AAAAAGTTTAGGGATCAATTTAAAACAATAGTTATAGTTTGAG
352630 GACATATGAT
Statistics
Matches: 82, Mismatches: 16, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
59 2 0.02
60 77 0.94
61 3 0.04
ACGTcount: A:0.42, C:0.04, G:0.21, T:0.33
Consensus pattern (61 bp):
AAAAAGTTTAGGGATCAATTTAAAACAATAGTTATAGTTTGAGAGATGAAATTAAAACATT
Found at i:357241 original size:60 final size:60
Alignment explanation
Indices: 357169--357301 Score: 162
Period size: 60 Copynumber: 2.2 Consensus size: 60
357159 ATAAAAGGGT
* * *
357169 AAAG-TACAAAAATGGTCCCCCGGCTATAGGATGTTGCTTTATTAAG-CCCTTCGACTATTA
1 AAAGTTAC-AAAATGATCCCCCGACTATAGAATGTTGCTTTATTAAGTCCC-TCGACTATTA
* * * * *
357229 AAAGTTACAAAATGATCCTCTGACTATAGAATGTTGTTTTATTAAGTCCCTCGACTGTTC
1 AAAGTTACAAAATGATCCCCCGACTATAGAATGTTGCTTTATTAAGTCCCTCGACTATTA
357289 AAAGTTACAAAAT
1 AAAGTTACAAAAT
357302 AGTAATCCGA
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
60 57 0.90
61 6 0.10
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (60 bp):
AAAGTTACAAAATGATCCCCCGACTATAGAATGTTGCTTTATTAAGTCCCTCGACTATTA
Found at i:357314 original size:60 final size:60
Alignment explanation
Indices: 357192--357315 Score: 153
Period size: 60 Copynumber: 2.1 Consensus size: 60
357182 GGTCCCCCGG
* ** *
357192 CTATAGGATGTTGCTTTATTAAGCCCTTCGACTATTAAAAGTTACAAAATGATCCTCTGA
1 CTATAGAATGTTGCTTTATTAAGCCCTTCGACTATTAAAAGTTACAAAATGATAATCCGA
* * *
357252 CTATAGAATGTTGTTTTATTAAGTCCC-TCGACTGTTCAAAGTTACAAAAT-AGTAATCCGA
1 CTATAGAATGTTGCTTTATTAAG-CCCTTCGACTATTAAAAGTTACAAAATGA-TAATCCGA
357312 CTAT
1 CTAT
357316 TTATTACTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
59 1 0.02
60 51 0.93
61 3 0.05
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (60 bp):
CTATAGAATGTTGCTTTATTAAGCCCTTCGACTATTAAAAGTTACAAAATGATAATCCGA
Found at i:358581 original size:2 final size:2
Alignment explanation
Indices: 358574--358643 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
358564 ATGTTCAATA
358574 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
358616 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
358644 CATTATTTTA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:370827 original size:5 final size:5
Alignment explanation
Indices: 370817--370841 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
370807 TAATCAACTG
370817 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
370842 CATGGACTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:371055 original size:27 final size:27
Alignment explanation
Indices: 371002--371055 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
370992 GAGATTCAAT
*
371002 CGGGAGGAACCGAGGCAGCGGAGTTTG
1 CGGGAGGAACCGAGGAAGCGGAGTTTG
* * * *
371029 CGGGTGGATCCGAGGAAGGGGATTTTG
1 CGGGAGGAACCGAGGAAGCGGAGTTTG
371056 AGAGGTCTGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.20, C:0.15, G:0.48, T:0.17
Consensus pattern (27 bp):
CGGGAGGAACCGAGGAAGCGGAGTTTG
Found at i:383322 original size:136 final size:136
Alignment explanation
Indices: 383062--383454 Score: 621
Period size: 136 Copynumber: 2.9 Consensus size: 136
383052 ATTAATGGAG
* * *
383062 ACGC-AACCGTGTCGAG-TCGTGATG-CTTCGATCGGACTGCGAGATCCTATAATCCTTCACGAA
1 ACGCAAACCGTATCGAGATCGTGATGTC-TCGATCGGACTGCGAGATCCTACAATCCTTCATGAA
* * *
383124 ACGCATATCCTTCATCCAATTAGCAATGACACCAATGCTATGTATGCAACAATTTGGAATTCATT
65 ACGCATATCCTTCATCCAATTAGCAATGACACTAATGTTATGTATGCAACAATTTGGCATTCATT
383189 ACTCAAA
130 ACTCAAA
* *
383196 ATGCAAACCGTATCGAGATCGTGATGTCTCGATCGGACTGCAAGATCCTACAATCCTTCATGAAA
1 ACGCAAACCGTATCGAGATCGTGATGTCTCGATCGGACTGCGAGATCCTACAATCCTTCATGAAA
**
383261 CGCATATCCTTCATCCAATTAGCAATGACACTAATGTTATGCGTGCAACAATTTGGCATTCATTA
66 CGCATATCCTTCATCCAATTAGCAATGACACTAATGTTATGTATGCAACAATTTGGCATTCATTA
*
383326 CTCGAA
131 CTCAAA
* *
383332 ACGCAAACCGTATCGAGATCGTGATGTTTCGATCGGACTGCGAGATCCTACAATCCTTCATGCAA
1 ACGCAAACCGTATCGAGATCGTGATGTCTCGATCGGACTGCGAGATCCTACAATCCTTCATGAAA
* *
383397 TGCATATCCTTCATCCAATTAGCAATGACACTAATGTTACGTATGCAACAATTTGGCA
66 CGCATATCCTTCATCCAATTAGCAATGACACTAATGTTATGTATGCAACAATTTGGCA
383455 ACTACAAGAT
Statistics
Matches: 237, Mismatches: 19, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
134 3 0.01
135 11 0.05
136 222 0.94
137 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (136 bp):
ACGCAAACCGTATCGAGATCGTGATGTCTCGATCGGACTGCGAGATCCTACAATCCTTCATGAAA
CGCATATCCTTCATCCAATTAGCAATGACACTAATGTTATGTATGCAACAATTTGGCATTCATTA
CTCAAA
Found at i:394845 original size:24 final size:24
Alignment explanation
Indices: 394751--394850 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
394741 ATATTTTATC
* *
394751 TGATTTCTGATTTGAATTCTGTTT
1 TGATATCTGATCTGAATTCTGTTT
* * *
394775 TGACATCTGATCTGAAATCTGTTC
1 TGATATCTGATCTGAATTCTGTTT
* * * *
394799 TGAT-TCCTAACCTGGATTCTGTTA
1 TGATAT-CTGATCTGAATTCTGTTT
*
394823 TGATATCTGATCTGAATTATGTTT
1 TGATATCTGATCTGAATTCTGTTT
394847 TGAT
1 TGAT
394851 TTTTGATATC
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 1 0.02
24 56 0.97
25 1 0.02
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.47
Consensus pattern (24 bp):
TGATATCTGATCTGAATTCTGTTT
Found at i:399726 original size:24 final size:24
Alignment explanation
Indices: 399628--399726 Score: 85
Period size: 24 Copynumber: 4.2 Consensus size: 24
399618 ATATTTTATC
* *
399628 TGATTTCTGATTTGAATTCTG-TT
1 TGATATCTGATCTGAATTCTGTTT
* * *
399651 TGACATCTGATCTGAAATCTGTTC
1 TGATATCTGATCTGAATTCTGTTT
* * * *
399675 TGAT-TCCTAACCTGGATTCTGTTA
1 TGATAT-CTGATCTGAATTCTGTTT
*
399699 TGATATCTGATCTGAATTATGTTT
1 TGATATCTGATCTGAATTCTGTTT
399723 TGAT
1 TGAT
399727 TTTTGATATC
Statistics
Matches: 57, Mismatches: 16, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
23 18 0.32
24 38 0.67
25 1 0.02
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.46
Consensus pattern (24 bp):
TGATATCTGATCTGAATTCTGTTT
Found at i:399899 original size:2 final size:2
Alignment explanation
Indices: 399892--399946 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
399882 GGGATGGGGG
399892 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
399934 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
399947 GTTTTGAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:402193 original size:21 final size:23
Alignment explanation
Indices: 402169--402215 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
402159 AAAAAAACCG
402169 AAAACTG-C-CAAAAG-ATGAGAT
1 AAAACTGTCACAAAAGTA-GAGAT
*
402190 AAAAGTGTCACAAAAGTAGAGAT
1 AAAACTGTCACAAAAGTAGAGAT
402213 AAA
1 AAA
402216 CATGTAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 6 0.27
22 1 0.05
23 14 0.64
24 1 0.05
ACGTcount: A:0.55, C:0.11, G:0.19, T:0.15
Consensus pattern (23 bp):
AAAACTGTCACAAAAGTAGAGAT
Found at i:402605 original size:25 final size:26
Alignment explanation
Indices: 402577--402629 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
402567 GGGTCGAGTT
402577 TTTTTAAAT-CGG-GTTCAGGTCTGGG
1 TTTTTAAATGCGGTGTTCAGGTC-GGG
* *
402602 TTTTTTAATGTGGTGTTCAGGTCGGG
1 TTTTTAAATGCGGTGTTCAGGTCGGG
402628 TT
1 TT
402630 GAATTCGGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 8 0.33
26 7 0.29
27 9 0.38
ACGTcount: A:0.13, C:0.09, G:0.32, T:0.45
Consensus pattern (26 bp):
TTTTTAAATGCGGTGTTCAGGTCGGG
Found at i:408876 original size:15 final size:13
Alignment explanation
Indices: 408842--408907 Score: 57
Period size: 14 Copynumber: 4.9 Consensus size: 13
408832 TTATTAACGG
408842 TAAAAAA-T-AAA
1 TAAAAAATTAAAA
408853 TAAATAAATTAGAATA
1 TAAA-AAATTA-AA-A
408869 TAAAAAATTATAAA
1 TAAAAAATTA-AAA
*
408883 -ATAAAATTAAACA
1 TAAAAAATTAAA-A
408896 TAAAAAATTAAA
1 TAAAAAATTAAA
408908 CAAATATAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
11 4 0.09
12 5 0.11
13 10 0.22
14 11 0.24
15 10 0.22
16 5 0.11
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (13 bp):
TAAAAAATTAAAA
Found at i:408912 original size:28 final size:28
Alignment explanation
Indices: 408842--408913 Score: 87
Period size: 27 Copynumber: 2.6 Consensus size: 28
408832 TTATTAACGG
*
408842 TAAAAAA-TAAATAAAT-AAATTAGAATA
1 TAAAAAATTAAA-AAATAAAATTAGAACA
*
408869 TAAAAAATTATAAAATAAAATTA-AACA
1 TAAAAAATTAAAAAATAAAATTAGAACA
408896 TAAAAAATTAAACAAATA
1 TAAAAAATTAAA-AAATA
408914 TAATATTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
27 25 0.64
28 14 0.36
ACGTcount: A:0.71, C:0.03, G:0.01, T:0.25
Consensus pattern (28 bp):
TAAAAAATTAAAAAATAAAATTAGAACA
Found at i:409202 original size:15 final size:14
Alignment explanation
Indices: 409168--409206 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
409158 AATTGGGAAC
*
409168 TAGGGATTTTGATT
1 TAGGAATTTTGATT
*
409182 TTGGAATTTTAGATT
1 TAGGAATTTT-GATT
409197 TAGGAATTTT
1 TAGGAATTTT
409207 TAGTGATGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (14 bp):
TAGGAATTTTGATT
Found at i:410577 original size:11 final size:11
Alignment explanation
Indices: 410561--410616 Score: 51
Period size: 11 Copynumber: 4.8 Consensus size: 11
410551 ATTATATAGT
410561 TTTTGAAAATA
1 TTTTGAAAATA
410572 TTTTGAAAATA
1 TTTTGAAAATA
*
410583 TATAT-AATATATA
1 T-TTTGAA-A-ATA
*
410596 GTTTTGAAAACA
1 -TTTTGAAAATA
410608 TTTTGAAAA
1 TTTTGAAAA
410617 CGTTTATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
11 23 0.62
12 5 0.14
13 6 0.16
14 3 0.08
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (11 bp):
TTTTGAAAATA
Found at i:410663 original size:38 final size:36
Alignment explanation
Indices: 410546--410782 Score: 224
Period size: 40 Copynumber: 6.5 Consensus size: 36
410536 TTCGAAAATT
*
410546 TATATAT-TATATAGTTTTTGAAAATATTTTGAAAA-
1 TATATATATATATAGTTTTT-AAAACATTTTGAAAAC
*
410581 TATATATAATATATAGTTTTGAAAACATTTTGAAAAC
1 TATATAT-ATATATAGTTTTTAAAACATTTTGAAAAC
410618 GTTTATATATATTATATAGTTTTTAAAACATTTTGAAAAC
1 ---TATATATA-TATATAGTTTTTAAAACATTTTGAAAAC
* * *
410658 -ATATATAGTATATAGTTTTAAAAACATTTTTTGTGAAAT
1 TATATATA-TATATAGTTTTTAAAACA--TTTTG-AAAAC
*
410697 TATATA-ATATATAGTTTTAAAAACATTTTTTGAAAAC
1 TATATATATATATAGTTTTTAAAACA--TTTTGAAAAC
*
410734 --T-TATATA-ATA-TTTTTAAAACGTTTTGAAAAC
1 TATATATATATATAGTTTTTAAAACATTTTGAAAAC
*
410765 TATGTA-ATATATAGTTTT
1 TATATATATATATAGTTTT
410783 GGAATTTTTT
Statistics
Matches: 174, Mismatches: 11, Indels: 34
0.79 0.05 0.16
Matches are distributed among these distances:
31 10 0.06
33 13 0.07
34 10 0.06
35 15 0.09
36 38 0.22
37 14 0.08
38 30 0.17
39 5 0.03
40 39 0.22
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (36 bp):
TATATATATATATAGTTTTTAAAACATTTTGAAAAC
Found at i:410672 original size:76 final size:73
Alignment explanation
Indices: 410497--410782 Score: 249
Period size: 76 Copynumber: 3.9 Consensus size: 73
410487 GTAAAAATGT
* *
410497 TTTTGACAAA-ATATA-ATATATAATTTTCAGAAAATGATTTTCGAAAA-TT-TATATATTATAT
1 TTTTGA-AAACATATATATATATAGTTTT-A-AAAA-CATTTT-GAAAACTTATATATATTATAT
*
410558 AGTTTTTGAAAATA
61 AGTTTTT-AAAACA
* *
410572 TTTTGAAAATATATATAATATATAGTTTTGAAAACATTTTGAAAACGTTTATATATATTATATAG
1 TTTTGAAAACATATAT-ATATATAGTTTTAAAAACATTTTGAAAAC--TTATATATATTATATAG
410637 TTTTTAAAACA
63 TTTTTAAAACA
*
410648 TTTTGAAAACATATATAGTATATAGTTTTAAAAACATTTTTTGTGAAA-TTATATA-A-TATATA
1 TTTTGAAAACATATATA-TATATAGTTTTAAAAACA--TTTTG-AAAACTTATATATATTATATA
*
410710 GTTTTAAAAACA
62 GTTTTTAAAACA
* * *
410722 TTTTTTGAAAAC-T-TATATA-ATA-TTTTTAAAACGTTTTGAAAAC-TATGTA-A-TATATAGT
1 --TTTTGAAAACATATATATATATAGTTTTAAAAACATTTTGAAAACTTATATATATTATATAGT
410780 TTT
64 TTT
410783 GGAATTTTTT
Statistics
Matches: 185, Mismatches: 12, Indels: 35
0.80 0.05 0.15
Matches are distributed among these distances:
68 20 0.11
69 5 0.03
71 9 0.05
72 3 0.02
73 7 0.04
74 29 0.16
75 18 0.10
76 56 0.30
77 30 0.16
78 5 0.03
79 3 0.02
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (73 bp):
TTTTGAAAACATATATATATATAGTTTTAAAAACATTTTGAAAACTTATATATATTATATAGTTT
TTAAAACA
Found at i:417640 original size:17 final size:17
Alignment explanation
Indices: 417618--417652 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
417608 AACAATAGGA
*
417618 TTAACCACACGTTTAAT
1 TTAACCACACGTGTAAT
417635 TTAACCACACGTGTAAT
1 TTAACCACACGTGTAAT
417652 T
1 T
417653 CGCGGTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (17 bp):
TTAACCACACGTGTAAT
Found at i:422750 original size:13 final size:13
Alignment explanation
Indices: 422723--422772 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 13
422713 AATTATAAAC
422723 TTTAAG-TTAGAG
1 TTTAAGTTTAGAG
*
422735 TTTAAGTTTAGGG
1 TTTAAGTTTAGAG
422748 TTTATAGTTTAGAG
1 TTTA-AGTTTAGAG
*
422762 ATTATAGTTTA
1 TTTA-AGTTTA
422773 CGATTTAGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
12 6 0.18
13 9 0.27
14 18 0.55
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (13 bp):
TTTAAGTTTAGAG
Found at i:422758 original size:14 final size:14
Alignment explanation
Indices: 422729--422772 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
422719 AAACTTTAAG
422729 TTAGAGTTTA-AGT
1 TTAGAGTTTATAGT
*
422742 TTAGGGTTTATAGT
1 TTAGAGTTTATAGT
*
422756 TTAGAGATTATAGT
1 TTAGAGTTTATAGT
422770 TTA
1 TTA
422773 CGATTTAGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 9 0.33
14 18 0.67
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.48
Consensus pattern (14 bp):
TTAGAGTTTATAGT
Found at i:422779 original size:21 final size:21
Alignment explanation
Indices: 422755--422799 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
422745 GGGTTTATAG
*
422755 TTTAGAGATTATAGTTTACGA
1 TTTAGAGATTATAATTTACGA
* * *
422776 TTTAGTGTTTATAATTTAGGA
1 TTTAGAGATTATAATTTACGA
422797 TTT
1 TTT
422800 TAAGTTAGAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.02, G:0.18, T:0.51
Consensus pattern (21 bp):
TTTAGAGATTATAATTTACGA
Found at i:427522 original size:3 final size:3
Alignment explanation
Indices: 427514--427539 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
427504 AATTTATCCG
427514 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
427540 ACTGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:428321 original size:14 final size:13
Alignment explanation
Indices: 428302--428339 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
428292 AAATATTCAA
428302 AAAAATTAAATATT
1 AAAAATTAAA-ATT
428316 AAAAATT-AAATT
1 AAAAATTAAAATT
428328 AAAATATTAAAA
1 AAAA-ATTAAAA
428340 AATATTCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.32
13 5 0.23
14 10 0.45
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAATTAAAATT
Found at i:428321 original size:35 final size:35
Alignment explanation
Indices: 428282--428356 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 35
428272 TTATGAATAT
*
428282 AAAATT-ATTCAAATATTCAAAAAA-ATTAAATATTA
1 AAAATTAATTAAAATATT-AAAAAATATT-AATATTA
*
428317 AAAATTAAATTAAAATATTAAAAAATATTCATATTA
1 AAAATT-AATTAAAATATTAAAAAATATTAATATTA
428353 AAAA
1 AAAA
428357 CACTAAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
35 6 0.17
36 16 0.46
37 13 0.37
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (35 bp):
AAAATTAATTAAAATATTAAAAAATATTAATATTA
Found at i:428334 original size:20 final size:17
Alignment explanation
Indices: 428292--428356 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 17
428282 AAAATTATTC
*
428292 AAATATTCAAAAAAATT
1 AAATATTAAAAAAAATT
428309 AAATATTAAAAATTAAATT
1 AAATATTAAAAA--AAATT
*
428328 AAAATATTAAAAAATATT
1 -AAATATTAAAAAAAATT
*
428346 -CATATTAAAAA
1 AAATATTAAAAA
428357 CACTAAAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
16 10 0.24
17 11 0.26
18 4 0.10
19 5 0.12
20 12 0.29
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATATTAAAAAAAATT
Found at i:429501 original size:55 final size:55
Alignment explanation
Indices: 429409--429538 Score: 197
Period size: 55 Copynumber: 2.4 Consensus size: 55
429399 GATTGTATGA
* * *
429409 GAGTGTATCGATACGCTCAAAACATCGAATGCCATTTGTGTATCGGTACACTTAG
1 GAGTGTATCGATACACCCAAAACATCGAATGCCATTTGTGTATCGGTACACTGAG
* * *
429464 GAGTGTATCGATACACCCAAAACATTGAGTGCTATTTGTGTATCGGTACACTGAG
1 GAGTGTATCGATACACCCAAAACATCGAATGCCATTTGTGTATCGGTACACTGAG
*
429519 GAGTGTATCGATACCCCCAA
1 GAGTGTATCGATACACCCAA
429539 GTATGAACCA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 68 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (55 bp):
GAGTGTATCGATACACCCAAAACATCGAATGCCATTTGTGTATCGGTACACTGAG
Found at i:430109 original size:23 final size:23
Alignment explanation
Indices: 430081--430155 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
430071 TTCGGGATAA
*
430081 TATGTGACACTTCGGTGCAACCC
1 TATGTGGCACTTCGGTGCAACCC
*
430104 TATGTGGCATTTCGGTGCAACCC
1 TATGTGGCACTTCGGTGCAACCC
* *
430127 TATGTGGCACTTTGGTGCAA-TC
1 TATGTGGCACTTCGGTGCAACCC
430149 TATGTGG
1 TATGTGG
430156 TCTTTCGGGA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 8 0.17
23 39 0.83
ACGTcount: A:0.19, C:0.23, G:0.27, T:0.32
Consensus pattern (23 bp):
TATGTGGCACTTCGGTGCAACCC
Found at i:430187 original size:43 final size:43
Alignment explanation
Indices: 430059--430189 Score: 133
Period size: 43 Copynumber: 3.0 Consensus size: 43
430049 GAGTTGATGG
* *
430059 TCTATGTGGTCCTTCGGGATAATATGTGACACTTCGGTGCAAC
1 TCTATGTGGTCTTTCGGGACAATATGTGACACTTCGGTGCAAC
* * *
430102 CCTATGTGG-CATTTCGGTG-CAACCCTATGTGGCACTTTGGTGCAA-
1 TCTATGTGGTC-TTTCGG-GACAA---TATGTGACACTTCGGTGCAAC
*
430147 TCTATGTGGTCTTTCGGGACAATTATGTGCCACTTCGGTGCAA
1 TCTATGTGGTCTTTCGGGACAA-TATGTGACACTTCGGTGCAA
430190 ATTACGAGCT
Statistics
Matches: 72, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
42 1 0.01
43 33 0.46
44 2 0.03
45 17 0.24
46 19 0.26
ACGTcount: A:0.19, C:0.22, G:0.26, T:0.33
Consensus pattern (43 bp):
TCTATGTGGTCTTTCGGGACAATATGTGACACTTCGGTGCAAC
Found at i:430607 original size:2 final size:2
Alignment explanation
Indices: 430600--430637 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
430590 TTTTGAATAA
430600 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
430638 TTGTATTTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:430926 original size:25 final size:25
Alignment explanation
Indices: 430897--430965 Score: 84
Period size: 25 Copynumber: 2.8 Consensus size: 25
430887 AAAATAGATA
430897 GTAAGTTTTGACTAATCCAAAATTT
1 GTAAGTTTTGACTAATCCAAAATTT
** *
430922 GTAAGTTTTGACTAATTTAAATTTT
1 GTAAGTTTTGACTAATCCAAAATTT
* * *
430947 ATAAATTTTGATTAATCCA
1 GTAAGTTTTGACTAATCCA
430966 GTAAAAATAT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (25 bp):
GTAAGTTTTGACTAATCCAAAATTT
Found at i:439504 original size:3 final size:3
Alignment explanation
Indices: 439496--439520 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
439486 TTATATTTTA
439496 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
439521 TTTTTTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:441439 original size:25 final size:26
Alignment explanation
Indices: 441384--441439 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
441374 TACTCACTGG
*
441384 ATTTTTGAATTATTTATGTTTTGATC
1 ATTTTTGAATTATTTATGTATTGATC
*
441410 A-TTTTGAATTATATTAT-TATT-ATT
1 ATTTTTGAATTAT-TTATGTATTGATC
441434 ATTTTT
1 ATTTTT
441440 AAATGATGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 3 0.12
25 18 0.69
26 5 0.19
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.64
Consensus pattern (26 bp):
ATTTTTGAATTATTTATGTATTGATC
Found at i:442644 original size:2 final size:2
Alignment explanation
Indices: 442637--442667 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
442627 ATTCTCAAAC
442637 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
442668 CCCACTTCAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:446666 original size:51 final size:50
Alignment explanation
Indices: 446611--446710 Score: 130
Period size: 50 Copynumber: 2.0 Consensus size: 50
446601 TGAAACTTGT
* *
446611 AATTAAAAACTATGTTGTTCATACATCGAA-CAATCTCAGTGCACCAATTGC
1 AATTAAAAAC--TGTTGTTCATACACCCAACCAATCTCAGTGCACCAATTGC
* * *
446662 AATTAAAGACTGTTGTTCATGCACCCAACCAATCTGAGTGCACCAATTG
1 AATTAAAAACTGTTGTTCATACACCCAACCAATCTCAGTGCACCAATTG
446711 GATATCTCTA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
49 15 0.35
50 19 0.44
51 9 0.21
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (50 bp):
AATTAAAAACTGTTGTTCATACACCCAACCAATCTCAGTGCACCAATTGC
Found at i:450478 original size:19 final size:19
Alignment explanation
Indices: 450451--450498 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
450441 AATGTTTTTA
* * *
450451 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTAATATT
450470 TGAACAGTAAATTAATATT
1 TGAACAGTAAATTAATATT
450489 TGAACAGTAA
1 TGAACAGTAA
450499 CCCGAGACTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (19 bp):
TGAACAGTAAATTAATATT
Found at i:450551 original size:20 final size:20
Alignment explanation
Indices: 450526--450563 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
450516 CCAGTATGTA
450526 AAAGGGGAACCGATTCCCCC
1 AAAGGGGAACCGATTCCCCC
*
450546 AAAGGGGTACCGATTCCC
1 AAAGGGGAACCGATTCCC
450564 TCACTGTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.32, G:0.26, T:0.13
Consensus pattern (20 bp):
AAAGGGGAACCGATTCCCCC
Found at i:450629 original size:21 final size:21
Alignment explanation
Indices: 450603--450642 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
450593 ATTTGAATAT
*
450603 TATGAAGGGGTATCGATTCTC
1 TATGAAGGGGTACCGATTCTC
450624 TATGAAGGGGTACCGATTC
1 TATGAAGGGGTACCGATTC
450643 CCCCCATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.30
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCTC
Found at i:450706 original size:21 final size:21
Alignment explanation
Indices: 450673--450712 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
450663 TTTTTGTAGA
*
450673 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
450695 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
450713 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:450955 original size:30 final size:32
Alignment explanation
Indices: 450919--450982 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 32
450909 TTTATCCTTT
450919 TGTAAAAG-GG-AAAGGTTCTAGCTTAGCCCG
1 TGTAAAAGAGGAAAAGGTTCTAGCTTAGCCCG
*
450949 TGTAAAAGCTAGGAAAAGGTTCTAGTTTAGCCCG
1 TGTAAAAG--AGGAAAAGGTTCTAGCTTAGCCCG
450983 GAAAAACTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 8 0.28
33 2 0.07
34 19 0.66
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (32 bp):
TGTAAAAGAGGAAAAGGTTCTAGCTTAGCCCG
Found at i:460856 original size:15 final size:15
Alignment explanation
Indices: 460836--460866 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
460826 TTTTGAAGCA
460836 GTTATGTTGTCCATT
1 GTTATGTTGTCCATT
460851 GTTATGTTGTCCATT
1 GTTATGTTGTCCATT
460866 G
1 G
460867 AGAGAGGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.23, T:0.52
Consensus pattern (15 bp):
GTTATGTTGTCCATT
Found at i:463748 original size:26 final size:23
Alignment explanation
Indices: 463688--463748 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 23
463678 CAGTTCTTGC
*
463688 TTAAAAATCATTTTATAAATTTCA
1 TTAAAAAT-ATTTTATAAATATCA
*
463712 TTCAAATATATTTTCATAAAATATCA
1 TT-AAAAATATTTT-AT-AAATATCA
463738 TATAAAAATAT
1 T-TAAAAATAT
463749 ATTGTATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 7 0.23
25 7 0.23
26 15 0.50
27 1 0.03
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (23 bp):
TTAAAAATATTTTATAAATATCA
Found at i:474090 original size:21 final size:21
Alignment explanation
Indices: 474066--474107 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
474056 GAAAACATGT
*
474066 ATACATGAAGTATCGACACAA
1 ATACATCAAGTATCGACACAA
* *
474087 ATACATCAAGTTTCGATACAA
1 ATACATCAAGTATCGACACAA
474108 TTTTGTCCAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.24
Consensus pattern (21 bp):
ATACATCAAGTATCGACACAA
Found at i:476275 original size:198 final size:196
Alignment explanation
Indices: 475755--476460 Score: 737
Period size: 198 Copynumber: 3.5 Consensus size: 196
475745 ATACATACGT
* * * *
475755 AAGAAT-ATGTGTCGATACATTTTCAAAA-GGTATCGACCCCAAAAACATCGAAACAAATAATTA
1 AAGAATAAAGTGTCGATACA-TTT-AAAATTGTATCGATCCCAAAAACATCGAAACGAATAATTA
** * * * * * * * * * *
475818 TAATGTAATATTTAAATTAACAATGTAACCAGTATACATATATCAG-TTAATTATAAAACAGGTC
64 TAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAAAAAATAGGTT
* * * *
475882 AACATAAAGTATCGACACTTTTTAAGTTTGTGTCGATACTTTTTTCCA-AAAGAAAGCACAAAC-
129 AA-ATAAAGTATCGACACTTTATAA-TTTGTGTCGATACTTTTTTCCATAATGAATGC-CCAACG
* *
475945 ATGTTC
191 AGGTGC
* * * *
475951 ATGCATAAAGTGTCGATACATTTAAAATTGTATCGATCACAAAAATATCGAAACCG-ATAATTAT
1 AAGAATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAA-CGAATAATTAT
* * * * *
476015 AATGTAATAGGTCAATTTACAATGTAACCGGTTTAAATTTACCGGTTGTATGAGAAAATAGGTTA
65 AATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAAAAAATAGGTTA
* *
476080 TAATAAAGTATCGACACTTGTGTAATTTGTGTCGATACATTTTGTCCATAATGAATGCCCAACGA
130 -AATAAAGTATCGACACTT-TATAATTTGTGTCGATAC-TTTTTTCCATAATGAATGCCCAACGA
476145 GGTGC
192 GGTGC
* * *
476150 AAGAATAACGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGACACGAA-AATTACA
1 AAGAATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACGAATAATTATA
* * *
476214 ATGTTATAGGAAAATTTACAATGTACCCGGTATAAATATACCGGTTTTATGAAAAAATAGGTCTA
66 ATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAAAAAATAGGT-TA
* * *
476279 AATAATGTATCGACACCTTTATAGTTTGTATCGATACTTTTTTCCAGAATAAATTAGGAATGCCC
130 AATAAAGTATCGACA-CTTTATAATTTGTGTCGATACTTTTTTCC---AT-AA-T--GAATGCCC
476344 AACGAGGTGC
187 AACGAGGTGC
** * *
476354 AAGCTTAAAGTGTCGATACATTTAAAATTGTATCGATCCAAAAAACAAT-GAAACCAATAATTAT
1 AAGAATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAAC-ATCGAAACGAATAATTAT
* *
476418 AATGCAATAGGTAAATTTGCAATGCT-ACCGGTATAAATATACC
65 AATGTAATAGGTAAATTTACAATG-TAACCGGTATAAATATACC
476461 AGTTAAATGC
Statistics
Matches: 425, Mismatches: 63, Indels: 35
0.81 0.12 0.07
Matches are distributed among these distances:
195 4 0.01
196 71 0.17
197 63 0.15
198 108 0.25
199 64 0.15
200 2 0.00
201 2 0.00
202 1 0.00
204 66 0.16
205 43 0.10
206 1 0.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (196 bp):
AAGAATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACGAATAATTATA
ATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAAAAAATAGGTTAA
ATAAAGTATCGACACTTTATAATTTGTGTCGATACTTTTTTCCATAATGAATGCCCAACGAGGTG
C
Found at i:476529 original size:23 final size:23
Alignment explanation
Indices: 476478--476522 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
476468 TGCCTATTTT
* *
476478 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGATACCTAATAC
476501 ATTATATAAGCGATACCTAATA
1 ATTATATAAGCGATACCTAATA
476523 TGTTATAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGATACCTAATAC
Found at i:477401 original size:3 final size:3
Alignment explanation
Indices: 477393--477429 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
477383 CAATAAATTA
477393 AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
477430 CTTTATAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:477415 original size:17 final size:17
Alignment explanation
Indices: 477393--477425 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
477383 CAATAAATTA
477393 AATAATAATAATAATAT
1 AATAATAATAATAATAT
477410 AATAATAATAATAATA
1 AATAATAATAATAATA
477426 ATAACTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAATAATAATAATAT
Found at i:480829 original size:16 final size:18
Alignment explanation
Indices: 480804--480841 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
480794 GACCCGAAAT
480804 AATATATTTATT-AA-AA
1 AATATATTTATTCAATAA
*
480820 AATATTTTTATTCAATAA
1 AATATATTTATTCAATAA
480838 AATA
1 AATA
480842 GGAATTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 11 0.58
17 2 0.11
18 6 0.32
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (18 bp):
AATATATTTATTCAATAA
Found at i:481088 original size:51 final size:51
Alignment explanation
Indices: 481012--481114 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
481002 TGATCATATC
481012 AGGTTAGATTGAAACCTGTCGGGTTCGGTCCATGCCCATCCTGCTTATTAT
1 AGGTTAGATTGAAACCTGTCGGGTTCGGTCCATGCCCATCCTGCTTATTAT
481063 AGGTTAGATTGAAACCTGTCGGGTTCGGTCCATGCCCATCCTGCTTATTAT
1 AGGTTAGATTGAAACCTGTCGGGTTCGGTCCATGCCCATCCTGCTTATTAT
481114 A
1 A
481115 CATGAAGTTG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.33
Consensus pattern (51 bp):
AGGTTAGATTGAAACCTGTCGGGTTCGGTCCATGCCCATCCTGCTTATTAT
Found at i:484137 original size:31 final size:31
Alignment explanation
Indices: 484059--484129 Score: 128
Period size: 31 Copynumber: 2.4 Consensus size: 31
484049 TCGATATAAC
484059 AATTGAATTTACAAAATGGTTTTTGGACTTG
1 AATTGAATTTACAAAATGGTTTTTGGACTTG
484090 AATTGAATTTACAAAAT-GTTTTTGGACTT-
1 AATTGAATTTACAAAATGGTTTTTGGACTTG
484119 AATTGAATTTA
1 AATTGAATTTA
484130 TTCAAAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 11 0.28
30 12 0.30
31 17 0.43
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (31 bp):
AATTGAATTTACAAAATGGTTTTTGGACTTG
Found at i:484221 original size:19 final size:19
Alignment explanation
Indices: 484211--484260 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
484201 TAATTTACTA
484211 TTTGAACAGTAAATCACTG
1 TTTGAACAGTAAATCACTG
484230 TTTGAACAGTAAATCACTG
1 TTTGAACAGTAAATCACTG
484249 TTTGAACAGTAA
1 TTTGAACAGTAA
484261 CCCGAGGCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (19 bp):
TTTGAACAGTAAATCACTG
Found at i:484391 original size:21 final size:21
Alignment explanation
Indices: 484365--484406 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
484355 ATTTGAATAT
*
484365 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
484386 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
484407 CCCATTCTGG
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:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:484473 original size:20 final size:22
Alignment explanation
Indices: 484435--484474 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
484425 TTTGAGTATA
484435 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
484457 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
484475 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:484728 original size:34 final size:32
Alignment explanation
Indices: 484689--484758 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
484679 TTTTGTAAAG
* *
484689 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
484723 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
484755 GGGA
1 GGGA
484759 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:485694 original size:231 final size:231
Alignment explanation
Indices: 485291--485753 Score: 856
Period size: 231 Copynumber: 2.0 Consensus size: 231
485281 AGTAAGCAAT
* *
485291 GGGAGAGAGTAATATTAATATTAGTATTTACGATACAGAAAATATAGAGACAACATTTGGGTAAA
1 GGGAGAGAGTAATATTAATATTAGTATTTACAATACAGAAAAGATAGAGACAACATTTGGGTAAA
* *
485356 TTACACGCTTACTAACTAAATTTTGCTCTCTTATTTCACTCACCATACTTTCAATTTTTAATTTA
66 TTACACGATTACTAACTAAATTTTACTCTCTTATTTCACTCACCATACTTTCAATTTTTAATTTA
*
485421 CTCACTGAACTTTAGACATTAAACTTTTTTGGCCACTCGACCGTGTTTACACAATAACCGGGTGG
131 CTCACTGAACTTTAGACATTAAACTTTTTTGGCCACTCGACCGTGTTCACACAATAACCGGGTGG
485486 TGACGTGGTTTATTTTAATAATAGAACATGTCACAC
196 TGACGTGGTTTATTTTAATAATAGAACATGTCACAC
485522 GGGAGAGAGTAATATTAATATTAGTATTTACAATACAGAAAAGATAG-GAACAACATTTGGGTAA
1 GGGAGAGAGTAATATTAATATTAGTATTTACAATACAGAAAAGATAGAG-ACAACATTTGGGTAA
485586 ATTACACGATTACTAACTAAATTTTACTCTCTTATTTCACTCACCATACTTTCAATTTTTAATTT
65 ATTACACGATTACTAACTAAATTTTACTCTCTTATTTCACTCACCATACTTTCAATTTTTAATTT
*
485651 ACTCACTGAACTTTAGACATTAAACTTTTTTGGCCACTCGACCGTGTTCACACAATAACGGGGTG
130 ACTCACTGAACTTTAGACATTAAACTTTTTTGGCCACTCGACCGTGTTCACACAATAACCGGGTG
485716 GTGACGTGGTTTATTTTAATAATAGAACATGTCACAC
195 GTGACGTGGTTTATTTTAATAATAGAACATGTCACAC
485753 G
1 G
485754 TTTACTTACT
Statistics
Matches: 225, Mismatches: 6, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
230 1 0.00
231 224 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (231 bp):
GGGAGAGAGTAATATTAATATTAGTATTTACAATACAGAAAAGATAGAGACAACATTTGGGTAAA
TTACACGATTACTAACTAAATTTTACTCTCTTATTTCACTCACCATACTTTCAATTTTTAATTTA
CTCACTGAACTTTAGACATTAAACTTTTTTGGCCACTCGACCGTGTTCACACAATAACCGGGTGG
TGACGTGGTTTATTTTAATAATAGAACATGTCACAC
Found at i:490431 original size:31 final size:33
Alignment explanation
Indices: 490385--490451 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
490375 ATTATATATA
*
490385 TATATATAATTTTTTTCTGATATTTTTGAATTT
1 TATATATAATTTTTTCCTGATATTTTTGAATTT
*
490418 TATATATAATTTTTCCCTGATATTTTTGAATTT
1 TATATATAATTTTTTCCTGATATTTTTGAATTT
490451 T
1 T
490452 GAAAAGGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (33 bp):
TATATATAATTTTTTCCTGATATTTTTGAATTT
Found at i:490721 original size:23 final size:22
Alignment explanation
Indices: 490685--490727 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
490675 ATAATTATTT
490685 AAAAATTAAATAAAAAATATAA
1 AAAAATTAAATAAAAAATATAA
*
490707 AAAATATTTAATAAAAAATAT
1 AAAA-ATTAAATAAAAAATAT
490728 TTTTTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (22 bp):
AAAAATTAAATAAAAAATATAA
Found at i:490722 original size:14 final size:14
Alignment explanation
Indices: 490703--490729 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
490693 AATAAAAAAT
490703 ATAAAAAATATTTA
1 ATAAAAAATATTTA
490717 ATAAAAAATATTT
1 ATAAAAAATATTT
490730 TTTTATATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATAAAAAATATTTA
Found at i:491649 original size:2 final size:2
Alignment explanation
Indices: 491642--491666 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
491632 TGTCCATCAA
491642 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
491667 AAAGGTCTTT
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:505426 original size:6 final size:6
Alignment explanation
Indices: 505415--505465 Score: 86
Period size: 6 Copynumber: 8.5 Consensus size: 6
505405 ACTCCCTTGC
505415 CTTCTG CTTCTG CTTCTG CTTCTG CTTCTG CTT-TG CTTCTG CTTCATG
1 CTTCTG CTTCTG CTTCTG CTTCTG CTTCTG CTTCTG CTTCTG CTTC-TG
505463 CTT
1 CTT
505466 TGGCACCGCT
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.12
6 33 0.77
7 5 0.12
ACGTcount: A:0.02, C:0.31, G:0.16, T:0.51
Consensus pattern (6 bp):
CTTCTG
Found at i:505476 original size:29 final size:29
Alignment explanation
Indices: 505419--505478 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
505409 CCTTGCCTTC
* *
505419 TGCTTCTGCTTCTGCTTCTGCTTCTGCTT
1 TGCTTCTGCTTCTGCTTCTGCTACCGCTT
505448 TGCTTCTGCTTCATGCTT-TGGC-ACCGCTT
1 TGCTTCTGCTTC-TGCTTCT-GCTACCGCTT
505477 TG
1 TG
505479 ACGCCACTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.03, C:0.30, G:0.20, T:0.47
Consensus pattern (29 bp):
TGCTTCTGCTTCTGCTTCTGCTACCGCTT
Found at i:508234 original size:22 final size:20
Alignment explanation
Indices: 508193--508239 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
508183 TTAAAGAAAA
*
508193 AATATATTTAATATATAATT
1 AATATAATTAATATATAATT
*
508213 AATATAATTAGTATATCGAATT
1 AATATAATTAATATAT--AATT
508235 AATAT
1 AATAT
508240 TTTTAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 14 0.61
22 9 0.39
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (20 bp):
AATATAATTAATATATAATT
Found at i:508294 original size:17 final size:17
Alignment explanation
Indices: 508274--508306 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
508264 ATATTTATTT
508274 ATAT-AAAATATAATATA
1 ATATGAAAA-ATAATATA
508291 ATATGAAAAATAATAT
1 ATATGAAAAATAATAT
508307 TGTGATCTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
ATATGAAAAATAATATA
Found at i:508644 original size:3 final size:3
Alignment explanation
Indices: 508631--508665 Score: 52
Period size: 3 Copynumber: 11.0 Consensus size: 3
508621 ATTGAACTCT
508631 TTA TATA TTA TTA TTA TTTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
508666 AGTTTATCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 24 0.80
4 6 0.20
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:508652 original size:13 final size:13
Alignment explanation
Indices: 508631--508665 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
508621 ATTGAACTCT
*
508631 TTATATATTATTA
1 TTATTTATTATTA
508644 TTATTTATTATTA
1 TTATTTATTATTA
508657 TTA-TTATTA
1 TTATTTATTA
508666 AGTTTATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATTTATTATTA
Found at i:516834 original size:17 final size:17
Alignment explanation
Indices: 516804--516837 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
516794 ATTCGAGTTT
* *
516804 GAGTTTGAGTTTGAATC
1 GAGTTCGAGCTTGAATC
516821 GAGTTCGAGCTTGAATC
1 GAGTTCGAGCTTGAATC
516838 AAGCTCAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.12, G:0.29, T:0.35
Consensus pattern (17 bp):
GAGTTCGAGCTTGAATC
Done.