Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold444
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: 554371
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
File 2 of 5
Found at i:141538 original size:13 final size:12
Alignment explanation
Indices: 141520--141566 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 12
141510 ATTTTAATTT
141520 TTTATTATCAATA
1 TTTATTAT-AATA
141533 TTTATTATAATTA
1 TTTATTATAA-TA
* *
141546 ATTATAATAATA
1 TTTATTATAATA
141558 TTTATTATA
1 TTTATTATA
141567 TTTATAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (12 bp):
TTTATTATAATA
Found at i:141562 original size:25 final size:27
Alignment explanation
Indices: 141529--141582 Score: 85
Period size: 25 Copynumber: 2.1 Consensus size: 27
141519 TTTTATTATC
141529 AATATTTATTATA-AT-TAATTATAAT
1 AATATTTATTATATATATAATTATAAT
*
141554 AATATTTATTATATTTATAATTATAAT
1 AATATTTATTATATATATAATTATAAT
141581 AA
1 AA
141583 ACACAATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 13 0.50
26 1 0.04
27 12 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
AATATTTATTATATATATAATTATAAT
Found at i:141909 original size:16 final size:16
Alignment explanation
Indices: 141872--141910 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
141862 TTTATGATAT
141872 AATTATATTTAAAATA
1 AATTATATTTAAAATA
**
141888 TTTTATATTTAAAATA
1 AATTATATTTAAAATA
141904 AATTATA
1 AATTATA
141911 ATACATTAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTATATTTAAAATA
Found at i:141954 original size:2 final size:2
Alignment explanation
Indices: 141949--142002 Score: 56
Period size: 2 Copynumber: 25.5 Consensus size: 2
141939 ATTTTGAAAC
*
141949 AT AT AT TT AT AT CAT AT CAT AT GAT A- AT AT AT CAT 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
141992 AT AT AT AT AT A
1 AT AT AT AT AT A
142003 ATCGAATTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
1 1 0.02
2 36 0.80
3 8 0.18
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:141982 original size:15 final size:14
Alignment explanation
Indices: 141962--142004 Score: 61
Period size: 15 Copynumber: 3.0 Consensus size: 14
141952 TATTTATATC
141962 ATATCATATGATAAT
1 ATATCATAT-ATAAT
141977 ATATCATATATATAT
1 ATATCATATATA-AT
141992 ATAT-ATATATAAT
1 ATATCATATATAAT
142005 CGAATTTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 2 0.07
14 10 0.37
15 15 0.56
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (14 bp):
ATATCATATATAAT
Found at i:144350 original size:20 final size:20
Alignment explanation
Indices: 144325--144365 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
144315 GAATTTAGTA
*
144325 AAAATAATTAC-TTTTAATAT
1 AAAATAA-TACATTATAATAT
144345 AAAATAATACATTATAATAT
1 AAAATAATACATTATAATAT
144365 A
1 A
144366 TTAAATATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAATAATACATTATAATAT
Found at i:146690 original size:19 final size:19
Alignment explanation
Indices: 146668--146715 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
146658 AATTTGATTT
146668 AAATTATTTTTAATA-ATA
1 AAATTATTTTTAATATATA
* *
146686 AAAATA-TATTAATATATA
1 AAATTATTTTTAATATATA
146704 AAATATATTTTT
1 AAAT-TATTTTT
146716 TAATTTTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
17 7 0.30
18 11 0.48
19 2 0.09
20 3 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AAATTATTTTTAATATATA
Found at i:146697 original size:17 final size:17
Alignment explanation
Indices: 146677--146712 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
146667 TAAATTATTT
146677 TTAATA-ATAAAAATATA
1 TTAATATAT-AAAATATA
146694 TTAATATATAAAATATA
1 TTAATATATAAAATATA
146711 TT
1 TT
146713 TTTTAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.89
18 2 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAATATATAAAATATA
Found at i:147015 original size:20 final size:20
Alignment explanation
Indices: 146964--147015 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
146954 AATTTAAAAG
*
146964 TTTATTTAATTATTTATTAT
1 TTTATTTAAATATTTATTAT
* *
146984 ATTATTAAAAATATTT-TTATT
1 TTTATT-TAAATATTTATTA-T
147005 TTTATTTAAAT
1 TTTATTTAAAT
147016 TTAATTATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTATTTAAATATTTATTAT
Found at i:148248 original size:22 final size:22
Alignment explanation
Indices: 148204--148248 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
148194 ATTATATATT
* **
148204 TATTAATATTTTTTTTGCCAAA
1 TATTAATAATTTTTTTAACAAA
*
148226 TATTAATAATTTTTTTAATAAA
1 TATTAATAATTTTTTTAACAAA
148248 T
1 T
148249 GTAATACTTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (22 bp):
TATTAATAATTTTTTTAACAAA
Found at i:148398 original size:25 final size:24
Alignment explanation
Indices: 148370--148423 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
148360 TTAATAATGT
148370 TATAAATTTAAATTATAATCACATA
1 TATAAATTTAAATTAT-ATCACATA
* * * *
148395 TAT-ATTTTTAATTATGTCACATT
1 TATAAATTTAAATTATATCACATA
148418 TATAAA
1 TATAAA
148424 AATTATTAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
23 9 0.39
24 11 0.48
25 3 0.13
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.46
Consensus pattern (24 bp):
TATAAATTTAAATTATATCACATA
Found at i:148606 original size:3 final size:3
Alignment explanation
Indices: 148598--148642 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
148588 CACTAAGCAT
148598 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
148643 TTTGTAAGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:149204 original size:68 final size:68
Alignment explanation
Indices: 149095--149311 Score: 299
Period size: 68 Copynumber: 3.2 Consensus size: 68
149085 TTAATTTATC
* ** * * *
149095 GATTTGGTGATTTGTCATTATTGATTAAATGAGAGATTTAGTAGTTTATCATTGTTGATTAAATA
1 GATTTGGTGGTTTACCATTATTGACTAAATGAGAGATTTAGTAGTTTACCATTGTTGATTAAATG
*
149160 AGT
66 GGT
* * * *
149163 GATTTGGTGGTTTACCATTGTTGACTAAATTAGAGATTTAGTAGTTTGCCATTATTGATTAAATG
1 GATTTGGTGGTTTACCATTATTGACTAAATGAGAGATTTAGTAGTTTACCATTGTTGATTAAATG
149228 GGT
66 GGT
* * *
149231 GATTTGGTGGTTTACTATTATTAACTAAATGAGAGATTTAGTAGTTTACCGTTGTTGATTAAATG
1 GATTTGGTGGTTTACCATTATTGACTAAATGAGAGATTTAGTAGTTTACCATTGTTGATTAAATG
149296 GGT
66 GGT
*
149299 GATTTGATGGTTT
1 GATTTGGTGGTTT
149312 TTACCAAACT
Statistics
Matches: 130, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
68 130 1.00
ACGTcount: A:0.28, C:0.05, G:0.23, T:0.44
Consensus pattern (68 bp):
GATTTGGTGGTTTACCATTATTGACTAAATGAGAGATTTAGTAGTTTACCATTGTTGATTAAATG
GGT
Found at i:149244 original size:102 final size:102
Alignment explanation
Indices: 149105--149294 Score: 238
Period size: 102 Copynumber: 1.9 Consensus size: 102
149095 GATTTGGTGA
* * * * * *
149105 TTTGTCATTATTGATTAAATGAGAGATTTAGTAGTTTA-TCATTGTTGATTAAATAAGTGATTTG
1 TTTGCCATTATTGATTAAATGAGAGATTTAGTAGTTTACT-ATTATTAACTAAATAAGAGATTTA
*
149169 GTGGTTTACCATTGTTGACTAAATTAGAGATTTAGTAG
65 GTAGTTTACCATTGTTGACTAAATTAGAGATTTAGTAG
* * * * *
149207 TTTGCCATTATTGATTAAATGGGTGATTTGGTGGTTTACTATTATTAACTAAATGAGAGATTTAG
1 TTTGCCATTATTGATTAAATGAGAGATTTAGTAGTTTACTATTATTAACTAAATAAGAGATTTAG
* *
149272 TAGTTTACCGTTGTTGATTAAAT
66 TAGTTTACCATTGTTGACTAAAT
149295 GGGTGATTTG
Statistics
Matches: 73, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
102 72 0.99
103 1 0.01
ACGTcount: A:0.29, C:0.06, G:0.21, T:0.44
Consensus pattern (102 bp):
TTTGCCATTATTGATTAAATGAGAGATTTAGTAGTTTACTATTATTAACTAAATAAGAGATTTAG
TAGTTTACCATTGTTGACTAAATTAGAGATTTAGTAG
Found at i:149303 original size:34 final size:34
Alignment explanation
Indices: 149110--149295 Score: 201
Period size: 34 Copynumber: 5.5 Consensus size: 34
149100 GGTGATTTGT
* *
149110 CATTATTGATTAAATGAGAGATTTAGTAGTTTAT
1 CATTGTTGATTAAATGAGAGATTTAGTAGTTTAC
* * * *
149144 CATTGTTGATTAAATAAGTGATTTGGTGGTTTAC
1 CATTGTTGATTAAATGAGAGATTTAGTAGTTTAC
* * *
149178 CATTGTTGACTAAATTAGAGATTTAGTAGTTTGC
1 CATTGTTGATTAAATGAGAGATTTAGTAGTTTAC
* * * * *
149212 CATTATTGATTAAATGGGTGATTTGGTGGTTTAC
1 CATTGTTGATTAAATGAGAGATTTAGTAGTTTAC
* * * *
149246 TATTATTAACTAAATGAGAGATTTAGTAGTTTAC
1 CATTGTTGATTAAATGAGAGATTTAGTAGTTTAC
*
149280 CGTTGTTGATTAAATG
1 CATTGTTGATTAAATG
149296 GGTGATTTGA
Statistics
Matches: 120, Mismatches: 32, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
34 120 1.00
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.43
Consensus pattern (34 bp):
CATTGTTGATTAAATGAGAGATTTAGTAGTTTAC
Found at i:153778 original size:34 final size:34
Alignment explanation
Indices: 153731--153932 Score: 280
Period size: 34 Copynumber: 5.9 Consensus size: 34
153721 GTTTGCCATT
* * *
153731 GATTTGGTGGTTTACCATTATTGATTAAATGAGA
1 GATTTGGTAGTTTACCATTGTTGATTAAATGGGA
*
153765 GATTTGGTAGTTTACCATTGTTGATTAAATGGGT
1 GATTTGGTAGTTTACCATTGTTGATTAAATGGGA
* *
153799 GATTTGGTGGTTTACCATTGTTGACTAAATGGGA
1 GATTTGGTAGTTTACCATTGTTGATTAAATGGGA
* * *
153833 GATTTGGTAGTTTGCCATTGTTGATTAAATGAGT
1 GATTTGGTAGTTTACCATTGTTGATTAAATGGGA
* *
153867 GATTTGGTGGTTTGA-CATTGTTGACTAAATGGGA
1 GATTTGGTAGTTT-ACCATTGTTGATTAAATGGGA
*
153901 GATTTGGTAGTTTGCCATTGTTGATTAAATGG
1 GATTTGGTAGTTTACCATTGTTGATTAAATGG
153933 TGATTTGATG
Statistics
Matches: 146, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
34 146 1.00
ACGTcount: A:0.24, C:0.06, G:0.28, T:0.42
Consensus pattern (34 bp):
GATTTGGTAGTTTACCATTGTTGATTAAATGGGA
Found at i:153807 original size:68 final size:68
Alignment explanation
Indices: 153730--153946 Score: 357
Period size: 68 Copynumber: 3.2 Consensus size: 68
153720 AGTTTGCCAT
* * * *
153730 TGATTTGGTGGTTTACCATTATTGATTAAATGAGAGATTTGGTAGTTTACCATTGTTGATTAAAT
1 TGATTTGGTGGTTTACCATTGTTGACTAAATGGGAGATTTGGTAGTTTGCCATTGTTGATTAAAT
153795 GGG
66 GGG
153798 TGATTTGGTGGTTTACCATTGTTGACTAAATGGGAGATTTGGTAGTTTGCCATTGTTGATTAAAT
1 TGATTTGGTGGTTTACCATTGTTGACTAAATGGGAGATTTGGTAGTTTGCCATTGTTGATTAAAT
*
153863 GAG
66 GGG
153866 TGATTTGGTGGTTTGA-CATTGTTGACTAAATGGGAGATTTGGTAGTTTGCCATTGTTGATTAAA
1 TGATTTGGTGGTTT-ACCATTGTTGACTAAATGGGAGATTTGGTAGTTTGCCATTGTTGATTAAA
153930 T-GG
65 TGGG
*
153933 TGATTTGATGGTTT
1 TGATTTGGTGGTTT
153947 TTACCAAACC
Statistics
Matches: 141, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
67 14 0.10
68 126 0.89
69 1 0.01
ACGTcount: A:0.24, C:0.06, G:0.28, T:0.43
Consensus pattern (68 bp):
TGATTTGGTGGTTTACCATTGTTGACTAAATGGGAGATTTGGTAGTTTGCCATTGTTGATTAAAT
GGG
Found at i:155534 original size:27 final size:26
Alignment explanation
Indices: 155489--155559 Score: 97
Period size: 27 Copynumber: 2.7 Consensus size: 26
155479 AACATGCCAT
*
155489 CATTTTTGACAAATAAAAAAAACCAC
1 CATTTTTGACAAACAAAAAAAACCAC
* *
155515 CATTTTTGACAAACACAAAATAACTAC
1 CATTTTTGACAAACA-AAAAAAACCAC
*
155542 CATTTTTTACAAACAAAA
1 CATTTTTGACAAACAAAA
155560 GGTGGCTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 17 0.43
27 23 0.57
ACGTcount: A:0.51, C:0.20, G:0.03, T:0.27
Consensus pattern (26 bp):
CATTTTTGACAAACAAAAAAAACCAC
Found at i:157470 original size:21 final size:22
Alignment explanation
Indices: 157432--157477 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
157422 ATCTGTTGAA
* **
157432 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTACGGAGTACT
157453 ACTCCACCTGCTACGGAGTACT
1 ACTCCACCTGCTACGGAGTACT
157475 ACT
1 ACT
157478 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.22, C:0.30, G:0.17, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTACGGAGTACT
Found at i:157743 original size:29 final size:29
Alignment explanation
Indices: 157700--157764 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
157690 AATCATAATC
*
157700 AGTAGCAATTAAAGAAGTCTAAGATTAAG
1 AGTAGTAATTAAAGAAGTCTAAGATTAAG
* *
157729 TGTAGTAATTGAAGAAGTCTAAGATTAAG
1 AGTAGTAATTAAAGAAGTCTAAGATTAAG
157758 AGTAGTA
1 AGTAGTA
157765 TTGGAAATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.45, C:0.05, G:0.23, T:0.28
Consensus pattern (29 bp):
AGTAGTAATTAAAGAAGTCTAAGATTAAG
Found at i:158013 original size:16 final size:16
Alignment explanation
Indices: 157992--158022 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
157982 ATTAATATGT
*
157992 ATTATATGAATTATAA
1 ATTATATAAATTATAA
158008 ATTATATAAATTATA
1 ATTATATAAATTATA
158023 TGAGTCAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
ATTATATAAATTATAA
Found at i:158509 original size:41 final size:42
Alignment explanation
Indices: 158427--158527 Score: 141
Period size: 41 Copynumber: 2.4 Consensus size: 42
158417 AGCTTGACTC
** * *
158427 ATTTATTTATTACAAAGACCAAGACTATTCGATATATTGGTT
1 ATTTATTTATTGTAAAGACCAAGACAATTCGATATACTGGTT
* *
158469 ATTTATTTATTGTAAA-ACCAAGACAATTGGCTATACTGGTT
1 ATTTATTTATTGTAAAGACCAAGACAATTCGATATACTGGTT
158510 ATTTATTTATTGTAAAGA
1 ATTTATTTATTGTAAAGA
158528 TGTACAGACC
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 37 0.71
42 15 0.29
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.42
Consensus pattern (42 bp):
ATTTATTTATTGTAAAGACCAAGACAATTCGATATACTGGTT
Found at i:159289 original size:9 final size:9
Alignment explanation
Indices: 159272--159312 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
159262 TTTGTTGGTT
*
159272 TATATATTA
1 TATAAATTA
159281 TATAAA-T-
1 TATAAATTA
159288 TATAAATTA
1 TATAAATTA
*
159297 TATTAATTA
1 TATAAATTA
159306 TATAAAT
1 TATAAAT
159313 CGGATTAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
7 6 0.22
8 2 0.07
9 19 0.70
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
TATAAATTA
Found at i:159296 original size:16 final size:16
Alignment explanation
Indices: 159271--159307 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
159261 TTTTGTTGGT
*
159271 TTATATATTATATAAA
1 TTATAAATTATATAAA
*
159287 TTATAAATTATATTAA
1 TTATAAATTATATAAA
159303 TTATA
1 TTATA
159308 TAAATCGGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTATAAATTATATAAA
Found at i:159352 original size:15 final size:16
Alignment explanation
Indices: 159332--159364 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
159322 ATATAAATTT
159332 TTTAATTTAA-ATTAA
1 TTTAATTTAATATTAA
159347 TTTAATTTAATATTAA
1 TTTAATTTAATATTAA
159363 TT
1 TT
159365 ATAAATCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTAATTTAATATTAA
Found at i:160470 original size:22 final size:22
Alignment explanation
Indices: 160445--160505 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 22
160435 TTAAATTATT
* *
160445 ATTTAATAATAAAAATATTTGA
1 ATTTAATAATAAAAATATATAA
160467 A-TT--TAATAAAAATATATAA
1 ATTTAATAATAAAAATATATAA
160486 ATATTAAT-ATAAAAATATAT
1 AT-TTAATAATAAAAATATAT
160506 TTTTTATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
19 15 0.45
21 4 0.12
22 13 0.39
23 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
ATTTAATAATAAAAATATATAA
Found at i:162402 original size:3 final size:3
Alignment explanation
Indices: 162394--162432 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
162384 AGGCATCTAA
162394 AAT 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 AAT
162433 TTTTATGTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:165854 original size:22 final size:22
Alignment explanation
Indices: 165778--165859 Score: 85
Period size: 22 Copynumber: 3.7 Consensus size: 22
165768 CAATTGGGTT
* *
165778 TTTAA-TTTAGGTTTAGATGGG
1 TTTAAGTTTAAGTTTAAATGGG
* * *
165799 CTTAAGTTTAGGTTTAAATAGG
1 TTTAAGTTTAAGTTTAAATGGG
*
165821 TATTTAGTTTAAGTTTAAATGGG
1 T-TTAAGTTTAAGTTTAAATGGG
*
165844 TTTAAGTTTAAATTTA
1 TTTAAGTTTAAGTTTA
165860 CAGTTTATTA
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
21 4 0.08
22 27 0.54
23 19 0.38
ACGTcount: A:0.30, C:0.01, G:0.21, T:0.48
Consensus pattern (22 bp):
TTTAAGTTTAAGTTTAAATGGG
Found at i:166218 original size:21 final size:22
Alignment explanation
Indices: 166194--166244 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
166184 TAAAAGGTTC
*
166194 AAAATTTAAA-TTATGAATGAA
1 AAAATTGAAATTTATGAATGAA
*
166215 AAAATTGAAATTTATGGATGAA
1 AAAATTGAAATTTATGAATGAA
166237 AGAAATTG
1 A-AAATTG
166245 TTTTGAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 9 0.35
22 11 0.42
23 6 0.23
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (22 bp):
AAAATTGAAATTTATGAATGAA
Found at i:166258 original size:2 final size:2
Alignment explanation
Indices: 166251--166286 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
166241 ATTGTTTTGA
166251 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
166287 GACAAGTACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:166671 original size:13 final size:12
Alignment explanation
Indices: 166653--166695 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
166643 TTTTAATTTT
166653 TTTATTATCAATA
1 TTTATTAT-AATA
166666 TTTATTATAATTA
1 TTTATTATAA-TA
* *
166679 ATTATAATAATA
1 TTTATTATAATA
166691 TTTAT
1 TTTAT
166696 AACGTCTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 8 0.31
13 18 0.69
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTATTATAATA
Found at i:167000 original size:23 final size:23
Alignment explanation
Indices: 166974--167023 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
166964 TATTTAATAC
* *
166974 AAAAATATATAATTATTAATTTTA
1 AAAAATA-ATAATAATTAATATTA
166998 AAAAATAATAATAATTAATATTA
1 AAAAATAATAATAATTAATATTA
167021 AAA
1 AAA
167024 GATTAGAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AAAAATAATAATAATTAATATTA
Found at i:167618 original size:3 final size:3
Alignment explanation
Indices: 167612--167644 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
167602 TTTTTTTAAA
167612 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
167645 TTGTAGCTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:167923 original size:29 final size:29
Alignment explanation
Indices: 167866--167925 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
167856 CGTTGGATGA
* * *
167866 TTCAAATATTGTTGTCTTGACGGAGAGCT
1 TTCAAATATTGTTGCCCTGACGGACAGCT
*
167895 TTCAAATATTGTTGCCCTGATGGACAGCT
1 TTCAAATATTGTTGCCCTGACGGACAGCT
167924 TT
1 TT
167926 ACGCAAAGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (29 bp):
TTCAAATATTGTTGCCCTGACGGACAGCT
Found at i:168282 original size:34 final size:34
Alignment explanation
Indices: 168236--168453 Score: 273
Period size: 34 Copynumber: 6.5 Consensus size: 34
168226 GTAAAAACCA
**
168236 CCATTTAATCAACAATGACAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
168270 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
168304 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
168338 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
168371 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
168405 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
168438 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
168454 TCTCCCACTT
Statistics
Matches: 161, Mismatches: 18, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 45 0.28
34 114 0.71
35 2 0.01
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:168411 original size:67 final size:67
Alignment explanation
Indices: 168234--168453 Score: 307
Period size: 67 Copynumber: 3.3 Consensus size: 67
168224 TGGTAAAAAC
* * *
168234 CACCATTTAATCAACAATGAC-AACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCA
1 CACCATTTAATCAACAATGGCAAACC-ACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
168298 AAT
65 AAT
* * * *
168301 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACCACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
168366 AAT
65 AAT
* * * * *
168369 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACCACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
168434 AT
66 AT
168436 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
168454 TCTCCCACTT
Statistics
Matches: 133, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
67 75 0.56
68 56 0.42
69 2 0.02
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACCACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:168412 original size:101 final size:101
Alignment explanation
Indices: 168234--168453 Score: 345
Period size: 101 Copynumber: 2.2 Consensus size: 101
168224 TGGTAAAAAC
* *
168234 CACCATTTAATCAACAATGACAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGACAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAA
*
168299 ATCACCCATTTAATCAACAATGGTAAGCTACCAAATTT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAA--T
** *
168337 C-CCATTTAATCAACAATGGTAAGCTACCAAATCT-CCATTTAGTCAACAATGGCAAACCACCAA
1 CACCATTTAATCAACAATGACAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAA
*
168400 ATCACCCATTTAATCAACAATGGTAAACTACTAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
168436 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
168454 TCTCCCACTT
Statistics
Matches: 109, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
99 2 0.02
100 16 0.15
101 60 0.55
102 30 0.28
103 1 0.01
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGACAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:172546 original size:19 final size:19
Alignment explanation
Indices: 172519--172581 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
172509 TCACGTGTAC
* *
172519 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
172538 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
172557 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
172576 AGTACC
1 AGTACC
172582 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:172928 original size:34 final size:34
Alignment explanation
Indices: 172882--173097 Score: 269
Period size: 34 Copynumber: 6.4 Consensus size: 34
172872 GTAAAAACCA
*
172882 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
172916 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
172950 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
172984 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
173017 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * * *
173051 CCATTTAATCAACAATGATAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
173084 CCATTTAATCAACA
1 CCATTTAATCAACA
173098 GGTACTTTGA
Statistics
Matches: 159, Mismatches: 18, Indels: 11
0.85 0.10 0.06
Matches are distributed among these distances:
33 43 0.27
34 114 0.72
35 2 0.01
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:172996 original size:68 final size:67
Alignment explanation
Indices: 172880--173097 Score: 310
Period size: 67 Copynumber: 3.2 Consensus size: 67
172870 TGGTAAAAAC
* * *
172880 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
172945 AT
66 AT
* * *
172947 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
173012 AAT
65 AAT
* * * * * * *
173015 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGATAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
173080 AT
66 AT
173082 CACCATTTAATCAACA
1 CACCATTTAATCAACA
173098 GGTACTTTGA
Statistics
Matches: 133, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 72 0.54
68 61 0.46
ACGTcount: A:0.41, C:0.28, G:0.07, T:0.24
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:175206 original size:29 final size:29
Alignment explanation
Indices: 175164--175234 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
175154 TTATGAGATA
**
175164 ATATTTTAAAAAATTATTATTATAATAATTTT
1 ATATTTT--AAAATTATTAAAATAAT-ATTTT
* *
175196 -TATTTTAAAATTTTTAAAATAATTTTTT
1 ATATTTTAAAATTATTAAAATAATATTTT
175224 ATATTTTAAAA
1 ATATTTTAAAA
175235 ACAATTATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
28 4 0.12
29 24 0.71
31 6 0.18
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
ATATTTTAAAATTATTAAAATAATATTTT
Found at i:175229 original size:21 final size:22
Alignment explanation
Indices: 175205--175254 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
175195 TTATTTTAAA
* * *
175205 ATTTTTAAAATAATTTTTTAT-
1 ATTTTTAAAACAATTATTAATC
*
175226 ATTTTAAAAACAATTATTAATC
1 ATTTTTAAAACAATTATTAATC
175248 ATTTTTA
1 ATTTTTA
175255 GTTCCTCTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTTTTAAAACAATTATTAATC
Found at i:180326 original size:27 final size:28
Alignment explanation
Indices: 180259--180329 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 28
180249 AAACAAGCCT
* * *
180259 CCATATTTGACAAATACAAAAGAAACTA
1 CCATTTTTGACAAACACAAAAGAAACCA
*
180287 CCATTTTTGACAAACACAAAA-TAACCA
1 CCATTTTTGACAAACACAAAAGAAACCA
*
180314 CCATTTTTTACAAACA
1 CCATTTTTGACAAACA
180330 AATGGGTGGC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
27 19 0.50
28 19 0.50
ACGTcount: A:0.48, C:0.23, G:0.04, T:0.25
Consensus pattern (28 bp):
CCATTTTTGACAAACACAAAAGAAACCA
Found at i:184713 original size:20 final size:20
Alignment explanation
Indices: 184688--184726 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
184678 AAGAATTGAA
184688 GAGGGATACAAGAGAAGGAT
1 GAGGGATACAAGAGAAGGAT
**
184708 GAGGGATACTTGAGAAGGA
1 GAGGGATACAAGAGAAGGA
184727 GGAGTGAGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.41, T:0.13
Consensus pattern (20 bp):
GAGGGATACAAGAGAAGGAT
Found at i:184849 original size:28 final size:27
Alignment explanation
Indices: 184789--184880 Score: 98
Period size: 28 Copynumber: 3.4 Consensus size: 27
184779 TAGTCACAAA
* * *
184789 TTTTGACAAAT--AAACAAGCCTCCAT
1 TTTTGACAAATACAAAAAAACCACCAT
*
184814 ATTTGACAAATACAAAAGAAACCACCAT
1 TTTTGACAAATACAAAA-AAACCACCAT
* *
184842 TTTTGACAAACACAAAATAACCACCAT
1 TTTTGACAAATACAAAAAAACCACCAT
*
184869 TTTTTACAAATA
1 TTTTGACAAATA
184881 AATAGGTGAC
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
25 10 0.18
27 22 0.40
28 23 0.42
ACGTcount: A:0.47, C:0.22, G:0.05, T:0.26
Consensus pattern (27 bp):
TTTTGACAAATACAAAAAAACCACCAT
Found at i:186489 original size:21 final size:21
Alignment explanation
Indices: 186463--186517 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
186453 AACAATTTCG
186463 AATATAACACAA-AAAAATAAA
1 AATATAACACAACAAAAA-AAA
* *
186484 AATATAATACAACATAAAAAA
1 AATATAACACAACAAAAAAAA
186505 AATACTAACACAA
1 AATA-TAACACAA
186518 TACTCACCCC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.71, C:0.13, G:0.00, T:0.16
Consensus pattern (21 bp):
AATATAACACAACAAAAAAAA
Found at i:187421 original size:123 final size:123
Alignment explanation
Indices: 187160--187554 Score: 472
Period size: 124 Copynumber: 3.2 Consensus size: 123
187150 CATTCAACAC
* * * * *
187160 TCATAAAATTTTAAAATTGAATTATACAACGTTTATTAAGACGCATAAGTAATTCTCAATCATAA
1 TCATAAAATATTAAAATTGAATTATACAACATTTATTAAGACGCATAA-AAATACTCAACCATAA
** ** *
187225 AAATCTTTAAAAAAAA-TCAAGAGAACTCAATGTTAGCATGAAGTCAATAGAGTTTTATG
65 AAA-AGTTAAAAAAAATTCAAGAGAACTCAATGTTAATATGAAGTCAATAGACTTTTATG
* * *
187284 -CTATAAAATGTTAAAATTGAATTATACAACATTTATTAAGACACATAAAAAAACTCAACCATAA
1 TC-ATAAAATATTAAAATTGAATTATACAACATTTATTAAGACGCATAAAAATACTCAACCATAA
** * * * *
187348 AAAAGTTAAAAAAAATTCAAGA-AGACTCAAAATTAATATGAAGTTAATAAATTTTTTTG
65 AAAAGTTAAAAAAAATTCAAGAGA-ACTCAATGTTAATATGAAGTCAATAGACTTTTATG
* * * * * * *
187407 TCATAAAATATTAAAATTAAATTATATAACATTTTTTGAGATGTATCAAAAATATTCAACCATAA
1 TCATAAAATATTAAAATTGAATTATACAACATTTATTAAGACGCAT-AAAAATACTCAACCATAA
*
187472 AAAAGTTAAAAGAAATTCAAGAGAACTCAATGTTAATATGAAGTCAATAGACTTTTATG
65 AAAAGTTAAAAAAAATTCAAGAGAACTCAATGTTAATATGAAGTCAATAGACTTTTATG
*
187531 CCATAAAATATTAAAATTGAATTA
1 TCATAAAATATTAAAATTGAATTA
187555 GATATATTAA
Statistics
Matches: 229, Mismatches: 36, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
122 11 0.05
123 85 0.37
124 132 0.58
125 1 0.00
ACGTcount: A:0.49, C:0.10, G:0.09, T:0.32
Consensus pattern (123 bp):
TCATAAAATATTAAAATTGAATTATACAACATTTATTAAGACGCATAAAAATACTCAACCATAAA
AAAGTTAAAAAAAATTCAAGAGAACTCAATGTTAATATGAAGTCAATAGACTTTTATG
Found at i:187590 original size:109 final size:108
Alignment explanation
Indices: 187445--187769 Score: 351
Period size: 109 Copynumber: 3.0 Consensus size: 108
187435 ACATTTTTTG
* * *
187445 AGATGTATCAAAAATATTCAACCATAAAAAAGTTAAAAGAAATTCAAGAGAACTCAATGTTAATA
1 AGATATATCAAAAATATTTAACCATAAAAAA-TTAAAAGAAATTCAAGAGAACTCAATGTTAACA
*
187510 TGAAGTCAATAGACTTTTATGCCATAAAATATTAAAATTGAATT
65 TGAAGTCAATAGACTTTTATGCCATAAAATGTTAAAATTGAATT
* * * *
187554 AGATATATTAAAAATATTTAGCGATACAAAAATTAAAAGAAATTCAAGATG-ACTCAATGTTAGC
1 AGATATATCAAAAATATTTAACCATA-AAAAATTAAAAGAAATTCAAGA-GAACTCAATGTTAAC
* * * * *
187618 ATGAAGTCAATGGAC--TT-TGTCATAAAATGTTAAAACTAAACT
64 ATGAAGTCAATAGACTTTTATGCCATAAAATGTTAAAATTGAATT
* * *
187660 AAATCTATCAAAAATATTTAACCACAAAAAAAATATAAAA-AAA-TCAAGA-ACACTCAATGTTA
1 AGATATATCAAAAATATTTAA-C-CATAAAAAAT-TAAAAGAAATTCAAGAGA-ACTCAATGTTA
* **
187722 ACATGAAGTCAA-AGGACTTTTATACCATAAAATGTTATTATTGAATT
62 ACATGAAGTCAATA-GACTTTTATGCCATAAAATGTTAAAATTGAATT
187769 A
1 A
187770 TACAAAGTTT
Statistics
Matches: 177, Mismatches: 28, Indels: 22
0.78 0.12 0.10
Matches are distributed among these distances:
106 68 0.38
107 12 0.07
108 9 0.05
109 82 0.46
110 6 0.03
ACGTcount: A:0.50, C:0.11, G:0.10, T:0.29
Consensus pattern (108 bp):
AGATATATCAAAAATATTTAACCATAAAAAATTAAAAGAAATTCAAGAGAACTCAATGTTAACAT
GAAGTCAATAGACTTTTATGCCATAAAATGTTAAAATTGAATT
Found at i:187715 original size:106 final size:105
Alignment explanation
Indices: 187450--187741 Score: 327
Period size: 106 Copynumber: 2.7 Consensus size: 105
187440 TTTTGAGATG
* * *
187450 TATCAAAAATATTCAACCATAAAAAAGTTAAAAGAAATTCAAGAGAACTCAATGTTAATATGAAG
1 TATCAAAAATATTTAACCATAAAAAAATTAAAAGAAATTCAAGA-AACTCAATGTTAACATGAAG
* * * * *
187515 TCAATAGACTTTTATGCCATAAAATATTAAAATTGAATTAGATA
65 TCAATGGAC--TT-TGCCATAAAATATTAAAACTAAACTAAATA
* * * * * *
187559 TATTAAAAATATTTAGCGATACAAAAATTAAAAGAAATTCAAGATGACTCAATGTTAGCATGAAG
1 TATCAAAAATATTTAACCATAAAAAAATTAAAAGAAATTCAAGA-AACTCAATGTTAACATGAAG
* * *
187624 TCAATGGACTTTGTCATAAAATGTTAAAACTAAACTAAATC
65 TCAATGGACTTTGCCATAAAATATTAAAACTAAACTAAATA
*
187665 TATCAAAAATATTTAACCACAAAAAAAATATAAAA-AAA-TCAAGAACACTCAATGTTAACATGA
1 TATCAAAAATATTTAACCA-TAAAAAAAT-TAAAAGAAATTCAAGAA-ACTCAATGTTAACATGA
*
187728 AGTCAAAGGACTTT
63 AGTCAATGGACTTT
187742 TATACCATAA
Statistics
Matches: 154, Mismatches: 26, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
106 74 0.48
107 12 0.08
108 5 0.03
109 63 0.41
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (105 bp):
TATCAAAAATATTTAACCATAAAAAAATTAAAAGAAATTCAAGAAACTCAATGTTAACATGAAGT
CAATGGACTTTGCCATAAAATATTAAAACTAAACTAAATA
Found at i:187922 original size:125 final size:124
Alignment explanation
Indices: 187666--187922 Score: 284
Period size: 125 Copynumber: 2.1 Consensus size: 124
187656 AACTAAATCT
187666 ATCAAAAATATTTAACCACAAAAAAAATATAAAAAAATCAAGAACACTCAATGTTAACATGAAGT
1 ATCAAAAATATTTAACCACAAAAAAAATATAAAAAAATCAAGAACACTCAATGTTAACATGAAGT
* ** * * *
187731 CAAAGGACTTTTATACCATAAAATGTTATTATTGAATTATACAAAGTTTACTAGGACGT
66 CAAAGGACTTTTATACCATAAAATATTAAAATTAAATTATACAAAGTTTACTAAGACGC
* * * * * ** *
187790 ATAAAAAATATTTAACTATAAAAAAAGT-TACAAGAAATTCAAGATGACTCAATGTTAACATTAA
1 ATCAAAAATATTTAACCACAAAAAAAATATA-AA-AAAATCAAGAACACTCAATGTTAACATGAA
* * * * ** *
187854 GTCAATA-GACTTTTATGCCATAAAATATTAAAATTAAATTCTATAATGTTTGTTAAGATGC
64 GTCAA-AGGACTTTTATACCATAAAATATTAAAATTAAATTATACAAAGTTTACTAAGACGC
187915 ATCAAAAA
1 ATCAAAAA
187923 ACATGTTAAA
Statistics
Matches: 108, Mismatches: 22, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
123 2 0.02
124 26 0.24
125 79 0.73
126 1 0.01
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.30
Consensus pattern (124 bp):
ATCAAAAATATTTAACCACAAAAAAAATATAAAAAAATCAAGAACACTCAATGTTAACATGAAGT
CAAAGGACTTTTATACCATAAAATATTAAAATTAAATTATACAAAGTTTACTAAGACGC
Found at i:188021 original size:111 final size:109
Alignment explanation
Indices: 187809--188033 Score: 263
Period size: 111 Copynumber: 2.0 Consensus size: 109
187799 ATTTAACTAT
* * * ** *
187809 AAAAAAAGTTACAAGAAATTCAAGATGACTCAATGTTAACATTAAGTCAATAGACTTTTATGCCA
1 AAAAAAAGTTAAAAGAAATTCAAAAGGACTCAATGTTAACACAAAGTCAATAGACTTTTATGACA
* * * * *
187874 TAAAATATTAAAATTAAATTCTATAATGTTTGTTAAGATGCATC
66 TAAAATATTAAAATTAAATTATACAATATTTATTAAGACGCATC
* * *
187918 AAAAAACATGTTAAAAGAAATTCAAAAGGACTTAATTTTAGCACAAAGTCAAT-GAACTTTTATG
1 AAAAAA-A-GTTAAAAGAAATTCAAAAGGACTCAATGTTAACACAAAGTCAATAG-ACTTTTATG
* * *
187982 ACATAAAATGTTAAAATTGAATTATACAATATTTATTAAGACGTATC
63 ACATAAAATATTAAAATTAAATTATACAATATTTATTAAGACGCATC
188029 AAAAA
1 AAAAA
188034 TATTTAACCG
Statistics
Matches: 96, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
109 6 0.06
110 2 0.02
111 88 0.92
ACGTcount: A:0.48, C:0.10, G:0.11, T:0.32
Consensus pattern (109 bp):
AAAAAAAGTTAAAAGAAATTCAAAAGGACTCAATGTTAACACAAAGTCAATAGACTTTTATGACA
TAAAATATTAAAATTAAATTATACAATATTTATTAAGACGCATC
Found at i:188189 original size:127 final size:124
Alignment explanation
Indices: 187929--188273 Score: 343
Period size: 127 Copynumber: 2.7 Consensus size: 124
187919 AAAAACATGT
* * * * *
187929 TAAAAGAAATTCAAAAGGACTTAATTTTAGCACAAAGTCAATGAACTTTTATGACATAAAATGTT
1 TAAAA-AAATTCAAAAGGACTTAATATTAGCACGAAGTTAATGGACTTTTATGCCATAAAATGTT
* * *
187994 AAAATTGAATTATACAATATTTATTAAGACGTATCAAAAATATTTAACCGTAAAAAAGTTTAA
65 AAAATTGAATTATACAACATTTATTAAGACGTATAAAAAATATTTAACCATAAAAAA---TAA
* * * * * *
188057 AAAAAAAATTCAAGAGGACTTAATATTGGTATGAAGTTAATGGACTTTTATGCCATAAACTGTTA
1 TAAAAAAATTCAAAAGGACTTAATATTAGCACGAAGTTAATGGACTTTTATGCCATAAAATGTTA
* * * *
188122 AACTTGAATTATATATACAACATTTATTGAGAC-TAATAAAAAATATTTAACTATTAAAAA-AA
66 AAATTG-A--AT-TATACAACATTTATTAAGACGT-ATAAAAAATATTTAACCATAAAAAATAA
* * * * * *
188184 TAAAAAACATTTAAAAGGACTCAATATTAGCACGAAGTTAATGGATTTTTATGCTATATAATGTA
1 TAAAAAA-ATTCAAAAGGACTTAATATTAGCACGAAGTTAATGGACTTTTATGCCATAAAATGTT
* * *
188249 AAAATTGTATTGTACAACGTTTATT
65 AAAATTGAATTATACAACATTTATT
188274 GAGATTAATT
Statistics
Matches: 177, Mismatches: 34, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
124 13 0.07
125 2 0.01
127 63 0.36
128 57 0.32
130 3 0.02
131 39 0.22
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (124 bp):
TAAAAAAATTCAAAAGGACTTAATATTAGCACGAAGTTAATGGACTTTTATGCCATAAAATGTTA
AAATTGAATTATACAACATTTATTAAGACGTATAAAAAATATTTAACCATAAAAAATAA
Found at i:188236 original size:128 final size:124
Alignment explanation
Indices: 187930--188273 Score: 341
Period size: 128 Copynumber: 2.7 Consensus size: 124
187920 AAAACATGTT
* * * * * *
187930 AAAAGAAATTCAAAAGGACTTAATTTTAGCACAAAGTCAATGAACTTTTATGACATAAAATGTTA
1 AAAAAAAATTCAAAAGGACTTAATATTAGCACGAAGTTAATGGACTTTTATGCCATAAAATGTTA
* * *
187995 AAATTGAATTATACAATATTTATTAAGACGTATCAAAAATATTTAACCGTAAAAAAGTTTAA
66 AAATTGAATTATACAACATTTATTAAGACGTATAAAAAATATTTAACAGTAAAAAA---TAA
* * * * *
188057 AAAAAAAATTCAAGAGGACTTAATATTGGTATGAAGTTAATGGACTTTTATGCCATAAACTGTTA
1 AAAAAAAATTCAAAAGGACTTAATATTAGCACGAAGTTAATGGACTTTTATGCCATAAAATGTTA
* * * *
188122 AACTTGAATTATATATACAACATTTATTGAGAC-TAATAAAAAATATTTAACTATTAAAAAA-AT
66 AAATTG-A--AT-TATACAACATTTATTAAGACGT-ATAAAAAATATTTAAC-AGTAAAAAATAA
* * * * * * *
188185 AAAAAACATTTAAAAGGACTCAATATTAGCACGAAGTTAATGGATTTTTATGCTATATAATGTAA
1 AAAAAAAATTCAAAAGGACTTAATATTAGCACGAAGTTAATGGACTTTTATGCCATAAAATGTTA
* * *
188250 AAATTGTATTGTACAACGTTTATT
66 AAATTGAATTATACAACATTTATT
188274 GAGATTAATT
Statistics
Matches: 177, Mismatches: 34, Indels: 15
0.78 0.15 0.07
Matches are distributed among these distances:
124 13 0.07
125 2 0.01
127 59 0.33
128 60 0.34
130 3 0.02
131 33 0.19
132 7 0.04
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.33
Consensus pattern (124 bp):
AAAAAAAATTCAAAAGGACTTAATATTAGCACGAAGTTAATGGACTTTTATGCCATAAAATGTTA
AAATTGAATTATACAACATTTATTAAGACGTATAAAAAATATTTAACAGTAAAAAATAA
Found at i:189135 original size:29 final size:31
Alignment explanation
Indices: 189101--189169 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
189091 AAAAAGTAAC
189101 ACAAATATAATA-TAA-AAATAAAAATTTAT
1 ACAAATATAATATTAACAAATAAAAATTTAT
* * * * *
189130 ATAAATAAAATATTAACATATCATAATTTAT
1 ACAAATATAATATTAACAAATAAAAATTTAT
189161 ACAAATATA
1 ACAAATATA
189170 TAATAATACA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
29 10 0.32
30 3 0.10
31 18 0.58
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (31 bp):
ACAAATATAATATTAACAAATAAAAATTTAT
Found at i:190030 original size:27 final size:27
Alignment explanation
Indices: 189996--190051 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
189986 TAAACGTAAT
*
189996 AAATATT-ATTAT--AATTAATTA-AA
1 AAATATTAATTATAAAATTAATAATAA
190019 AAATATTAATTATAAAATTAATAATAA
1 AAATATTAATTATAAAATTAATAATAA
190046 AAATAT
1 AAATAT
190052 CAAAATAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 7 0.25
24 5 0.18
26 8 0.29
27 8 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
AAATATTAATTATAAAATTAATAATAA
Found at i:190047 original size:26 final size:24
Alignment explanation
Indices: 189992--190042 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
189982 ATTATAAACG
189992 TAAT-AAATATTATTATAATTAAT
1 TAATAAAATATTATTATAATTAAT
190015 TAA-AAAATATTAATTATAA--AAT
1 TAATAAAATATT-ATTATAATTAAT
190037 TAATAA
1 TAATAA
190043 TAAAAATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
22 6 0.24
23 12 0.48
24 7 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
TAATAAAATATTATTATAATTAAT
Found at i:190059 original size:26 final size:26
Alignment explanation
Indices: 190008--190059 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
189998 ATATTATTAT
* * *
190008 AATTAATTAAAAAATATTAATTATAA
1 AATTAATAAAAAAATATCAATAATAA
190034 AATTAATAATAAAAATATCAA-AATAA
1 AATTAATAA-AAAAATATCAATAATAA
190060 TTGAATAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
AATTAATAAAAAAATATCAATAATAA
Found at i:190668 original size:22 final size:22
Alignment explanation
Indices: 190601--190665 Score: 59
Period size: 23 Copynumber: 3.1 Consensus size: 22
190591 TCAATATTTA
190601 TAATTAAATTTAAAAT-AAAAA-
1 TAATTAAA-TTAAAATAAAAAAT
* *
190622 TAA-T--ATTAAAATAATAATT
1 TAATTAAATTAAAATAAAAAAT
190641 TAATTAAATTAAAATTAAAAAAT
1 TAATTAAATTAAAA-TAAAAAAT
190664 TA
1 TA
190666 TTATCATAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
17 7 0.21
18 4 0.12
19 3 0.09
20 2 0.06
21 3 0.09
22 7 0.21
23 8 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TAATTAAATTAAAATAAAAAAT
Found at i:191100 original size:20 final size:20
Alignment explanation
Indices: 191075--191114 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
191065 TTAATGTATG
191075 TTATAATATCTCTTTTGTTT
1 TTATAATATCTCTTTTGTTT
191095 TTATAATATCTCTTTTGTTT
1 TTATAATATCTCTTTTGTTT
191115 ATGAAATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.10, G:0.05, T:0.65
Consensus pattern (20 bp):
TTATAATATCTCTTTTGTTT
Found at i:194140 original size:109 final size:109
Alignment explanation
Indices: 194018--194395 Score: 496
Period size: 107 Copynumber: 3.5 Consensus size: 109
194008 GTCAAAAGAA
*
194018 ATTAGCATGAAGTCAATAAACTTTTATGTCATAAAATGTTAAAATTAAATTAGACATATCAAAAA
1 ATTAGCATGAAGTCAATAGACTTTTATGTCATAAAATGTTAAAATTAAATTAGACATATCAAAAA
*
194083 TACTTAACCATAAAAAAATTAAAAGAAATTCAAGAAGAATCAAT
66 TACTTAACCATAAAAAAATTAAAAGAAATTCAAGAAGACTCAAT
* * * * * *
194127 ATTAGTATGAAGTCAGTGGACTTTTATATCATAAAATTTTAAAATTGAATTAGACATATCAAAAA
1 ATTAGCATGAAGTCAATAGACTTTTATGTCATAAAATGTTAAAATTAAATTAGACATATCAAAAA
194192 TACTTAACCATAAAAAAA-TAAAA-AAATTCAAGAAGACTCAAT
66 TACTTAACCATAAAAAAATTAAAAGAAATTCAAGAAGACTCAAT
* * * * *
194234 TTTAGCATGAAGTCAATGGACGTTTATG-CTATAAAATGTTAAAATTGAATTAGACGTATCAAAA
1 ATTAGCATGAAGTCAATAGACTTTTATGTC-ATAAAATGTTAAAATTAAATTAGACATATCAAAA
* * * *
194298 ATATTTAACTATAAAATAAAATTAAAAGAAATTCAA-TAGTACTTAAT
65 ATACTTAACCAT-AAA-AAAATTAAAAGAAATTCAAGAAG-ACTCAAT
* * * *
194345 GTTAGCATGAAGTAAATAGA-TTTTATGCCATAAAATGTTAAGATTAAATTA
1 ATTAGCATGAAGTCAATAGACTTTTATGTCATAAAATGTTAAAATTAAATTA
194396 TACAACATTT
Statistics
Matches: 237, Mismatches: 25, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
106 1 0.00
107 83 0.35
108 8 0.03
109 80 0.34
110 33 0.14
111 32 0.14
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (109 bp):
ATTAGCATGAAGTCAATAGACTTTTATGTCATAAAATGTTAAAATTAAATTAGACATATCAAAAA
TACTTAACCATAAAAAAATTAAAAGAAATTCAAGAAGACTCAAT
Found at i:194763 original size:106 final size:108
Alignment explanation
Indices: 194569--194847 Score: 271
Period size: 106 Copynumber: 2.6 Consensus size: 108
194559 GATATTTAAA
* * * *
194569 AGGACTTAATGTTAGCACGAAGTCAATGGACTTTTATGCTATAAAATGTTAAAATTGTATTATAC
1 AGGACTCAATGTTAGCACGAAGTCAATAGATTTTTATGCTATAAAATGTTAAAATTG-AAT-TAC
* * * * *
194634 AATGTTTATTGAGACTAATAAAAAATT-A-A-AAAAAA-TTCAAG
64 AATATATAATGAGAATAAAAAAAAATTAACATAAAAAATTTCAAG
* * *
194675 AGGACTCAATGTTAACACGAAGTCAATAGATTTTTATGCCACAAAATGTTAAAATTGAATTAC-A
1 AGGACTCAATGTTAGCACGAAGTCAATAGATTTTTATGCTATAAAATGTTAAAATTGAATTACAA
*
194739 TATATAATGAGATGGATAAAAAAAATTTAATCATAAAAAATTTCAAG
66 TATATAATGAGA---ATAAAAAAAAATTAA-CATAAAAAATTTCAAG
* * * * * * * * *
194786 AGGATTCAATATTAGCATGAAATCAGTCGGTTTTTATTCTTTAAAATGTTAAAATTGAATTA
1 AGGACTCAATGTTAGCACGAAGTCAATAGATTTTTATGCTATAAAATGTTAAAATTGAATTA
194848 TGCAAATGTT
Statistics
Matches: 140, Mismatches: 25, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
103 10 0.07
104 3 0.02
105 2 0.01
106 61 0.44
107 1 0.01
109 1 0.01
110 6 0.04
111 56 0.40
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (108 bp):
AGGACTCAATGTTAGCACGAAGTCAATAGATTTTTATGCTATAAAATGTTAAAATTGAATTACAA
TATATAATGAGAATAAAAAAAAATTAACATAAAAAATTTCAAG
Found at i:195596 original size:28 final size:30
Alignment explanation
Indices: 195545--195601 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 30
195535 TAATAATACA
* *
195545 TTAAAAGAATAACTTATATTAAGATGAATT
1 TTAAAAGAATAAATTATATTAAGACGAATT
*
195575 TTAAAA-AATAAATT-TTTTAAGACGAAT
1 TTAAAAGAATAAATTATATTAAGACGAAT
195602 AAAATAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 11 0.46
29 7 0.29
30 6 0.25
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.37
Consensus pattern (30 bp):
TTAAAAGAATAAATTATATTAAGACGAATT
Found at i:195905 original size:17 final size:15
Alignment explanation
Indices: 195872--195910 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 15
195862 ACATCATGAT
195872 TATAATATAAAAATAA
1 TATAA-ATAAAAATAA
195888 TATAAATAAAATATTAA
1 TATAAATAAAA-A-TAA
195905 TATAAA
1 TATAAA
195911 AATTATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.29
16 6 0.29
17 9 0.43
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TATAAATAAAAATAA
Found at i:195999 original size:23 final size:25
Alignment explanation
Indices: 195963--196012 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
195953 TTTAAAATTT
195963 AAATTAATTCATTT-ATATAATTTAA
1 AAATTAATTCATTTAATA-AATTTAA
195988 AAATTAA-T-ATTTAATAAATTTAA
1 AAATTAATTCATTTAATAAATTTAA
196011 AA
1 AA
196013 TTTCAATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 13 0.54
24 4 0.17
25 7 0.29
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
AAATTAATTCATTTAATAAATTTAA
Found at i:196396 original size:37 final size:37
Alignment explanation
Indices: 196355--196427 Score: 85
Period size: 37 Copynumber: 2.0 Consensus size: 37
196345 TATCTAATTT
* * *
196355 TTAA-TAATATATTTATTATTTAAATTTAAAATTTAAA
1 TTAATTAATATATATAAT-TTTAAAATTAAAATTTAAA
* *
196392 TTAATTAATTTATATAATTTTAAAATTAATATTTAA
1 TTAATTAATATATATAATTTTAAAATTAAAATTTAA
196428 TAAATTTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
37 20 0.67
38 10 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (37 bp):
TTAATTAATATATATAATTTTAAAATTAAAATTTAAA
Found at i:196417 original size:31 final size:32
Alignment explanation
Indices: 196370--196435 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
196360 AATATATTTA
* *
196370 TTATTTAAATTTAAAATTTAA-A-TTAATTAAT
1 TTATATAAATTTAAAA-TTAATATTTAATAAAT
*
196401 TTATATAATTTTAAAATTAATATTTAATAAAT
1 TTATATAAATTTAAAATTAATATTTAATAAAT
196433 TTA
1 TTA
196436 AAATTTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 4 0.13
31 15 0.50
32 11 0.37
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
TTATATAAATTTAAAATTAATATTTAATAAAT
Found at i:196425 original size:23 final size:24
Alignment explanation
Indices: 196383--196440 Score: 77
Period size: 22 Copynumber: 2.5 Consensus size: 24
196373 TTTAAATTTA
196383 AAATTT-AAATTAATTAATTTATAT
1 AAATTTAAAATTAATTAATTTA-AT
*
196407 AATTTTAAAATTAA-T-ATTTAAT
1 AAATTTAAAATTAATTAATTTAAT
196429 AAATTTAAAATT
1 AAATTTAAAATT
196441 TAAATTTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 13 0.42
23 5 0.16
24 6 0.19
25 7 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AAATTTAAAATTAATTAATTTAAT
Found at i:196696 original size:426 final size:426
Alignment explanation
Indices: 195903--196759 Score: 1507
Period size: 426 Copynumber: 2.0 Consensus size: 426
195893 ATAAAATATT
*
195903 AATATAAAAATTATTATATTTAATTTTTAATAATATATTTATTATTTAAATTTAAAATTTAAATT
1 AATATAAAAATTATTATATCTAATTTTTAATAATATATTTATTATTTAAATTTAAAATTTAAATT
* * * *
195968 AATTCATTTATATAATTTAAAAATTAATATTTAATAAATTTAAAATTTCAATTTCAATTTGAGTG
66 AATTAATTTATATAATTTAAAAATTAATATTTAATAAATTTAAAATTTAAATTTCAACTTCAGTG
196033 AATTTTTCTTACTCCTAAACGACTGCCACTTGAAAAGGAAATCTCAGCCCTTCTTTTCCTTGGCC
131 AATTTTTCTTACTCCTAAACGACTGCCACTTGAAAAGGAAATCTCAGCCCTTCTTTTCCTTGGCC
* *
196098 GCGACCCAAGCCAATGGATATCCTCTAATATTCTAAAGTCAATTTACTTGCCGTGCCAGAAAAGC
196 ACGACCCAAGCCAATGGATATCCTCTAATATTCTAAAATCAATTTACTTGCCGTGCCAGAAAAGC
* ** *
196163 AAAATAAATAGTTAAATCTTCGCTATCTAACGTTGATATGGAAGGACCTTCCAAAGAGACAAAGA
261 AAAACAAATAGTTAAATCTTCGCTATCTAACGTTGATATGGAAAAACCTTCCAAAAAGACAAAGA
* * *
196228 TATAGAAATAATGAAAACTAATAAATGGTGGAGGGAGGAGCCGACAAATTCTTAGCCAAGATCTT
326 TATAAAAATAATGAAAACTAATAAATGGTGGAGAGAGGAGCCGACAAATTCTTAGCAAAGATCTT
196293 CCTCAACCTCAATCTCAATTACAGAAATTATAAGTC
391 CCTCAACCTCAATCTCAATTACAGAAATTATAAGTC
196329 AATATAAAAATTATTATATCTAATTTTTAATAATATATTTATTATTTAAATTTAAAATTTAAATT
1 AATATAAAAATTATTATATCTAATTTTTAATAATATATTTATTATTTAAATTTAAAATTTAAATT
*
196394 AATTAATTTATATAATTTTAAAATTAATATTTAATAAATTTAAAATTTAAATTTCAACTTCAGTG
66 AATTAATTTATATAATTTAAAAATTAATATTTAATAAATTTAAAATTTAAATTTCAACTTCAGTG
* * *
196459 AATTTTTCTTACTCCTAAACGACTGCCACTTGAAAAGGACATCTTAGCCTTTCTTTTCCTTGGCC
131 AATTTTTCTTACTCCTAAACGACTGCCACTTGAAAAGGAAATCTCAGCCCTTCTTTTCCTTGGCC
196524 ACGACCCAAGCCAATGGATATCCTCTAATATTCTAAAATCAATTTACTTGCCGTGCCAGAAAAGC
196 ACGACCCAAGCCAATGGATATCCTCTAATATTCTAAAATCAATTTACTTGCCGTGCCAGAAAAGC
* * *
196589 AAAACAAATAGTTAAATCTTCGCTATCTAACGTTGATATTGAAAAATCTTCTAAAAAGACAAAGA
261 AAAACAAATAGTTAAATCTTCGCTATCTAACGTTGATATGGAAAAACCTTCCAAAAAGACAAAGA
*
196654 TATAAAAATAATGAAAACTAATAAATGGTGGAGAGAGGAGCCGATAAATTCTTAGCAAAGATCTT
326 TATAAAAATAATGAAAACTAATAAATGGTGGAGAGAGGAGCCGACAAATTCTTAGCAAAGATCTT
*
196719 CCTCAACCTCAATCTCAATTACAGAAATTATAAGTT
391 CCTCAACCTCAATCTCAATTACAGAAATTATAAGTC
196755 AATAT
1 AATAT
196760 CATTGTCAAA
Statistics
Matches: 408, Mismatches: 23, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
426 408 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (426 bp):
AATATAAAAATTATTATATCTAATTTTTAATAATATATTTATTATTTAAATTTAAAATTTAAATT
AATTAATTTATATAATTTAAAAATTAATATTTAATAAATTTAAAATTTAAATTTCAACTTCAGTG
AATTTTTCTTACTCCTAAACGACTGCCACTTGAAAAGGAAATCTCAGCCCTTCTTTTCCTTGGCC
ACGACCCAAGCCAATGGATATCCTCTAATATTCTAAAATCAATTTACTTGCCGTGCCAGAAAAGC
AAAACAAATAGTTAAATCTTCGCTATCTAACGTTGATATGGAAAAACCTTCCAAAAAGACAAAGA
TATAAAAATAATGAAAACTAATAAATGGTGGAGAGAGGAGCCGACAAATTCTTAGCAAAGATCTT
CCTCAACCTCAATCTCAATTACAGAAATTATAAGTC
Found at i:196806 original size:14 final size:15
Alignment explanation
Indices: 196780--196817 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
196770 GATTTAAATT
*
196780 ATAATTATTTTTATC
1 ATAATTATATTTATC
*
196795 AT-ATTATATTTATT
1 ATAATTATATTTATC
196809 ATAATTATA
1 ATAATTATA
196818 AACATAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
ATAATTATATTTATC
Found at i:197769 original size:29 final size:29
Alignment explanation
Indices: 197733--197788 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
197723 AAATTTTTAT
*
197733 TAATATTTATAATTA-AATTTAAATAAAAA
1 TAATATTTA-AATAATAATTTAAATAAAAA
*
197762 TAATATTTAAATAATAATTTGAATAAA
1 TAATATTTAAATAATAATTTAAATAAA
197789 TCAAAATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (29 bp):
TAATATTTAAATAATAATTTAAATAAAAA
Found at i:198304 original size:19 final size:21
Alignment explanation
Indices: 198280--198327 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
198270 TGAAGTTGAG
*
198280 AAATTAATTTTT-TAA-AAAA
1 AAATTAATTTTTAAAATAAAA
198299 AAATTATATTTTTAAAATAAAA
1 AAATTA-ATTTTTAAAATAAAA
198321 AAATTAA
1 AAATTAA
198328 AAATAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 6 0.24
20 6 0.24
21 3 0.12
22 10 0.40
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATTAATTTTTAAAATAAAA
Found at i:198311 original size:20 final size:19
Alignment explanation
Indices: 198280--198321 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
198270 TGAAGTTGAG
198280 AAATTAATTTTTTAAAA-AA
1 AAATTAA-TTTTTAAAATAA
198299 AAATTATATTTTTAAAATAA
1 AAATTA-ATTTTTAAAATAA
198319 AAA
1 AAA
198322 AATTAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATTAATTTTTAAAATAA
Found at i:200773 original size:2 final size:2
Alignment explanation
Indices: 200762--200801 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
200752 CAAATCACAC
* *
200762 TA TA -A TA TA TA TA TA TG TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
200802 TCCTCTTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:200785 original size:14 final size:14
Alignment explanation
Indices: 200766--200801 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
200756 TCACACTATA
200766 ATATATATATATGT
1 ATATATATATATGT
200780 ATATATATATATGT
1 ATATATATATATGT
200794 ATATATAT
1 ATATATAT
200802 TCCTCTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (14 bp):
ATATATATATATGT
Found at i:201038 original size:124 final size:125
Alignment explanation
Indices: 200857--201088 Score: 312
Period size: 124 Copynumber: 1.9 Consensus size: 125
200847 TTATATTCAG
*
200857 TGAATAAAAAATATTTAATCATAACAAATGTTAAAAAAAATTTAAGAGAATTCAATGTTAACACG
1 TGAATAAAAAATATTTAATCATAACAAATGTTAAAAAAAATTCAAGAGAATTCAATGTTAACACG
* ** *
200922 AAGTCAAT-AGATTTTTATGTCATAAAATGTTAAAATTGAATTATGTAACATTTTTTTGAGA
66 AAATCAATGA-ATTTTTATACCAT-AAATGTTAAAATTAAATTATGTAACATTTTTTTGAGA
* * * *
200983 TGAATCAAAAATATTTAATTATGAA-AAA-GTT-AAAAAAATTCAAGAGGACTT-AATGTTACCA
1 TGAATAAAAAATATTTAATCAT-AACAAATGTTAAAAAAAATTCAAGA-GAATTCAATGTTAACA
201044 CGAAATCAATGAATTTTTATACCATAAATGTTAAAATTAAATTAT
64 CGAAATCAATGAATTTTTATACCATAAATGTTAAAATTAAATTAT
201089 AAAATAAAAA
Statistics
Matches: 94, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
123 19 0.20
124 42 0.45
125 8 0.09
126 23 0.24
127 2 0.02
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.34
Consensus pattern (125 bp):
TGAATAAAAAATATTTAATCATAACAAATGTTAAAAAAAATTCAAGAGAATTCAATGTTAACACG
AAATCAATGAATTTTTATACCATAAATGTTAAAATTAAATTATGTAACATTTTTTTGAGA
Found at i:201513 original size:113 final size:110
Alignment explanation
Indices: 201007--201643 Score: 620
Period size: 110 Copynumber: 5.7 Consensus size: 110
200997 TTAATTATGA
* * * * * *
201007 AAAAGTTAAAA-AAATTCAAGAGGACTTAATGTTACCACGAAATCAATGAATTTTTATACCAT-A
1 AAAA-TTAAAAGAAATTCAAGAGGACTCAATGTTAACACGAAGTCAATGGACTTTTATGCCATAA
* * *
201070 AATGTTAAAATTAAATTATAAAATAAAAAATATTTAACCA-TAAAG
65 AATGTTAAAATTAAATTAGAATATAAAAAATATTTAACCATTAAAT
* * * ** * * **
201115 AAAAGTCAAAAGAAATTTAAAAAAAACTCAATGTT-AGACGAAATCAATGGACTTTTATGTTATA
1 AAAA-TTAAAAGAAA-TTCAAGAGGACTCAATGTTAACACGAAGTCAATGGACTTTTATGCCATA
* * * *
201179 AAATGTTAAAATTAAATTATAAAATAAAAAATATTTAACC-GTAAAA
64 AAATGTTAAAATTAAATTAGAATATAAAAAATATTTAACCATTAAAT
* * * ** * * *
201225 AAAAGGTCAAAAGAAATTTAAAAAAAACTCAATGTTAGCACAAAGTCAATGGACTTTTGTGCCAT
1 AAAA--TTAAAAGAAA-TTCAAGAGGACTCAATGTTAACACGAAGTCAATGGACTTTTATGCCAT
* * *
201290 AAAATGTTAAAATTGAATTGGATATATAAAAAA-ATTTAACCATAAAAT
63 AAAATGTTAAAATTAAATTAGA-ATATAAAAAATATTTAACCATTAAAT
* * **
201338 AAAATTAAAAGAAATTCAAGAGGACTCAATATTAGCATAAAGTCAATGGACTTTTATGCCATAAA
1 AAAATTAAAAGAAATTCAAGAGGACTCAATGTTAACACGAAGTCAATGGACTTTTATGCCATAAA
*
201403 ATGTTAAAATTAAATTAGACGTATAAAAAATATTTAACCATTAAAT
66 ATGTTAAAATTAAATTAGA-ATATAAAAAATATTTAACCATTAAAT
* * * * * *
201449 AAAATTAGAAAAAAAATTTAAGAGGACTCAATGTTAACATGAAGTTAATGAACTTTTATACCATA
1 AAAATT--AAAAGAAATTCAAGAGGACTCAATGTTAACACGAAGTCAATGGACTTTTATGCCATA
* * *
201514 AAATGTTAAAATTAAATTAGACGTATCAAAAATATTTAACCATAAAAT
64 AAATGTTAAAATTAAATTAGA-ATATAAAAAATATTTAACCATTAAAT
* ** * * * * * *
201562 AAAATTAAAAGCAATTCAAGAGGACTCAATGTTAGTATGAAATCAATAGATTTTTATGTCAGAAA
1 AAAATTAAAAGAAATTCAAGAGGACTCAATGTTAACACGAAGTCAATGGACTTTTATGCCATAAA
*
201627 ATGTTAAAATTGAATTA
66 ATGTTAAAATTAAATTA
201644 TATATATATA
Statistics
Matches: 453, Mismatches: 65, Indels: 19
0.84 0.12 0.04
Matches are distributed among these distances:
108 10 0.02
109 24 0.05
110 132 0.29
111 122 0.27
112 48 0.11
113 117 0.26
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.30
Consensus pattern (110 bp):
AAAATTAAAAGAAATTCAAGAGGACTCAATGTTAACACGAAGTCAATGGACTTTTATGCCATAAA
ATGTTAAAATTAAATTAGAATATAAAAAATATTTAACCATTAAAT
Found at i:201585 original size:224 final size:218
Alignment explanation
Indices: 201014--201643 Score: 708
Period size: 224 Copynumber: 2.8 Consensus size: 218
201004 TGAAAAAGTT
* * * * *
201014 AAAAAAATTCAAGAGGACTTAATGTTACCACGAAATCAATGAATTTTTATACCAT-AAATGTTAA
1 AAAAAAATTTAAGAGGACTCAATGTTAACACGAAGTCAATGAACTTTTATACCATAAAATGTTAA
* * * * * * **
201078 AATTAAATTATAAAATAAAAAATATTTAACCATAAAGA-AAAGTCAAAAGAAATTTAAAAAAAAC
66 AATTAAATTAGAATAT-AAAAATATTTAACCATAAA-ATAAAATTAAAAGAAA-TTCAAGAGGAC
* * *
201142 TCAATGTTAGACGAAATCAATGGACTTTTATGTTATAAAATGTTAAAATTAAATTATAAAATAAA
128 TCAATGTTAGA-TAAATCAATGGACTTTTATGTCATAAAATGTTAAAATTAAATTAGAAAATAAA
201207 AAATATTTAACCGTAAAAAAAAGGTCA
192 AAATATTTAACCGTAAAAAAAAGGTCA
* * ** * * * * *
201234 AAAGAAATTTAAAAAAAACTCAATGTTAGCACAAAGTCAATGGACTTTTGTGCCATAAAATGTTA
1 AAAAAAATTT-AAGAGGACTCAATGTTAACACGAAGTCAATGAACTTTTATACCATAAAATGTTA
* * *
201299 AAATTGAATTGGATATATAAAAAAATTTAACCATAAAATAAAATTAAAAGAAATTCAAGAGGACT
65 AAATTAAATTAGA-ATATAAAAATATTTAACCATAAAATAAAATTAAAAGAAATTCAAGAGGACT
* * **
201364 CAATATTAGCATAAAGTCAATGGACTTTTATGCCATAAAATGTTAAAATTAAATTAGACGTATAA
129 CAATGTTAG-ATAAA-TCAATGGACTTTTATGTCATAAAATGTTAAAATTAAATTAGA-AAATAA
* * * *
201429 AAAATATTTAACCATTAAATAAAA-TTAGA
191 AAAATATTTAACC-GTAAAAAAAAGGT-CA
* *
201458 AAAAAAATTTAAGAGGACTCAATGTTAACATGAAGTTAATGAACTTTTATACCATAAAATGTTAA
1 AAAAAAATTTAAGAGGACTCAATGTTAACACGAAGTCAATGAACTTTTATACCATAAAATGTTAA
* *
201523 AATTAAATTAGACGTATCAAAAATATTTAACCATAAAATAAAATTAAAAGCAATTCAAGAGGACT
66 AATTAAATTAGA-ATAT-AAAAATATTTAACCATAAAATAAAATTAAAAGAAATTCAAGAGGACT
* * * *
201588 CAATGTTAGTATGAAATCAATAGATTTTTATGTCAGAAAATGTTAAAATTGAATTA
129 CAATGTTAG-AT-AAATCAATGGACTTTTATGTCATAAAATGTTAAAATTAAATTA
201644 TATATATATA
Statistics
Matches: 340, Mismatches: 59, Indels: 18
0.82 0.14 0.04
Matches are distributed among these distances:
220 8 0.02
221 54 0.16
222 88 0.26
223 79 0.23
224 108 0.32
225 3 0.01
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.30
Consensus pattern (218 bp):
AAAAAAATTTAAGAGGACTCAATGTTAACACGAAGTCAATGAACTTTTATACCATAAAATGTTAA
AATTAAATTAGAATATAAAAATATTTAACCATAAAATAAAATTAAAAGAAATTCAAGAGGACTCA
ATGTTAGATAAATCAATGGACTTTTATGTCATAAAATGTTAAAATTAAATTAGAAAATAAAAAAT
ATTTAACCGTAAAAAAAAGGTCA
Found at i:201906 original size:18 final size:19
Alignment explanation
Indices: 201885--201931 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
201875 TTTAAAATTT
* *
201885 ATATAATATAATT-TATTA
1 ATATAAAATAATTATATAA
201903 ATATATAAATAATTATATAA
1 ATATA-AAATAATTATATAA
201923 ATATAAAAT
1 ATATAAAAT
201932 TTTTTAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.20
19 11 0.44
20 9 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATATAAAATAATTATATAA
Found at i:201909 original size:20 final size:20
Alignment explanation
Indices: 201884--201931 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
201874 TTTTAAAATT
*
201884 TATATAATATAATT-TATTAA
1 TATATAA-ATAATTATATAAA
201904 TATATAAATAATTATATAAA
1 TATATAAATAATTATATAAA
201924 TATA-AAAT
1 TATATAAAT
201932 TTTTTAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TATATAAATAATTATATAAA
Found at i:203903 original size:50 final size:50
Alignment explanation
Indices: 203839--204143 Score: 493
Period size: 50 Copynumber: 6.1 Consensus size: 50
203829 TATACTTAGA
* * *
203839 GTCAACAATTATGGCCACCTTTCTCTATTGTCAAAGGTTAGTGAAGAATC
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
** * *
203889 GTCAACAACAATGGCCACCTCTTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
203939 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
203989 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
204039 GTCAACAATTACGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * * *
204089 GTCAACAATTACGGCCACATCTCTCTATTATCAAAGGTTGGTGAAGGATA
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
204139 GTCAA
1 GTCAA
204144 TAATGACAAA
Statistics
Matches: 238, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 238 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (50 bp):
GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:208599 original size:50 final size:50
Alignment explanation
Indices: 208535--208839 Score: 448
Period size: 50 Copynumber: 6.1 Consensus size: 50
208525 TATACTTAGA
* * *
208535 GTCAACAATTATGGCCACCTTTCTCTATTGTTAAAGGTTGGTGAAGAATC
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * * * * *
208585 GTCAACAATAATGGCTACCTCTTTTTATTGTCAAAGGTTGGTAAAGAATC
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * *
208635 ATCAACAATTACGGTCACCACTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
208685 GTCAACAATTACGGCCACCTCTCTTTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
208735 GTCAACAATTACAGCCACCTCTCTCTATTGTCAGAGGTTGGTGAAGAATC
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * *
208785 GTCAACAATTACGGCCACCTCTCTCTATTATCAAAGGTTAGTGAAGAATA
1 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
208835 GTCAA
1 GTCAA
208840 TAATGACAAC
Statistics
Matches: 227, Mismatches: 28, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 227 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (50 bp):
GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:209657 original size:15 final size:15
Alignment explanation
Indices: 209609--209650 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
209599 GATATTGAAC
* *
209609 AAATT-TATAAGTCA
1 AAATTATATAAATAA
*
209623 AAATTATTTAAATAA
1 AAATTATATAAATAA
209638 AAATTATATAAAT
1 AAATTATATAAAT
209651 TTAAATTTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (15 bp):
AAATTATATAAATAA
Found at i:210927 original size:34 final size:34
Alignment explanation
Indices: 210871--211088 Score: 269
Period size: 34 Copynumber: 6.4 Consensus size: 34
210861 TGGGTTTGGT
* *
210871 TTGTTGATTAAATGGTA-ATTTGGTAATTTACCA
1 TTGTTGATTAAATGGGAGATTTGGTAGTTTACCA
**
210904 TTGTTGATTAAATGGGTA-ATTTGGTAGTTTGTCA
1 TTGTTGATTAAATGGG-AGATTTGGTAGTTTACCA
* *
210938 TTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGAGATTTGGTAGTTTACCA
* *
210972 TTGTTGATTAAATAGGAGATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGAGATTTGGTAGTTTACCA
* * *
211006 TTGTTGATTAAATGAGTGATTTGGTGGTTTACCA
1 TTGTTGATTAAATGGGAGATTTGGTAGTTTACCA
* * * **
211040 TTGTTGACTAAATGGGAGATTTAGTAGGTTGTCA
1 TTGTTGATTAAATGGGAGATTTGGTAGTTTACCA
211074 TTGTTGATTAAATGG
1 TTGTTGATTAAATGG
211089 TGGTTTTTAC
Statistics
Matches: 159, Mismatches: 24, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
33 16 0.10
34 143 0.90
ACGTcount: A:0.27, C:0.06, G:0.25, T:0.42
Consensus pattern (34 bp):
TTGTTGATTAAATGGGAGATTTGGTAGTTTACCA
Found at i:211076 original size:102 final size:101
Alignment explanation
Indices: 210871--211089 Score: 314
Period size: 102 Copynumber: 2.2 Consensus size: 101
210861 TGGGTTTGGT
* * **
210871 TTGTTGATTAAATGGTAATTTGGTAATTTACCATTGTTGATTAAATGGGTAATTTGGTAGTTTGT
1 TTGTTGATTAAATGGTAATTTGGTAACTTACCATTGTTGATTAAATGAGTAATTTGGTAGTTTAC
*
210936 CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
66 CATTGTTGACTAAATGGGAGATTTAGTAGCTTACCA
* * *
210972 TTGTTGATTAAATAGG-AGATTTGGTAGCTTACCATTGTTGATTAAATGAGTGATTTGGTGGTTT
1 TTGTTGATTAAAT-GGTA-ATTTGGTAACTTACCATTGTTGATTAAATGAGTAATTTGGTAGTTT
* **
211036 ACCATTGTTGACTAAATGGGAGATTTAGTAGGTTGTCA
64 ACCATTGTTGACTAAATGGGAGATTTAGTAGCTTACCA
211074 TTGTTGATTAAATGGT
1 TTGTTGATTAAATGGT
211090 GGTTTTTACC
Statistics
Matches: 104, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
101 16 0.15
102 88 0.85
ACGTcount: A:0.26, C:0.06, G:0.25, T:0.42
Consensus pattern (101 bp):
TTGTTGATTAAATGGTAATTTGGTAACTTACCATTGTTGATTAAATGAGTAATTTGGTAGTTTAC
CATTGTTGACTAAATGGGAGATTTAGTAGCTTACCA
Found at i:211452 original size:19 final size:19
Alignment explanation
Indices: 211392--211444 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
211382 GTTGTCGAGG
211392 TACTATTCACGTATATAAA
1 TACTATTCACGTATATAAA
* **
211411 TACTATTCACATATATAGG
1 TACTATTCACGTATATAAA
211430 TACTATTCACGTATA
1 TACTATTCACGTATA
211445 CAATTACTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (19 bp):
TACTATTCACGTATATAAA
Found at i:215587 original size:34 final size:34
Alignment explanation
Indices: 215520--215736 Score: 253
Period size: 34 Copynumber: 6.4 Consensus size: 34
215510 GGAAGAATTA
*
215520 TTGATTAAATGGG-GTAATTTGGTAGTTTACCATTG
1 TTGATTAAATGGGAG--ATTTGGTGGTTTACCATTG
* *
215555 TTGATTAAATGGGTGATTTGGTGGTTTGCCATTG
1 TTGATTAAATGGGAGATTTGGTGGTTTACCATTG
* * * *
215589 TTGACTAAATGGAAGATTTGATAGCTTT-CCATTG
1 TTGATTAAATGGGAGATTTGGT-GGTTTACCATTG
* * *
215623 TTGATTAAATGGGAGATTTGGTAGCTTACCATTA
1 TTGATTAAATGGGAGATTTGGTGGTTTACCATTG
*
215657 TTGATTAAATGGGTGATTTGGTGGTTTACCATTG
1 TTGATTAAATGGGAGATTTGGTGGTTTACCATTG
*
215691 TTGATTAAATGGGAGATTTAGTAGGTTGT--CATTG
1 TTGATTAAATGGGAGATTTGGT-GGTT-TACCATTG
215725 TTGATTAAATGG
1 TTGATTAAATGG
215737 TGGTTTTTAC
Statistics
Matches: 157, Mismatches: 20, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
33 2 0.01
34 132 0.84
35 21 0.13
36 2 0.01
ACGTcount: A:0.25, C:0.06, G:0.27, T:0.41
Consensus pattern (34 bp):
TTGATTAAATGGGAGATTTGGTGGTTTACCATTG
Found at i:215661 original size:102 final size:102
Alignment explanation
Indices: 215520--215736 Score: 323
Period size: 102 Copynumber: 2.1 Consensus size: 102
215510 GGAAGAATTA
* * *
215520 TTGATTAAATGGGGTAATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TTGATTAAATGGGG-AATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTACC
215585 ATTGTTGACTAAATGGAAGATTT-GATAGCTT-TCCATTG
65 ATTGTTGACTAAATGGAAGATTTAG-TAGCTTGT-CATTG
215623 TTGATTAAAT-GGGAGATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 TTGATTAAATGGGGA-ATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTACC
* * *
215687 ATTGTTGATTAAATGGGAGATTTAGTAGGTTGTCATTG
65 ATTGTTGACTAAATGGAAGATTTAGTAGCTTGTCATTG
215725 TTGATTAAATGG
1 TTGATTAAATGG
215737 TGGTTTTTAC
Statistics
Matches: 104, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
101 1 0.01
102 90 0.87
103 13 0.12
ACGTcount: A:0.25, C:0.06, G:0.27, T:0.41
Consensus pattern (102 bp):
TTGATTAAATGGGGAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTACCA
TTGTTGACTAAATGGAAGATTTAGTAGCTTGTCATTG
Found at i:217098 original size:19 final size:19
Alignment explanation
Indices: 217074--217124 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
217064 TTATTTAAAA
217074 ATATTAAAATATTAT-TTTT
1 ATATTAAAAT-TTATATTTT
*
217093 ATATTAATATTTATATTTT
1 ATATTAAAATTTATATTTT
217112 ATAATT-AAATTTA
1 AT-ATTAAAATTTA
217125 ATTAATAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 4 0.14
19 21 0.75
20 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATTAAAATTTATATTTT
Found at i:217138 original size:20 final size:21
Alignment explanation
Indices: 217115--217181 Score: 52
Period size: 21 Copynumber: 3.4 Consensus size: 21
217105 ATATTTTATA
217115 ATTAAATTTAATT-AATAATT
1 ATTAAATTTAATTAAATAATT
* *
217135 ATT--ATTTTATTAAATAAAT
1 ATTAAATTTAATTAAATAATT
* * * *
217154 AATAATTTTAATTGAATCATT
1 ATTAAATTTAATTAAATAATT
217175 -TTAAATT
1 ATTAAATT
217182 ATTAAAATAC
Statistics
Matches: 34, Mismatches: 10, Indels: 6
0.68 0.20 0.12
Matches are distributed among these distances:
18 7 0.21
19 8 0.24
20 8 0.24
21 11 0.32
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (21 bp):
ATTAAATTTAATTAAATAATT
Found at i:217143 original size:31 final size:32
Alignment explanation
Indices: 217090--217153 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
217080 AAATATTATT
* *
217090 TTTATATTAATATTTATATTTTA-TAATTAAA
1 TTTATATTAATAATTATATTTTATTAAATAAA
217121 TTTA-ATTAATAATTATTATTTTATTAAATAAA
1 TTTATATTAATAATTA-TATTTTATTAAATAAA
217153 T
1 T
217154 AATAATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 10 0.34
31 11 0.38
32 8 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (32 bp):
TTTATATTAATAATTATATTTTATTAAATAAA
Found at i:217715 original size:3 final size:3
Alignment explanation
Indices: 217707--217735 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
217697 AATTAGAAAG
217707 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
217736 GCATGGATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:219892 original size:18 final size:18
Alignment explanation
Indices: 219869--219905 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
219859 AGTGACAAGA
*
219869 TAGCGGACTTGAAATCAT
1 TAGCGGACTCGAAATCAT
219887 TAGCGGACTCGAAATCAT
1 TAGCGGACTCGAAATCAT
219905 T
1 T
219906 TAGGACAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (18 bp):
TAGCGGACTCGAAATCAT
Found at i:220322 original size:73 final size:73
Alignment explanation
Indices: 220203--220349 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
220193 TCACATCTTC
220203 AATGCATTCAGGGCTAGCTTCAAGAAACTTGTATAAAAGATTCTCGTATAAAAAATATGAGTCTC
1 AATGCATTCAGGGCTAGCTTCAAGAAACTTGTATAAAAGATTCTCGTATAAAAAATATGAGTCTC
220268 CTATCGTT
66 CTATCGTT
220276 AATGCATTCAGGGCTAGCTTCAAGAAACTTGTATAAAAGATTCTCGTATAAAAAATATGAGTCTC
1 AATGCATTCAGGGCTAGCTTCAAGAAACTTGTATAAAAGATTCTCGTATAAAAAATATGAGTCTC
220341 CTATCGTT
66 CTATCGTT
220349 A
1 A
220350 CTACGTAATG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (73 bp):
AATGCATTCAGGGCTAGCTTCAAGAAACTTGTATAAAAGATTCTCGTATAAAAAATATGAGTCTC
CTATCGTT
Found at i:222859 original size:817 final size:818
Alignment explanation
Indices: 221456--223096 Score: 2529
Period size: 817 Copynumber: 2.0 Consensus size: 818
221446 TATGAATTTT
** *
221456 TTTTATAAATTAAAAATCATATAGGTAGTATCCTAAATTTTTCTAAAAATTATTAAAAGAATTTA
1 TTTTATAAATTAAAAATCATATAGGTAGTATCCTAAATTTTTAAAAAAATTATTAAAAAAATTTA
* * *
221521 TGTATGTAATTATAATTATTATATTCTATAATAAGTTGTGAAAATGAAAAAAAAAATTATGATCA
66 TGTATGCAATTATAATTATTATATTCTATAATAAATTGTCAAAATGAAAAAAAAAATTATGATCA
* * *
221586 TAATGTTCATAATGATCAAACTAGCATCAATTATATCTATAATCATAATAAATTTAATGTAACTA
131 TAATGTTCATAATGATCAAACTAACATCAATTACATCTATAATCATAATAAACTTAATGTAACTA
* * * *
221651 AAAATATATTCACGATGGTAATTTAAATCTTTACTAACAACGAATAGGTCATTAGGCTATCGGTG
196 AAAATATATTCACGATAGCAATTTAAATCTTTAATAACAACGAATAGGTCATTAGGCTATCGATG
* * * * *
221716 ATTAATTATACTAGTGAAATTATAACTTAGAAATTATTAAAGCCTTTTGTATGCTTAAATTAAAT
261 ATTAATCATACTAATGAAATTATAACTTAGAAATGATTAAAGCCTTTTGCATGATTAAATTAAAT
**
221781 TAAAATTTTTGTTTAATAATGATTTTTTGTCATTTTTTATAATTGTTTAATTTTCTCAACAATTT
326 TAAAATTTTCATTTAATAATGATTTTTTGTCATTTTTTATAATTGTTTAATTTTCTCAACAATTT
* *
221846 AATCTTTCAAAAGGTAAATATATAAAAACAATTCCAAATATCTGTCAATGGAATCAAAAGTTACA
391 AATCTTTCAAAAAGTAAATAAATAAAAACAATTCCAAATATCTGTCAATGGAATCAAAAGTTACA
* * *
221911 AAATTTGATTGTAAAGAATATGTCCTAGTTGCTTCGCTTTGACTAAAGAATGATTCAAAATGATG
456 AAATTTGATTGTAAAGAATATGTCCTAGTTGCTTCACTTTGACAAAAGAATGATTCAAAATAATG
* * *
221976 GTTAAAATGAAAGCAAACAAACTAAAGTGACAATCTTCCTCTTAAAATTTATCTCTGCATTCTTG
521 GTTAAAATGAAAGCAAACAAACTAAAATGACAATCTTCCTCTTAAAATTTATCTCTACACTCTTG
* *
222041 AAAAGTGATAACTCAAACCTAAAGAAAAGAATAGGATAAATTACTTTATTTTTATAAAAAATCAT
586 AAAAGTGATAACTCAAACCTAAAGAAAAGAATAGGATAAATTACTCTATTTCTATAAAAAATCAT
* * * * * *
222106 TGTATATATTCGATATTTTAGATAATTAAAGTTTAATTTAGCATTAATGTTGAAAAAAAA-ATGT
651 TGTAAATATTCGAGATTTTAGACAAATAAAGTTTAATATAGCATTAATATTGAAAAAAAAGATGT
*
222170 TTTTCTAAAATTTCTTGGGAAAATGTAGTTTAAGAATTTTAAGGGTTGAAAATATGTTATAGTGA
716 TTTCCTAAAATTTCTTGGGAAAATGTAGTTTAAGAATTTTAAGGGTTGAAAATATGTTATAGTGA
222235 ATTGAAATATTCAAAA-AGATATATATACATAAAATAA
781 ATTGAAATATTCAAAATAGATATATATACATAAAATAA
*
222272 TTTTATAAATTAAAAATCATATAGGTAGTGTCC-AAATTTTTAAAAAAAATTATTAAAAAAATTT
1 TTTTATAAATTAAAAATCATATAGGTAGTATCCTAAATTTTT-AAAAAAATTATTAAAAAAATTT
* * *
222336 ATGTTTGCAATTATAATTATTATTTTCTATAATAAATTGTCAAAATG-GAAAAAAAATTCATGAT
65 ATGTATGCAATTATAATTATTATATTCTATAATAAATTGTCAAAATGAAAAAAAAAATT-ATGAT
* * *
222400 CATGATTTTCATAATGATCAAACTAACATCAATTACATCTATAATCATGATAAACTTAATGTAAC
129 CATAATGTTCATAATGATCAAACTAACATCAATTACATCTATAATCATAATAAACTTAATGTAAC
* * * *
222465 TAAAAATATATTCATGATAGCAATTTAAATCTTTAATAATAACG-ATATGTCATTAGGTTATCGA
194 TAAAAATATATTCACGATAGCAATTTAAATCTTTAATAACAACGAATAGGTCATTAGGCTATCGA
* * *
222529 TGATTAGTCGTACTAATGAAATTATGA-TTGAGAAATGATTAAAGCCTTTTGCATGATTAAATTA
259 TGATTAATCATACTAATGAAATTATAACTT-AGAAATGATTAAAGCCTTTTGCATGATTAAATTA
* * *
222593 AATTAAAATTTTCATTTAATATTGATTTTTTGTCCCTTTTTTTATTATTGTTTAATTTTCTCAAC
323 AATTAAAATTTTCATTTAATAATGATTTTTTGT--CATTTTTTATAATTGTTTAATTTTCTCAAC
* ** * * * * *
222658 AGTTTGGTCTTTCAAAAAGTAAATAAATCAAAGCTATTCTAAATATCTGTCAATGGAATCAAAGG
386 AATTTAATCTTTCAAAAAGTAAATAAATAAAAACAATTCCAAATATCTGTCAATGGAATCAAAAG
*
222723 TTACAAAATTTGATTGTAAAGAATATGTCCTAGTTGCTTCACTTTGACAAAAGAATGATTCAAAG
451 TTACAAAATTTGATTGTAAAGAATATGTCCTAGTTGCTTCACTTTGACAAAAGAATGATTCAAAA
* * * * * *
222788 TAATGGTTAAAGTGAAAGCAAACTAACTAAAATGACAATCTTCTTTTTAAAATTTGTCTTTACAC
516 TAATGGTTAAAATGAAAGCAAACAAACTAAAATGACAATCTTCCTCTTAAAATTTATCTCTACAC
222853 TCTTGAAAAGTGATAACTCAAACCTAAAGAAAAGAATAGGATAAATTACTCTATTTCTATAAAAA
581 TCTTGAAAAGTGATAACTCAAACCTAAAGAAAAGAATAGGATAAATTACTCTATTTCTATAAAAA
*
222918 TTCATTGTAAATATTCGAGATTTTAGACAAATAAAGTTTAATATAGCATTAATATTGAAAAAAAA
646 ATCATTGTAAATATTCGAGATTTTAGACAAATAAAGTTTAATATAGCATTAATATTGAAAAAAAA
* *
222983 GGGTGTTTTCCTAAAATTTCTTGGGAAAATGTAGTTTAAGAATTTTAAGTGTTGAAAATATGTTA
711 -GATGTTTTCCTAAAATTTCTTGGGAAAATGTAGTTTAAGAATTTTAAGGGTTGAAAATATGTTA
*
223048 TAGTGAATTGAAATATTCAAAATATATATATATACATAAAATAA
775 TAGTGAATTGAAATATTCAAAATAGATATATATACATAAAATAA
223092 TTTTA
1 TTTTA
223097 ATTGTAAAGA
Statistics
Matches: 744, Mismatches: 73, Indels: 12
0.90 0.09 0.01
Matches are distributed among these distances:
814 2 0.00
815 118 0.16
816 196 0.26
817 321 0.43
819 82 0.11
820 25 0.03
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (818 bp):
TTTTATAAATTAAAAATCATATAGGTAGTATCCTAAATTTTTAAAAAAATTATTAAAAAAATTTA
TGTATGCAATTATAATTATTATATTCTATAATAAATTGTCAAAATGAAAAAAAAAATTATGATCA
TAATGTTCATAATGATCAAACTAACATCAATTACATCTATAATCATAATAAACTTAATGTAACTA
AAAATATATTCACGATAGCAATTTAAATCTTTAATAACAACGAATAGGTCATTAGGCTATCGATG
ATTAATCATACTAATGAAATTATAACTTAGAAATGATTAAAGCCTTTTGCATGATTAAATTAAAT
TAAAATTTTCATTTAATAATGATTTTTTGTCATTTTTTATAATTGTTTAATTTTCTCAACAATTT
AATCTTTCAAAAAGTAAATAAATAAAAACAATTCCAAATATCTGTCAATGGAATCAAAAGTTACA
AAATTTGATTGTAAAGAATATGTCCTAGTTGCTTCACTTTGACAAAAGAATGATTCAAAATAATG
GTTAAAATGAAAGCAAACAAACTAAAATGACAATCTTCCTCTTAAAATTTATCTCTACACTCTTG
AAAAGTGATAACTCAAACCTAAAGAAAAGAATAGGATAAATTACTCTATTTCTATAAAAAATCAT
TGTAAATATTCGAGATTTTAGACAAATAAAGTTTAATATAGCATTAATATTGAAAAAAAAGATGT
TTTCCTAAAATTTCTTGGGAAAATGTAGTTTAAGAATTTTAAGGGTTGAAAATATGTTATAGTGA
ATTGAAATATTCAAAATAGATATATATACATAAAATAA
Found at i:223443 original size:362 final size:362
Alignment explanation
Indices: 222735--223428 Score: 1133
Period size: 362 Copynumber: 1.9 Consensus size: 362
222725 ACAAAATTTG
* * *
222735 ATTGTAAAGAATATGTCCTAGTTGCTTCACTTTGACAAAAGAATGATTCAAAGTAATGGTTAAAG
1 ATTGTAAAGAACATGTCCTAGTTGCTTCACTTTAACAAAAGAATGATTCAAAGTAATAGTTAAAG
* * ** * *
222800 TGAAAGCAAACTAACTAAAATGACAATCTTCTTTTTAAAATTTGTCTTTACACTCTTGAAAAGTG
66 TGAAAGCAAACTAAATAAAATGACAATCTTCCTCCTAAAATTTGTCTCTACACTCATGAAAAGTG
*
222865 ATAACTCAAACCTAAAGAAAAGAATAGGATAAATTACTCTATTTCTATAAAAATTCATTGTAAAT
131 ATAACTCAAACCTAAAGAAAAGAATAGGACAAATTACTCTATTTCTATAAAAATTCATTGTAAAT
*
222930 ATTCGAGATTTTAGACAAATAAAGTTTAATATAGCATTAATATTGAAAAAAAAGGGTGTTTTCCT
196 ATTCGAGATTTTAGACAAATAAAGTTTAATATAGCATTAATATTGAAAAAAAAGAGTGTTTTCCT
* *
222995 AAAATTTCTTGGGAAAATGTAGTTTAAGAATTTTAAGTGTTGAAAATATGTTATAGTGAATTGAA
261 AAAATTTCATGGGAAAATGTAGTTTAAGAATTTTAAGTGTTGAAAATATGTTATAGTCAATTGAA
223060 ATATTCAAAATATATATATATACATAAAATAATTTTA
326 ATATTCAAAATATATATATATACATAAAATAATTTTA
* ** * * *
223097 ATTGTAAAGAACATGTCCTAGTTTCTTCACTTTAATTAAAGAATGATTCGAAGTGATAGTTAAGG
1 ATTGTAAAGAACATGTCCTAGTTGCTTCACTTTAACAAAAGAATGATTCAAAGTAATAGTTAAAG
** *
223162 TGAGCGCAAACTAAATAAAATGACAATTTTCCTCCTAAAATTTGTCTCTACACTCATGAAAAGTG
66 TGAAAGCAAACTAAATAAAATGACAATCTTCCTCCTAAAATTTGTCTCTACACTCATGAAAAGTG
*
223227 ATAACTCAAACCTAAAGAAAAGAATAGGACAAATTACTCTATTTCTATAAAAATTCATTGTATAT
131 ATAACTCAAACCTAAAGAAAAGAATAGGACAAATTACTCTATTTCTATAAAAATTCATTGTAAAT
* * *
223292 ATTCGA-TTTTTAGACAAATAAAGTTTAATATAGCATTAATGTTG-AAAAAAAGAGTGTTTTTCT
196 ATTCGAGATTTTAGACAAATAAAGTTTAATATAGCATTAATATTGAAAAAAAAGAGTGTTTTCCT
223355 AAAATTTCATGGGAAAATGTAGTTTAAGAATTTTAAGTGTT-AAAATATGTTATAGTCAATTGAA
261 AAAATTTCATGGGAAAATGTAGTTTAAGAATTTTAAGTGTTGAAAATATGTTATAGTCAATTGAA
223419 ATATTCAAAA
326 ATATTCAAAA
223429 AGATATCTAT
Statistics
Matches: 306, Mismatches: 26, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
359 32 0.10
360 57 0.19
361 36 0.12
362 181 0.59
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (362 bp):
ATTGTAAAGAACATGTCCTAGTTGCTTCACTTTAACAAAAGAATGATTCAAAGTAATAGTTAAAG
TGAAAGCAAACTAAATAAAATGACAATCTTCCTCCTAAAATTTGTCTCTACACTCATGAAAAGTG
ATAACTCAAACCTAAAGAAAAGAATAGGACAAATTACTCTATTTCTATAAAAATTCATTGTAAAT
ATTCGAGATTTTAGACAAATAAAGTTTAATATAGCATTAATATTGAAAAAAAAGAGTGTTTTCCT
AAAATTTCATGGGAAAATGTAGTTTAAGAATTTTAAGTGTTGAAAATATGTTATAGTCAATTGAA
ATATTCAAAATATATATATATACATAAAATAATTTTA
Found at i:225880 original size:840 final size:832
Alignment explanation
Indices: 223097--225927 Score: 4160
Period size: 840 Copynumber: 3.4 Consensus size: 832
223087 AATAATTTTA
* * *
223097 ATTGTAAAGAACATGTCCTAGTTTCTTCACTTTAATTAAAGAATGATTCGAAGTGATAGTTAAGG
1 ATTGTAAAGAACATGTCCTAGTTGCTTCACTTTGATTAAAGAATGATTCAAAGTGATAGTTAAGG
*
223162 TGAGCGCAAACTAAATAAAATGACAAT-TTTCCTCCTAAAATTTGTCTCTACACTCATGAAAAGT
66 TGAGAGCAAACTAAATAAAATGACAATCTTT-CTCCTAAAATTTGTCTCTACACTCATGAAAAGT
* *
223226 GATAACTCAAACCTAAAGAAAAGAATAGGACAAATTACTCTATTTCTATAAAAATTCATTGTATA
130 GATAACTCAAACCTAAAGAAAAGAATAGGATAAATTACTCTATTTCTATAAAAAATCATTGTATA
* *
223291 TATTCGA-TTTTTAGACAAATAAAGTTTAATATAGCATTAATGTTGAAAAAAAGAGTGTTTTTCT
195 TATTCGAGATTTTAGACAATTAAAGTTTAATATAGCATTAATGTTGAAAAAAA-AGTGTTTTTCT
*
223355 AAAATTTCATGGGAAAATGTAGTTTAAGAATTTTAAGTGTTAAAATATGTTATAGTCAATTGAAA
259 AAAATTTCATGAGAAAATGTAGTTTAAGAATTTTAAGTGTTAAAATATGTTATAGTCAATTGAAA
223420 TATTCAAAAAGATATCTATATATATATATATATACATAAAATAATTTTATAAATTAAAAATCATA
324 TATTCAAAAAGATATCTATATATATATATATATACATAAAATAATTTTATAAATTAAAAATCATA
* * *
223485 TAGCTACTGTCCTAAATTTTTTTAAAAATTATTAAGAAAATTTATGTTTGTAATTATAATTATTA
389 TAGCTAATGTCCTAAATTTTTTTAAAAATTATTAAAAAAATTTATGTTTTTAATTATAATTATTA
* * *
223550 TGTTCCATAATAAGTTGTCAAAATGAAAAAAAAAAATCATGATCATGATGCTCATAATGATCAAA
454 TGTTCTATAATAAGTTGTCAAATTG-AAAAAAAAAATCATGATCATGATGTTCATAATGATCAAA
* * *
223615 CTAGCATCAATTATATCTATAATCATAATAAACTTAATGTAACCAAAAATATATTTACGATGGTA
518 -TAGCATCAATTACATCTATAATCATAATAAATTTAATGTAACTAAAAATATATTTACGATGGTA
* * * *
223680 ATTTAAATATTTAATAACAACAAATAGGTCATTTGGCTATCGGTGATTAGTTGTATTAGTGAAAT
582 ATTTAAATATTTAATAACAACGAATAGGTCATTAGGCTATCGATGATTAGTTGTACTAGTGAAAT
* * *
223745 TATGACTTAAAAATTATTAAGGCCTTTTGCATGCTTAAATTAAATTAAAATTTTCACTTAATAAT
647 TATGATTTAGAAATTATTAAAGCCTTTTGCATGCTTAAATTAAATTAAAATTTTCA-TTAATAAT
* *
223810 GATTTTTTGT-CCCTTTTTTTTTATGATAGTTTAATTTTCTCAACAAGTTGGTCCTTCAAAAAGT
711 GATTTTTTGTCCCCTTTTTTTTTATGATTGTTTAATTTTCTCAACAAGTTAGTCCTTCAAAAAGT
*
223874 AAATATATCAAAATTGTTCCAAATATCTGTCAATAGAATCAAAGGTTACAAAATTTG
776 AAATATATCAAAACTGTTCCAAATATCTGTCAATAGAATCAAAGGTTACAAAATTTG
*
223931 ATTGTAAAGAACATGTCCTAGTTACTTCACTTTGATTAAAAGAATGATTCAAAGTGATAGTTAAG
1 ATTGTAAAGAACATGTCCTAGTTGCTTCACTTTGATT-AAAGAATGATTCAAAGTGATAGTTAAG
* * * *
223996 GTGAGAGCAAAGTAACTAAAATGACAATCTTTCTCTTAAAGTTTGTCTCTACACTCATGAAAAGT
65 GTGAGAGCAAACTAAATAAAATGACAATCTTTCTCCTAAAATTTGTCTCTACACTCATGAAAAGT
* *
224061 GATAACTCAAA-CTCAAAGAAAAGAATAGGATAAATTACTCAATTTTTATAAAAAATCA----A-
130 GATAACTCAAACCT-AAAGAAAAGAATAGGATAAATTACTCTATTTCTATAAAAAATCATTGTAT
*
224120 ATATTCGAGATTTTAGACGATTAAAGTTTAATATAGCATTAATGTTGAAAAAAAAAGTGTTTTTC
194 ATATTCGAGATTTTAGACAATTAAAGTTTAATATAGCATTAATGTTG-AAAAAAAAGTGTTTTTC
* *
224185 TAAAATTTCATGAGAAACTGTAGTTTAAGAATTTTAAGTGTTGAAAATATGTTATAGTGAATTGA
258 TAAAATTTCATGAGAAAATGTAGTTTAAGAATTTTAAGTGTT-AAAATATGTTATAGTCAATTGA
224250 AATATTCAAAAAG--------------ATATATATACATAAAATAATTTTATAAATTAAAAATCA
322 AATATTCAAAAAGATATCTATATATATATATATATACATAAAATAATTTTATAAATTAAAAATCA
224301 TATAGCTAATGTCCTAAATTTTTTTAAAAATTATTAAAAAAATTTAT-TTTTGTAATTATAATTA
387 TATAGCTAATGTCCTAAATTTTTTTAAAAATTATTAAAAAAATTTATGTTTT-TAATTATAATTA
* * *
224365 TTATGTTCTATAATAAGTTGTCAAAATGGAAAAACAAAATCATGATCATGATGTTTATAATGATC
451 TTATGTTCTATAATAAGTTGTC-AAATTGAAAAAAAAAATCATGATCATGATGTTCATAATGATC
* * *
224430 AAAATAGCATCAACTACATCTATAATCATAATAAACTTAAATGTAA-TAAAAAATATATTCACGA
515 -AAATAGCATCAATTACATCTATAATCATAATAAA-TTTAATGTAACT-AAAAATATATTTACGA
* * * *
224494 TGATAATTTAAATTTTTAATAACAACG-ATAGGTCATTAGGCTATCGATGATTAGTCGTACTAAT
577 TGGTAATTTAAATATTTAATAACAACGAATAGGTCATTAGGCTATCGATGATTAGTTGTACTAGT
* * * **
224558 GAAATTATGATTGAGAAATGATTAAAGTCTTTTGCATGCTTAAATTAAATTAAAATTTTTGTTTA
642 GAAATTATGATTTAGAAATTATTAAAGCCTTTTGCATGCTTAAATTAAATTAAAA-TTTTCATTA
* * * * *
224623 ATAATAATTTTTTGTCCCC---TATTTTATGATTATTTAATTTTCTCAACAATTTAGTCTTTCAA
706 ATAATGATTTTTTGTCCCCTTTTTTTTTATGATTGTTTAATTTTCTCAACAAGTTAGTCCTTCAA
* * *
224685 AAAGTAAATATATTAAAACTGTTCCAAATATCTGTCAATGGAGTCAAAGGTTACAAAATTTG
771 AAAGTAAATATATCAAAACTGTTCCAAATATCTGTCAATAGAATCAAAGGTTACAAAATTTG
* *
224747 ATTGTAAAGAACATATCCTAGTTGCTTCACTTTGATTAAAGAATGATTCAAAGTGATGGTTAAGG
1 ATTGTAAAGAACATGTCCTAGTTGCTTCACTTTGATTAAAGAATGATTCAAAGTGATAGTTAAGG
* * * * * * * * *
224812 TGAAAACAAACCAAATAAAATGGCAATCTTCCTTCTAAAATTTGTTTCTACACTCGTAAAAAGTG
66 TGAGAGCAAACTAAATAAAATGACAATCTTTCTCCTAAAATTTGTCTCTACACTCATGAAAAGTG
* * *
224877 ATAACTCAAACCTAAAGAAAAGAATAGGATAAATTACTCTATTTCTATAAAAAAATCTTTATAAA
131 ATAACTCAAACCTAAAGAAAAGAATAGGATAAATTACTCTATTTCTAT-AAAAAATCATTGTATA
*
224942 TATTCGAGATTTTAGACAATTAAAGTTTAATTTAGCATTAATGTTGAAAAAAAAGTGTTTTTCTA
195 TATTCGAGATTTTAGACAATTAAAGTTTAATATAGCATTAATGTTGAAAAAAAAGTGTTTTTCTA
225007 AAATTTCATG-GAAAAATGTAGTTTAAGAATTTTAAGTGTTAAAATATGTTATAGTCAATTGAAA
260 AAATTTCATGAG-AAAATGTAGTTTAAGAATTTTAAGTGTTAAAATATGTTATAGTCAATTGAAA
225071 TATTCAAAAAGATATCTATATATATATATATATATATACATAAAATAATTTTATAAATTAAAAAT
324 TATTCAAAAAGATATC----TATATATATATATATATACATAAAATAATTTTATAAATTAAAAAT
* *
225136 CATATAGCTAGTGTCCTAAATTTTTTTAAAAATTATTAAAAAATATTTATGTTTTTAATTATGAT
385 CATATAGCTAATGTCCTAAATTTTTTTAAAAATTATTAAAAAA-ATTTATGTTTTTAATTATAAT
* * ** *
225201 TATTATATTCTATAATAAGTTGTCAAATTGAAAAAAAAAATCATTATCGCGATGTTCGTAATGAT
449 TATTATGTTCTATAATAAGTTGTCAAATTGAAAAAAAAAATCATGATCATGATGTTCATAATGAT
* * * * *
225266 CATGATAGTATTAATTACATCTATATTCATAATAAATTTAATGTAACTAAAAATATATTTACAAT
514 CA-AATAGCATCAATTACATCTATAATCATAATAAATTTAATGTAACTAAAAATATATTTACGAT
* *
225331 GGTAATTTAAATCTTTAATAACAACGAATAAGTCATTAGGCTATCGATGATTAGTTGTACTAGT-
578 GGTAATTTAAATATTTAATAACAACGAATAGGTCATTAGGCTATCGATGATTAGTTGTACTAGTG
225395 AAAGTTATGATTTAGAAATTATTAAAGCCTTTTGCATGCTTAAATTAAATTAAAATTTTCATTAA
643 AAA-TTATGATTTAGAAATTATTAAAGCCTTTTGCATGCTTAAATTAAATTAAAATTTTCATT-A
* *
225460 ATAATGATTTTTGGTCCCCTTTTTTTTTATAATTGTTTAATTTTCTCAACAAGTTAGTCCTTCAA
706 ATAATGATTTTTTGTCCCCTTTTTTTTTATGATTGTTTAATTTTCTCAACAAGTTAGTCCTTCAA
* * *
225525 AAGGTAAATATATCAAAACTGTTCTAAATATCTGTCCATAGAATCAAAGGTTACAAAATTTG
771 AAAGTAAATATATCAAAACTGTTCCAAATATCTGTCAATAGAATCAAAGGTTACAAAATTTG
*
225587 ATTGTAAAGAACATGTCCTAGTTGCTTCACTTTGATTAAAGAATGATTCAAAGTGATGGTTAAGG
1 ATTGTAAAGAACATGTCCTAGTTGCTTCACTTTGATTAAAGAATGATTCAAAGTGATAGTTAAGG
* * * * ** *
225652 CGAGAGCAAACTAAGTAAAATGACAGTCTTTTTTTTAAAATTTATCTCTACACTCATGAAAAGTG
66 TGAGAGCAAACTAAATAAAATGACAATCTTTCTCCTAAAATTTGTCTCTACACTCATGAAAAGTG
* * *
225717 ATAACTCAAACCTAAAAAAAAGAATAAGATAAATTACTCTATTTTTATAAAAAAAATCATTGTAT
131 ATAACTCAAACCTAAAGAAAAGAATAGGATAAATTACTCTATTTCTAT--AAAAAATCATTGTAT
*
225782 ATATTCGAGATTTTAGACAATTAAAATTTAATATAGCATTAATGTTG-AAAAAAAGTGTTTTTCT
194 ATATTCGAGATTTTAGACAATTAAAGTTTAATATAGCATTAATGTTGAAAAAAAAGTGTTTTTCT
* * * * * *
225846 AAAATTTCATGAGAAAATGTAATTTAAAAATTTTAAGCGTCAAAAAATATGTTATAGTGAATCGA
259 AAAATTTCATGAGAAAATGTAGTTTAAGAATTTTAAGTGT--TAAAATATGTTATAGTCAATTGA
225911 AATATTCAAAAAGATAT
322 AATATTCAAAAAGATAT
225928 ATACACATAA
Statistics
Matches: 1791, Mismatches: 153, Indels: 98
0.88 0.07 0.05
Matches are distributed among these distances:
815 122 0.07
816 140 0.08
817 3 0.00
818 276 0.15
819 96 0.05
820 57 0.03
821 45 0.03
830 8 0.00
831 86 0.05
832 41 0.02
834 37 0.02
835 133 0.07
836 61 0.03
837 242 0.14
838 38 0.02
839 4 0.00
840 306 0.17
841 59 0.03
842 37 0.02
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (832 bp):
ATTGTAAAGAACATGTCCTAGTTGCTTCACTTTGATTAAAGAATGATTCAAAGTGATAGTTAAGG
TGAGAGCAAACTAAATAAAATGACAATCTTTCTCCTAAAATTTGTCTCTACACTCATGAAAAGTG
ATAACTCAAACCTAAAGAAAAGAATAGGATAAATTACTCTATTTCTATAAAAAATCATTGTATAT
ATTCGAGATTTTAGACAATTAAAGTTTAATATAGCATTAATGTTGAAAAAAAAGTGTTTTTCTAA
AATTTCATGAGAAAATGTAGTTTAAGAATTTTAAGTGTTAAAATATGTTATAGTCAATTGAAATA
TTCAAAAAGATATCTATATATATATATATATACATAAAATAATTTTATAAATTAAAAATCATATA
GCTAATGTCCTAAATTTTTTTAAAAATTATTAAAAAAATTTATGTTTTTAATTATAATTATTATG
TTCTATAATAAGTTGTCAAATTGAAAAAAAAAATCATGATCATGATGTTCATAATGATCAAATAG
CATCAATTACATCTATAATCATAATAAATTTAATGTAACTAAAAATATATTTACGATGGTAATTT
AAATATTTAATAACAACGAATAGGTCATTAGGCTATCGATGATTAGTTGTACTAGTGAAATTATG
ATTTAGAAATTATTAAAGCCTTTTGCATGCTTAAATTAAATTAAAATTTTCATTAATAATGATTT
TTTGTCCCCTTTTTTTTTATGATTGTTTAATTTTCTCAACAAGTTAGTCCTTCAAAAAGTAAATA
TATCAAAACTGTTCCAAATATCTGTCAATAGAATCAAAGGTTACAAAATTTG
Found at i:226294 original size:2 final size:2
Alignment explanation
Indices: 226287--226320 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
226277 TGTTTCTATG
226287 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
226321 GACAAGTACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:228382 original size:2 final size:2
Alignment explanation
Indices: 228375--228405 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
228365 CATAGAAGTG
*
228375 TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
228406 TTACAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:228657 original size:16 final size:16
Alignment explanation
Indices: 228636--228667 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
228626 AACTATGTGT
228636 TGAACATGGCTGTCGA
1 TGAACATGGCTGTCGA
228652 TGAACATGGCTGTCGA
1 TGAACATGGCTGTCGA
228668 ACATAGATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (16 bp):
TGAACATGGCTGTCGA
Found at i:229900 original size:2 final size:2
Alignment explanation
Indices: 229895--229925 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
229885 AAAAAAAAGC
229895 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
229926 CACCCATATT
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:231712 original size:16 final size:15
Alignment explanation
Indices: 231691--231726 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
231681 AGGCAACCAG
*
231691 AAAAAAGCTGAAAAAA
1 AAAAAAGC-CAAAAAA
231707 AAAAAAGCCAAAAAA
1 AAAAAAGCCAAAAAA
231722 AAAAA
1 AAAAA
231727 CAGAGTAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.81, C:0.08, G:0.08, T:0.03
Consensus pattern (15 bp):
AAAAAAGCCAAAAAA
Found at i:232104 original size:20 final size:19
Alignment explanation
Indices: 232081--232126 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 19
232071 AATTATTATA
232081 AATATAATAAATAAAATATT
1 AATATAAT-AATAAAATATT
232101 AATAT--T-ATAAAATATT
1 AATATAATAATAAAATATT
232117 AATTATAATA
1 AA-TATAATA
232127 TTATATTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 8
0.73 0.00 0.27
Matches are distributed among these distances:
16 12 0.55
17 3 0.14
18 1 0.05
19 1 0.05
20 5 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATATAATAATAAAATATT
Found at i:232112 original size:16 final size:16
Alignment explanation
Indices: 232069--232119 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
232059 TATATATTAT
232069 TTAATTATTAT-AAATA
1 TTAA-TATTATAAAATA
*
232085 -TAATA-AATAAAATA
1 TTAATATTATAAAATA
232099 TTAATATTATAAAATA
1 TTAATATTATAAAATA
232115 TTAAT
1 TTAAT
232120 TATAATATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 2 0.07
14 7 0.23
15 8 0.27
16 13 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TTAATATTATAAAATA
Found at i:232134 original size:17 final size:17
Alignment explanation
Indices: 232112--232145 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
232102 ATATTATAAA
232112 ATATTA-ATTATAATATT
1 ATATTACATT-TAATATT
232129 ATATTACATTTAATATT
1 ATATTACATTTAATATT
232146 TAAATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATTACATTTAATATT
Found at i:232284 original size:17 final size:17
Alignment explanation
Indices: 232247--232281 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
232237 AATTTAATTT
232247 AATTTAATTTATAAATA
1 AATTTAATTTATAAATA
*
232264 AATTTAA-TTATTAATA
1 AATTTAATTTATAAATA
232280 AA
1 AA
232282 ATTATAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTTAATTTATAAATA
Found at i:232685 original size:40 final size:42
Alignment explanation
Indices: 232626--232720 Score: 106
Period size: 41 Copynumber: 2.3 Consensus size: 42
232616 ATCATAAAAT
232626 ATATATTTAATACAAA-TTTTTATTT-TATTTTAAAAAAATTTC
1 ATATA-TTAATACAAATTTTTTATTTATA-TTTAAAAAAATTTC
* * *
232668 ATATATTAAT-CATATTTTTTATTTATATTTAAATATATTTC
1 ATATATTAATACAAATTTTTTATTTATATTTAAAAAAATTTC
* *
232709 AAATATAAATAC
1 ATATATTAATAC
232721 TTACATTTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
40 3 0.07
41 34 0.76
42 8 0.18
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (42 bp):
ATATATTAATACAAATTTTTTATTTATATTTAAAAAAATTTC
Found at i:235059 original size:33 final size:33
Alignment explanation
Indices: 235013--235076 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 33
235003 GACAAATAAT
235013 ATTTAAAATAAAAATTAT-TTTATATATTTAAAG
1 ATTTAAAATAAAAATTATATTT-TATATTTAAAG
235046 ATTTATAAA-AAAAATTATACTTTTATATTTA
1 ATTTA-AAATAAAAATTATA-TTTTATATTTA
235077 TATTAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
33 14 0.50
34 11 0.39
35 3 0.11
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (33 bp):
ATTTAAAATAAAAATTATATTTTATATTTAAAG
Found at i:236507 original size:15 final size:16
Alignment explanation
Indices: 236476--236509 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
236466 CCCGTATTAG
236476 ATATAAATATTTATTTA
1 ATATAAATA-TTATTTA
236493 ATATAAATA-TATTTA
1 ATATAAATATTATTTA
236508 AT
1 AT
236510 TTTTATTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
17 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATAAATATTATTTA
Found at i:242171 original size:2 final size:2
Alignment explanation
Indices: 242164--242197 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
242154 CACTATAAAC
242164 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
242198 GTGCGAACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:242552 original size:17 final size:17
Alignment explanation
Indices: 242516--242553 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
242506 TGATTATGTC
*
242516 GATTATAGATTTGATAA
1 GATTATAGATTTCATAA
242533 GATTATAGATATTCAT-A
1 GATTATAGAT-TTCATAA
242550 GATT
1 GATT
242554 GAATTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.39, C:0.03, G:0.16, T:0.42
Consensus pattern (17 bp):
GATTATAGATTTCATAA
Found at i:242652 original size:22 final size:20
Alignment explanation
Indices: 242622--242665 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
242612 ATAGGTTAAA
242622 AAATGAATTTGAGCAAAAAATT
1 AAATGAATTTGA--AAAAAATT
* *
242644 AAATTAATTTTAAAAAAATT
1 AAATGAATTTGAAAAAAATT
242664 AA
1 AA
242666 CTTAGCTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 10 0.50
22 10 0.50
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (20 bp):
AAATGAATTTGAAAAAAATT
Found at i:246860 original size:2 final size:2
Alignment explanation
Indices: 246853--246886 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
246843 GGCTGTTAAA
246853 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
246887 TAGCTTGACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:247573 original size:22 final size:21
Alignment explanation
Indices: 247527--247573 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
247517 TTTCAAAAAT
* *
247527 TTTTAAAAATAATATTTTATC
1 TTTTAAAAATAATATTTGATA
247548 TTTTAAAAATAAT-TATTGACTA
1 TTTTAAAAATAATAT-TTGA-TA
247570 TTTT
1 TTTT
247574 TATTTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 1 0.05
21 16 0.73
22 5 0.23
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (21 bp):
TTTTAAAAATAATATTTGATA
Found at i:248390 original size:21 final size:21
Alignment explanation
Indices: 248366--248405 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
248356 TTTAAAAAAT
*
248366 TATTTT-TTATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
248387 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
248406 AATAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:248583 original size:20 final size:20
Alignment explanation
Indices: 248545--248583 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
248535 TAGCCATTGG
** *
248545 ATGATTTTATTTTATTATTT
1 ATGATTTTATTAAAATATTT
248565 ATGATTTTATTAAAATATT
1 ATGATTTTATTAAAATATT
248584 ATTTTCATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (20 bp):
ATGATTTTATTAAAATATTT
Found at i:248609 original size:21 final size:21
Alignment explanation
Indices: 248579--248655 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 21
248569 TTTTATTAAA
248579 ATAT-TATTTTCATAATATAT
1 ATATATATTTTCATAATATAT
* *
248599 TTATATATTTTTATAAT-TA-
1 ATATATATTTTCATAATATAT
*
248618 AAATACTATTTTCATAATATAT
1 ATATA-TATTTTCATAATATAT
* **
248640 CTACGTATTTTCATAA
1 ATATATATTTTCATAA
248656 CAAGTTAGCG
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
19 3 0.07
20 16 0.36
21 24 0.55
22 1 0.02
ACGTcount: A:0.39, C:0.08, G:0.01, T:0.52
Consensus pattern (21 bp):
ATATATATTTTCATAATATAT
Found at i:248629 original size:20 final size:19
Alignment explanation
Indices: 248573--248635 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 19
248563 TTATGATTTT
248573 ATTAAAATATTATTTTCATA
1 ATTAAAATA-TATTTTCATA
** *
248593 ATATATTTATATATTTTTATA
1 AT-TA-AAATATATTTTCATA
248614 ATTAAAATACTATTTTCATA
1 ATTAAAATA-TATTTTCATA
248634 AT
1 AT
248636 ATATCTACGT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 3 0.09
20 15 0.44
21 13 0.38
22 3 0.09
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTAAAATATATTTTCATA
Found at i:248649 original size:41 final size:41
Alignment explanation
Indices: 248573--248655 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
248563 TTATGATTTT
* * * *
248573 ATTAAAATATTATTTTCATAATATATTTATATATTTTTATA
1 ATTAAAATACTATTTTCATAATATATCTACATATTTTCATA
*
248614 ATTAAAATACTATTTTCATAATATATCTACGTATTTTCATA
1 ATTAAAATACTATTTTCATAATATATCTACATATTTTCATA
248655 A
1 A
248656 CAAGTTAGCG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.51
Consensus pattern (41 bp):
ATTAAAATACTATTTTCATAATATATCTACATATTTTCATA
Found at i:252346 original size:2 final size:2
Alignment explanation
Indices: 252334--252371 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
252324 CAACAAATGA
252334 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
252372 GCATTGCTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:252448 original size:2 final size:2
Alignment explanation
Indices: 252441--252469 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
252431 TGTCATAGTG
252441 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
252470 TGTATATGGG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.