Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold5
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: 1536239
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.33
Warning! 124408 characters in sequence are not A, C, G, or T
File 2 of 14
Found at i:198548 original size:15 final size:15
Alignment explanation
Indices: 198519--198567 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
198509 ATTAATTTTA
198519 TATATTTA-TATAATT
1 TATATTTATTA-AATT
198534 TATATTTATTAAATT
1 TATATTTATTAAATT
*
198549 TA-A-TTATTATATT
1 TATATTTATTAAATT
198562 T-TATTT
1 TATATTT
198568 TTTATTTATG
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 11 0.37
14 3 0.10
15 14 0.47
16 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TATATTTATTAAATT
Found at i:200774 original size:78 final size:78
Alignment explanation
Indices: 200645--200789 Score: 202
Period size: 78 Copynumber: 1.9 Consensus size: 78
200635 TTCTACTATA
** * * *
200645 ATAAACTTAACAAAGTGTAACTGACTAAATGAGTCAATTTGATAAACTCGACAAAGTGTAGCCGA
1 ATAAACTTAACAAAGTCCAACTAAATAAATGAGTCAATTTGATAAACTCGACAAAGTGTAACCGA
200710 CTGAGCAACTTCG
66 CTGAGCAACTTCG
* * *
200723 ATAAACTTGACAAAGTCCAACTAAATAAATTAGT-ATATTTGATAAATTCGACAAAGTGTAACCG
1 ATAAACTTAACAAAGTCCAACTAAATAAATGAGTCA-ATTTGATAAACTCGACAAAGTGTAACCG
200787 ACT
65 ACT
200790 AAGTGAACTT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
77 1 0.02
78 57 0.98
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (78 bp):
ATAAACTTAACAAAGTCCAACTAAATAAATGAGTCAATTTGATAAACTCGACAAAGTGTAACCGA
CTGAGCAACTTCG
Found at i:201158 original size:18 final size:20
Alignment explanation
Indices: 201131--201182 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
201121 TTATTATTAT
201131 ATTATATTT-AATA-TTAAA
1 ATTATATTTAAATATTTAAA
*
201149 ATTATTTTTAAATATTTAAA
1 ATTATATTTAAATATTTAAA
201169 ATCT-TATTTAAATA
1 AT-TATATTTAAATA
201183 AATAAATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 8 0.28
19 4 0.14
20 16 0.55
21 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTATATTTAAATATTTAAA
Found at i:201336 original size:20 final size:20
Alignment explanation
Indices: 201292--201336 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
201282 ATTTTGGTAC
*
201292 TAAATATAAAAAAAAATTAA
1 TAAATATAAAAAAAAAATAA
201312 TAAATATAAAAAATAAAATAA
1 TAAATATAAAAAA-AAAATAA
201333 -AAAT
1 TAAAT
201337 GACATAACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (20 bp):
TAAATATAAAAAAAAAATAA
Found at i:202487 original size:31 final size:34
Alignment explanation
Indices: 202421--202484 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
202411 ATTTTTTCCA
* *
202421 ATTTTTTTTGAAAATAAATTGTATGTAAACATTT
1 ATTTTTTTTGAAAATAAATAGTATATAAACATTT
202455 ATTTTTTTT-AAAA-AAA-AGTATAT-AACATTT
1 ATTTTTTTTGAAAATAAATAGTATATAAACATTT
202485 TATATTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 7 0.25
31 5 0.18
32 3 0.11
33 4 0.14
34 9 0.32
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (34 bp):
ATTTTTTTTGAAAATAAATAGTATATAAACATTT
Found at i:202640 original size:2 final size:2
Alignment explanation
Indices: 202633--202710 Score: 111
Period size: 2 Copynumber: 39.0 Consensus size: 2
202623 TTTAAATTTA
* * * *
202633 AT AT AT AT AT AT AT AT AT GT GT AT AT AT AT AT AT AT AT GT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
202675 GT 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
202711 CATCTATTGT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:202659 original size:20 final size:20
Alignment explanation
Indices: 202634--202710 Score: 127
Period size: 20 Copynumber: 3.9 Consensus size: 20
202624 TTAAATTTAA
202634 TATATATATATATATATGTG
1 TATATATATATATATATGTG
202654 TATATATATATATATATGTG
1 TATATATATATATATATGTG
* * *
202674 TGTATATATATATATATATA
1 TATATATATATATATATGTG
202694 TATATATATATATATAT
1 TATATATATATATATAT
202711 CATCTATTGT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (20 bp):
TATATATATATATATATGTG
Found at i:203061 original size:24 final size:23
Alignment explanation
Indices: 203034--203104 Score: 74
Period size: 23 Copynumber: 3.0 Consensus size: 23
203024 ATTATTAAAA
*
203034 ATAAAAATTTAATAATATAATTT
1 ATAAAAATTTAATATTATAATTT
*
203057 GAT-AAAATTAAATATTTATAATTT
1 -ATAAAAATTTAATA-TTATAATTT
*
203081 ATATAAAAATTAATATTA-AATTT
1 ATA-AAAATTTAATATTATAATTT
203104 A
1 A
203105 ATGGTTCAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
23 18 0.45
24 13 0.32
25 9 0.22
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (23 bp):
ATAAAAATTTAATATTATAATTT
Found at i:204695 original size:11 final size:11
Alignment explanation
Indices: 204681--204785 Score: 67
Period size: 11 Copynumber: 9.1 Consensus size: 11
204671 TAAGTAATTT
204681 TTATATTTATA
1 TTATATTTATA
*
204692 TTATAATTATA
1 TTATATTTATA
204703 TTTATGAGATTTATA
1 -TTAT---ATTTATA
204718 TTATATATT-TA
1 TTATAT-TTATA
204729 TCATATAATTTATA
1 T--TAT-ATTTATA
*
204743 TTATATATCATA
1 TTATAT-TTATA
204755 TTATATTT-TAA
1 TTATATTTAT-A
204766 TTATATTT-TA
1 TTATATTTATA
204776 -TATA-TTATA
1 TTATATTTATA
204785 T
1 T
204786 GAAAAGTTAT
Statistics
Matches: 77, Mismatches: 4, Indels: 27
0.71 0.04 0.25
Matches are distributed among these distances:
8 2 0.03
9 6 0.08
10 2 0.03
11 28 0.36
12 19 0.25
13 5 0.06
14 9 0.12
15 6 0.08
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (11 bp):
TTATATTTATA
Found at i:204705 original size:25 final size:27
Alignment explanation
Indices: 204677--204785 Score: 79
Period size: 26 Copynumber: 4.1 Consensus size: 27
204667 TATTTAAGTA
204677 ATTTTTATATT-TATATTATA-ATTAT
1 ATTTTTATATTATATATTATATATTAT
* *
204702 ATTTATGAGATT-TATATTATATATTTAT
1 ATTT-TTATATTATATATTATATA-TTAT
*
204730 CATATAATTTATATTATATA-T-CATATTAT
1 -AT-T--TTTATATTATATATTATATATTAT
*
204759 A-TTTTA-ATTATATTTTATATATTAT
1 ATTTTTATATTATATATTATATATTAT
204784 AT
1 AT
204786 GAAAAGTTAT
Statistics
Matches: 66, Mismatches: 7, Indels: 21
0.70 0.07 0.22
Matches are distributed among these distances:
23 7 0.11
24 5 0.08
25 12 0.18
26 15 0.23
27 1 0.02
28 5 0.08
29 6 0.09
30 4 0.06
31 6 0.09
32 5 0.08
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (27 bp):
ATTTTTATATTATATATTATATATTAT
Found at i:204723 original size:5 final size:5
Alignment explanation
Indices: 204681--204785 Score: 63
Period size: 5 Copynumber: 20.2 Consensus size: 5
204671 TAAGTAATTT
* * *
204681 TTATA TTTATA TTATAA TTATA TT-TA TGAGA TTTATA TTATA TATTTA
1 TTATA -TTATA TTAT-A TTATA TTATA TTATA -TTATA TTATA T-TATA
* * * *
204729 TCATA TAAT- TTATA TTATA TATCATA TTATA TTTTAA TTATA TTTTA
1 TTATA TTATA TTATA TTATA T-T-ATA TTATA TTAT-A TTATA TTATA
204776 -TATA TTATA T
1 TTATA TTATA T
204786 GAAAAGTTAT
Statistics
Matches: 77, Mismatches: 13, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
4 9 0.12
5 41 0.53
6 23 0.30
7 4 0.05
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:205090 original size:16 final size:15
Alignment explanation
Indices: 205069--205146 Score: 57
Period size: 17 Copynumber: 4.5 Consensus size: 15
205059 GTGTTATAAT
205069 ATATTTAAAAATTTA
1 ATATTTAAAAATTTA
205084 GATATTTATATAAAATTTA
1 -ATA-TT-TA-AAAATTTA
205103 ATATATTAAAAATTTATA
1 ATAT-TTAAAAA-TT-TA
*
205121 ATATTATATAAAATCTA
1 ATATT-TA-AAAATTTA
205138 ATATATTAA
1 ATAT-TTAA
205147 TGTATTTATA
Statistics
Matches: 52, Mismatches: 1, Indels: 18
0.73 0.01 0.25
Matches are distributed among these distances:
16 8 0.15
17 16 0.31
18 16 0.31
19 12 0.23
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (15 bp):
ATATTTAAAAATTTA
Found at i:205100 original size:19 final size:18
Alignment explanation
Indices: 205076--205141 Score: 66
Period size: 19 Copynumber: 3.7 Consensus size: 18
205066 AATATATTTA
205076 AAAATTTAGATATTTATAT
1 AAAATTTA-ATATTTATAT
*
205095 AAAATTTAATATAT-TA-
1 AAAATTTAATATTTATAT
205111 AAAATTT-ATAATATTATAT
1 AAAATTTAAT-AT-TTATAT
*
205130 AAAATCTAATAT
1 AAAATTTAATAT
205142 ATTAATGTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
15 2 0.05
16 9 0.23
17 3 0.08
18 7 0.18
19 16 0.41
20 2 0.05
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
AAAATTTAATATTTATAT
Found at i:205116 original size:35 final size:35
Alignment explanation
Indices: 205065--205146 Score: 121
Period size: 35 Copynumber: 2.3 Consensus size: 35
205055 TGTAGTGTTA
*
205065 TAATATATTTAAAAATTTAG-ATATTTATATAAAATT
1 TAATATA-TTAAAAATTTAGAATA-TTATATAAAATC
*
205101 TAATATATTAAAAATTTATAATATTATATAAAATC
1 TAATATATTAAAAATTTAGAATATTATATAAAATC
205136 TAATATATTAA
1 TAATATATTAA
205147 TGTATTTATA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
35 33 0.77
36 10 0.23
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (35 bp):
TAATATATTAAAAATTTAGAATATTATATAAAATC
Found at i:205187 original size:20 final size:19
Alignment explanation
Indices: 205149--205193 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
205139 TATATTAATG
*
205149 TATTTATATTTTATTTATA
1 TATTTATATTTTATATATA
205168 TTATTTATTATTTTA-ATATA
1 -TATTTA-TATTTTATATATA
205188 TATTTA
1 TATTTA
205194 AAATTATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 6 0.26
20 10 0.43
21 7 0.30
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TATTTATATTTTATATATA
Found at i:206786 original size:24 final size:22
Alignment explanation
Indices: 206726--206787 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 22
206716 AATATATATT
206726 TATTATTTTTT-TATTTTATAAA
1 TATTATTTTTTATA-TTTATAAA
*
206748 TATTATTTTAATATATTTACTAATA
1 TATTATTTT-TTATATTTA-TAA-A
*
206773 TTTTATTTTTTATAT
1 TATTATTTTTTATAT
206788 AATAATATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
22 9 0.27
23 5 0.15
24 10 0.30
25 9 0.27
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (22 bp):
TATTATTTTTTATATTTATAAA
Found at i:206982 original size:17 final size:17
Alignment explanation
Indices: 206938--207000 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 17
206928 TTATTTTATT
206938 ATAATTATATTTAAAATA
1 ATAATT-TATTTAAAATA
*
206956 ATATATTTATTTAAAATT
1 ATA-ATTTATTTAAAATA
* * *
206974 TTAATTTA-TTATATTA
1 ATAATTTATTTAAAATA
206990 ATAATTTATTT
1 ATAATTTATTT
207001 TTATATATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
16 12 0.32
17 7 0.19
18 15 0.41
19 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATAATTTATTTAAAATA
Found at i:206983 original size:21 final size:22
Alignment explanation
Indices: 206954--206996 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
206944 ATATTTAAAA
206954 TAATATATT-TATTTAA-AATTT
1 TAATATATTATA-TTAATAATTT
*
206975 TAATTTATTATATTAATAATTT
1 TAATATATTATATTAATAATTT
206997 ATTTTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TAATATATTATATTAATAATTT
Found at i:207051 original size:22 final size:21
Alignment explanation
Indices: 206934--207052 Score: 65
Period size: 22 Copynumber: 5.7 Consensus size: 21
206924 ATTTTTATTT
206934 TATTATAATTATATTTAAA--A
1 TATTAT-ATTATATTTAAATTA
* *
206954 TAATATATT-TATTTAAAATTT
1 TATTATATTATATTT-AAATTA
*
206975 TAATT-TATTATATTAATAATT-
1 T-ATTATATTATATTTA-AATTA
* **
206996 TATTTTTATATATATTTTGA-TA
1 TA-TTATAT-TATATTTAAATTA
207018 TATT-TA-TATATTTAAATTAA
1 TATTATATTATATTTAAATT-A
207038 TATTATATTATATTT
1 TATTATATTATATTT
207053 TTTTTCTTAC
Statistics
Matches: 76, Mismatches: 9, Indels: 26
0.68 0.08 0.23
Matches are distributed among these distances:
18 13 0.17
19 7 0.09
20 13 0.17
21 14 0.18
22 23 0.30
23 6 0.08
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (21 bp):
TATTATATTATATTTAAATTA
Found at i:210658 original size:13 final size:13
Alignment explanation
Indices: 210640--210664 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
210630 GTAATGCTCT
210640 TTTATGAACTACA
1 TTTATGAACTACA
210653 TTTATGAACTAC
1 TTTATGAACTAC
210665 TGAACTTGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (13 bp):
TTTATGAACTACA
Found at i:214247 original size:15 final size:15
Alignment explanation
Indices: 214227--214268 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
214217 GTGATTAAAA
214227 AAAATTATAAATTTT
1 AAAATTATAAATTTT
*
214242 AAAATT-TTAATTTT
1 AAAATTATAAATTTT
*
214256 AAATTTATTAAAT
1 AAAATTA-TAAAT
214269 ATTATTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 12 0.55
15 6 0.27
16 4 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AAAATTATAAATTTT
Found at i:214275 original size:21 final size:21
Alignment explanation
Indices: 214229--214277 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
214219 GATTAAAAAA
* *
214229 AATTATAAATTTTAAAATTTT
1 AATTTTAAATTTTAAAATATT
*
214250 AATTTTAAATTTATTAAATATT
1 AATTTTAAATTT-TAAAATATT
*
214272 ATTTTT
1 AATTTT
214278 TTAAATTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
AATTTTAAATTTTAAAATATT
Found at i:214863 original size:6 final size:6
Alignment explanation
Indices: 214852--214880 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
214842 CTTCCACCTA
214852 TCAATT TCAATT TCAATT TCAATT TCAAT
1 TCAATT TCAATT TCAATT TCAATT TCAAT
214881 GTCTATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.48
Consensus pattern (6 bp):
TCAATT
Found at i:214888 original size:18 final size:18
Alignment explanation
Indices: 214852--214888 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
214842 CTTCCACCTA
*
214852 TCAATTTCAATTTCAATT
1 TCAATTTCAATGTCAATT
*
214870 TCAATTTCAATGTCTATT
1 TCAATTTCAATGTCAATT
214888 T
1 T
214889 TATTTTCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.16, G:0.03, T:0.51
Consensus pattern (18 bp):
TCAATTTCAATGTCAATT
Found at i:215399 original size:3 final size:3
Alignment explanation
Indices: 215391--215422 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
215381 CTTATAAACA
215391 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
215423 AAATTTACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:216193 original size:13 final size:13
Alignment explanation
Indices: 216177--216235 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
216167 ATTTAATAAT
216177 TCATATATTTATA
1 TCATATATTTATA
216190 TCATATA-TTAT-
1 TCATATATTTATA
*
216201 TTATATATTTTATA
1 TCATATA-TTTATA
**
216215 TTTTATATTTCATAA
1 TCATATATTT-AT-A
216230 TCATAT
1 TCATAT
216236 TTAAATTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 6 0.16
12 4 0.11
13 14 0.38
14 8 0.22
15 5 0.14
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.58
Consensus pattern (13 bp):
TCATATATTTATA
Found at i:216223 original size:14 final size:14
Alignment explanation
Indices: 216198--216333 Score: 52
Period size: 13 Copynumber: 9.4 Consensus size: 14
216188 TATCATATAT
216198 TATTTATATATTTTA
1 TATTT-TATATTTTA
*
216213 TATTTTATATTTCA
1 TATTTTATATTTTA
* *
216227 TA-ATCATA-TTTA
1 TATTTTATATTTTA
*
216239 AATTATTATAAATTTATA
1 TATT-TTAT--ATTT-TA
*
216257 TAAATTTTAATATATTAA
1 T--ATTTT-ATAT-TTTA
*
216275 TAATTTT-TATTATA
1 T-ATTTTATATTTTA
*
216289 TAATTT-T-TTTTA
1 TATTTTATATTTTA
*
216301 TATATTTATATCTT-
1 TAT-TTTATATTTTA
216315 TATTTTATA-TTTA
1 TATTTTATATTTTA
216328 TATTTT
1 TATTTT
216334 TTTATCGTAT
Statistics
Matches: 91, Mismatches: 16, Indels: 30
0.66 0.12 0.22
Matches are distributed among these distances:
12 12 0.13
13 24 0.26
14 20 0.22
15 11 0.12
16 1 0.01
17 8 0.09
18 6 0.07
19 4 0.04
20 5 0.05
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTTTATATTTTA
Found at i:216282 original size:18 final size:18
Alignment explanation
Indices: 216256--216306 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
216246 ATAAATTTAT
*
216256 ATAAATTTTAATATATTA
1 ATAATTTTTAATATATTA
*
216274 ATAATTTTTATTATA-TA
1 ATAATTTTTAATATATTA
* *
216291 AT-TTTTTTTATATATT
1 ATAATTTTTAATATATT
216307 TATATCTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 9 0.33
17 5 0.19
18 13 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATAATTTTTAATATATTA
Found at i:224280 original size:21 final size:22
Alignment explanation
Indices: 224227--224281 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 22
224217 TATATATTTT
224227 ATAA-TTAAATTTAAATAAAAATA
1 ATAATTTAAATTT--ATAAAAATA
224250 A-AATTT--ATTTAT-AAAATA
1 ATAATTTAAATTTATAAAAATA
224268 ATAATTTAAATTTA
1 ATAATTTAAATTTA
224282 AAACCAATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
18 7 0.25
19 7 0.25
21 9 0.32
22 2 0.07
23 3 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATAATTTAAATTTATAAAAATA
Found at i:224283 original size:19 final size:18
Alignment explanation
Indices: 224233--224303 Score: 58
Period size: 17 Copynumber: 4.0 Consensus size: 18
224223 TTTTATAATT
*
224233 AAATTTAAA-TAAAAATA
1 AAATTTAAATTTAAAATA
*
224250 AAATTT-ATTTATAAAATA
1 AAATTTAAATT-TAAAATA
*
224268 ATAATTTAAATTTAAAA-C
1 A-AATTTAAATTTAAAATA
* *
224286 CAATTCAAATTTAAAATA
1 AAATTTAAATTTAAAATA
224304 TTTATGTAAC
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
16 1 0.02
17 21 0.50
18 7 0.17
19 10 0.24
20 3 0.07
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATTTAAATTTAAAATA
Found at i:226686 original size:40 final size:39
Alignment explanation
Indices: 226607--226698 Score: 109
Period size: 40 Copynumber: 2.3 Consensus size: 39
226597 CAATAGATAT
226607 TAAATTTAAATATTTAAATTTATTATTTATATAAATAAAA
1 TAAATTTAAATATTTAAA-TTATTATTTATATAAATAAAA
226647 TAAATTTAAATA-TTAAA-TATTATTTGA-ATTAAAATTAAAA
1 TAAATTTAAATATTTAAATTATTATTT-ATA-T-AAA-TAAAA
*
226687 TAAATTCAAATA
1 TAAATTTAAATA
226699 ATGTGATATT
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
37 9 0.19
38 2 0.04
39 8 0.17
40 28 0.60
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (39 bp):
TAAATTTAAATATTTAAATTATTATTTATATAAATAAAA
Found at i:226988 original size:2 final size:2
Alignment explanation
Indices: 226983--227024 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
226973 TTAGCGCATG
*
226983 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
227025 CATGTGGAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:228271 original size:20 final size:20
Alignment explanation
Indices: 228246--228283 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
228236 TATATAAAAT
*
228246 TATTTTTTTAAAATATTTAA
1 TATTTTTATAAAATATTTAA
*
228266 TATTTTTATATAATATTT
1 TATTTTTATAAAATATTT
228284 TGAGTTTACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTTTTATAAAATATTTAA
Found at i:228544 original size:15 final size:15
Alignment explanation
Indices: 228524--228566 Score: 63
Period size: 13 Copynumber: 3.0 Consensus size: 15
228514 TTAGAGTTTA
228524 AATATTTTATAAAAT
1 AATATTTTATAAAAT
228539 AATA--TTATAAAAT
1 AATATTTTATAAAAT
*
228552 AATATTTAATAAAAT
1 AATATTTTATAAAAT
228567 TTAAATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 13 0.52
15 12 0.48
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATATTTTATAAAAT
Found at i:229962 original size:24 final size:27
Alignment explanation
Indices: 229902--229962 Score: 76
Period size: 24 Copynumber: 2.4 Consensus size: 27
229892 ATATTATGAT
*
229902 TAAAATATTAAACATATTATATAAATA
1 TAAATTATTAAACATATTATATAAATA
*
229929 TATATT-TTAAA-AT-TTATATAAA-A
1 TAAATTATTAAACATATTATATAAATA
229952 TAAATTATTAA
1 TAAATTATTAA
229963 CTTATTAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 6 0.20
24 13 0.43
25 2 0.07
26 5 0.17
27 4 0.13
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (27 bp):
TAAATTATTAAACATATTATATAAATA
Found at i:230030 original size:21 final size:20
Alignment explanation
Indices: 229968--230041 Score: 61
Period size: 21 Copynumber: 3.9 Consensus size: 20
229958 ATTAACTTAT
*
229968 TAATCTTAT-TTAAAT-T-A
1 TAATATTATATTAAATATAA
*
229985 TAAAATT-TATTAAATATAA
1 TAATATTATATTAAATATAA
*
230004 TTATATTATAATTAAATATACA
1 TAATATTAT-ATTAAATATA-A
230026 -AATATTATA-TAAATAT
1 TAATATTATATTAAATAT
230042 TTAAATAATA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
16 1 0.02
17 11 0.24
18 1 0.02
19 13 0.28
20 2 0.04
21 17 0.37
22 1 0.02
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (20 bp):
TAATATTATATTAAATATAA
Found at i:241203 original size:2 final size:2
Alignment explanation
Indices: 241191--241238 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
241181 TAATCAACTC
* *
241191 AT AT A- AT AT AT AT AT AT AT AT AT AT AT A- AA AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
241231 GT AT AT AT
1 AT AT AT AT
241239 TTCTTTTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:241219 original size:23 final size:23
Alignment explanation
Indices: 241191--241238 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
241181 TAATCAACTC
* *
241191 ATATAATATATATATATATATAT
1 ATATAAAATATAAATATATATAT
*
241214 ATATAAAATATAAATATGTATAT
1 ATATAAAATATAAATATATATAT
241237 AT
1 AT
241239 TTCTTTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
ATATAAAATATAAATATATATAT
Found at i:241387 original size:2 final size:2
Alignment explanation
Indices: 241341--241368 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
241331 TAAAAAGCCC
241341 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
241369 CTTATTTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:241402 original size:13 final size:13
Alignment explanation
Indices: 241379--241411 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
241369 CTTATTTTAC
*
241379 AAAAT-ATATTAT
1 AAAATAATATTAA
241391 AAAATAATATTAA
1 AAAATAATATTAA
241404 AAAATAAT
1 AAAATAAT
241412 TCTTTTCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AAAATAATATTAA
Found at i:241714 original size:14 final size:14
Alignment explanation
Indices: 241697--241779 Score: 98
Period size: 14 Copynumber: 6.1 Consensus size: 14
241687 TATATATATT
241697 TATGTATGTATGTA
1 TATGTATGTATGTA
*
241711 TATGTATATATGTA
1 TATGTATGTATGTA
* * *
241725 TGTATATTTATG--
1 TATGTATGTATGTA
* *
241737 TATGTATGTATATG
1 TATGTATGTATGTA
241751 TATGTATGTATGTA
1 TATGTATGTATGTA
241765 TATGTATGTATGTA
1 TATGTATGTATGTA
241779 T
1 T
241780 GTATAACCCC
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
12 8 0.14
14 49 0.86
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (14 bp):
TATGTATGTATGTA
Found at i:241722 original size:18 final size:18
Alignment explanation
Indices: 241691--241784 Score: 161
Period size: 18 Copynumber: 5.2 Consensus size: 18
241681 TATATATATA
*
241691 TATATTTATGTATGTATG
1 TATATGTATGTATGTATG
*
241709 TATATGTATATATGTATG
1 TATATGTATGTATGTATG
*
241727 TATATTTATGTATGTATG
1 TATATGTATGTATGTATG
241745 TATATGTATGTATGTATG
1 TATATGTATGTATGTATG
241763 TATATGTATGTATGTATG
1 TATATGTATGTATGTATG
241781 TATA
1 TATA
241785 ACCCCTCCCA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 71 1.00
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (18 bp):
TATATGTATGTATGTATG
Found at i:241731 original size:36 final size:36
Alignment explanation
Indices: 241679--241784 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
241669 CTCTTTCTTA
* *
241679 TATATATATATATATATTTATGTATGTATGTATATG
1 TATATATGTATGTATATTTATGTATGTATGTATATG
241715 TATATATGTATGTATATTTATGTATGTATGTATATG
1 TATATATGTATGTATATTTATGTATGTATGTATATG
* *
241751 TATGTATGTATGTATATGTATGTATGTATGTATA
1 TATATATGTATGTATATTTATGTATGTATGTATA
241785 ACCCCTCCCA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (36 bp):
TATATATGTATGTATATTTATGTATGTATGTATATG
Found at i:241740 original size:4 final size:4
Alignment explanation
Indices: 241697--241783 Score: 100
Period size: 4 Copynumber: 23.8 Consensus size: 4
241687 TATATATATT
* *
241697 TATG TATG TATG TA-- TATG TATA TATG TATG TA-- TATT TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
241741 TATG TA-- TATG TATG TATG TATG TA-- TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
241784 AACCCCTCCC
Statistics
Matches: 72, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
2 8 0.11
4 64 0.89
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:246504 original size:20 final size:19
Alignment explanation
Indices: 246460--246505 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
246450 TATTAAATTC
246460 CAAAAAAAAAAAAAATCAA
1 CAAAAAAAAAAAAAATCAA
*
246479 -ATAAAAAACAATAAAATCAA
1 CA-AAAAAA-AAAAAAATCAA
246499 CAAAAAA
1 CAAAAAA
246506 TTATCAACGA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 1 0.04
19 6 0.26
20 15 0.65
21 1 0.04
ACGTcount: A:0.80, C:0.11, G:0.00, T:0.09
Consensus pattern (19 bp):
CAAAAAAAAAAAAAATCAA
Found at i:247362 original size:15 final size:16
Alignment explanation
Indices: 247342--247372 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
247332 TATACAAGAT
247342 AAGTTAGTC-AAAAAA
1 AAGTTAGTCGAAAAAA
247357 AAGTTAGTCGAAAAAA
1 AAGTTAGTCGAAAAAA
247373 GAAAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.58, C:0.06, G:0.16, T:0.19
Consensus pattern (16 bp):
AAGTTAGTCGAAAAAA
Found at i:252186 original size:12 final size:12
Alignment explanation
Indices: 252166--252221 Score: 60
Period size: 12 Copynumber: 4.7 Consensus size: 12
252156 CCTATTTTAT
252166 TATTTAAAATAA
1 TATTTAAAATAA
* *
252178 TATTAAAAATTA
1 TATTTAAAATAA
* *
252190 TTTTTATAATAA
1 TATTTAAAATAA
252202 TATTTAAAATTAA
1 TATTTAAAA-TAA
252215 -ATTTAAA
1 TATTTAAA
252222 TAAATAGTAA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
12 32 0.91
13 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TATTTAAAATAA
Found at i:252200 original size:24 final size:25
Alignment explanation
Indices: 252162--252221 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 25
252152 AAAGCCTATT
252162 TTATTATTTAAAATAATATTAAAAA
1 TTATTATTTAAAATAATATTAAAAA
* *
252187 TTATT-TTTATAATAATATTTAAAA
1 TTATTATTTAAAATAATATTAAAAA
*
252211 TTA-AATTTAAA
1 TTATTATTTAAA
252222 TAAATAGTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 25 0.83
25 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TTATTATTTAAAATAATATTAAAAA
Found at i:253787 original size:2 final size:2
Alignment explanation
Indices: 253780--253809 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
253770 TAGTAAGTAA
*
253780 AT AT AT AT CT 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
253810 TTGACATTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:255781 original size:2 final size:2
Alignment explanation
Indices: 255774--255814 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
255764 TGTGAGAACA
* * *
255774 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT TT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
255815 CCGGCACATG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:257738 original size:17 final size:17
Alignment explanation
Indices: 257704--257751 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
257694 AATATATTTT
* *
257704 ATATT-TATATTTAAAA
1 ATATTATATATATATAA
257720 ATATTATATATATATAA
1 ATATTATATATATATAA
* *
257737 ATTTTAAATATATAT
1 ATATTATATATATAT
257752 GTATCAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 5 0.19
17 22 0.81
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTATATATATATAA
Found at i:258065 original size:26 final size:27
Alignment explanation
Indices: 258039--258090 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
258029 ATTACATATA
258039 AATATA-ATATTAAAATA-ATTAAAAT
1 AATATATATATTAAAATATATTAAAAT
* *
258064 AATATATATTTTAAAATATTTTAAAAT
1 AATATATATATTAAAATATATTAAAAT
258091 TTATAAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 6 0.26
26 10 0.43
27 7 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
AATATATATATTAAAATATATTAAAAT
Found at i:263818 original size:80 final size:80
Alignment explanation
Indices: 263701--263865 Score: 276
Period size: 80 Copynumber: 2.1 Consensus size: 80
263691 CTACAGATGT
* * *
263701 ATAAAGAAGAGTCATACGTGCTGTAATCTCTAAATATTTATAATTTTGTTGTAGCAGGCTTCTTA
1 ATAAAGAAGAGTCATACGTGCTGTAATCTCCAAATATTTATAATTCTATTGTAGCAGGCTTCTTA
263766 CTTTCTTTTGGATAA
66 CTTTCTTTTGGATAA
* *
263781 ATAAAGTAGAGTCATACGTGTTGTAATCTCCAAATATTTATAATTCTATTGTAGCAGGCTTCTTA
1 ATAAAGAAGAGTCATACGTGCTGTAATCTCCAAATATTTATAATTCTATTGTAGCAGGCTTCTTA
*
263846 CTTTCTTTTGGATGA
66 CTTTCTTTTGGATAA
263861 ATAAA
1 ATAAA
263866 AATTTTTTAA
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.41
Consensus pattern (80 bp):
ATAAAGAAGAGTCATACGTGCTGTAATCTCCAAATATTTATAATTCTATTGTAGCAGGCTTCTTA
CTTTCTTTTGGATAA
Found at i:269788 original size:17 final size:17
Alignment explanation
Indices: 269766--269799 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
269756 GCAAGTTATT
*
269766 AAAAAATAAAGACAATA
1 AAAAAAGAAAGACAATA
*
269783 AAAAAAGAAATACAATA
1 AAAAAAGAAAGACAATA
269800 CCAAAAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.12
Consensus pattern (17 bp):
AAAAAAGAAAGACAATA
Found at i:270020 original size:26 final size:26
Alignment explanation
Indices: 269968--270020 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
269958 TCATCCATAA
*
269968 TTTTTTACAAATAAAAATTTATCTTT
1 TTTTTTACAAATAAAAATTGATCTTT
269994 TTTTTTACATTAATAAAAA-TGAT-TTT
1 TTTTTTACA--AATAAAAATTGATCTTT
270020 T
1 T
270021 ATTGATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 13 0.54
27 3 0.12
28 8 0.33
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.55
Consensus pattern (26 bp):
TTTTTTACAAATAAAAATTGATCTTT
Found at i:270611 original size:340 final size:343
Alignment explanation
Indices: 269936--270624 Score: 1199
Period size: 340 Copynumber: 2.0 Consensus size: 343
269926 ATTCTTTATT
* *
269936 TTATAATAAAAAGAGTCACCAATCATCCATAATTTTTTACAAATAAAAATTTATCTTTTTTTTTA
1 TTATAATAAAAAGAGTCACCAATCACCCATAATTTTTTACAAATAAAAATTTATCTTTTTTTTGA
* *
270001 CATTAATAAAAATGATTTTTATTGATTAAAGAGAGCCACCCACTACGGTTTCCTCCCAACCTGCC
66 CATTAATAAAAATGATTTTTATTGATTAAAGAGAG---CCCACTACAGTTTCCTCCCAACCTGAC
270066 TGCCTGAGTTTTTAACTTCATTAAGGAGTAGGTTGAAAAAGATAGGCCGTGGAGTTAGCAGTGGT
128 TGCCTGAGTTTTTAACTTCATTAAGGAGTAGGTTGAAAAAGATAGGCCGTGGAGTTAGCAGTGGT
270131 GGTGGACAGAGCTCATTGGGCTATCTGTTTCGGAGTGGAGAAGCTCCAAAATCAGCCATAAACAA
193 GGTGGACAGAGCTCATTGGGCTATCTGTTTCGGAGTGGAGAAGCTCCAAAATCAGCCATAAACAA
270196 TTCCCAAGCTGCTCCAACCGAAGAACCAGCTGCCTCCAAAGCTGCTTCTCAACCAGTAGATATTA
258 TTCCCAAGCTGCTCCAACCGAAGAACCAGCTGCCTCCAAAGCTGCTTCTCAACCAGTAGATATTA
270261 CGAATCAAATTCCTGACGGTA
323 CGAATCAAATTCCTGACGGTA
*
270282 TTATAATAAAAAAGAGTCATCAA-CTACCCATAATTTTTTACAAAT-AAAATTT-T-TTTTTTTT
1 TTATAAT-AAAAAGAGTCACCAATC-ACCCATAATTTTTTACAAATAAAAATTTATCTTTTTTTT
** **
270343 GACATTAATAAAGGTGATTTTTATTGATTAAAGAGAG-CCACTACAGTTTCCTCCTGACCTGACT
64 GACATTAATAAAAATGATTTTTATTGATTAAAGAGAGCCCACTACAGTTTCCTCCCAACCTGACT
* *
270407 GCCTGAGTTTTTAACTTCATTTAGGAGTAGGTTGAAAAAGATAGGTCGTGGAGTTAGCAGTGGTG
129 GCCTGAGTTTTTAACTTCATTAAGGAGTAGGTTGAAAAAGATAGGCCGTGGAGTTAGCAGTGGTG
270472 GTGGACAGAGCTCATTGGGCTATCTGTTTCGGAGTGGAGAAGCTCCAAAATCAGCCATAAACAAT
194 GTGGACAGAGCTCATTGGGCTATCTGTTTCGGAGTGGAGAAGCTCCAAAATCAGCCATAAACAAT
270537 TCCCAAGCTGCTCCAACCGAAGAACCAGCTGCCTCCAAAGCTGCTTCTCAACCAGTAGATATTAC
259 TCCCAAGCTGCTCCAACCGAAGAACCAGCTGCCTCCAAAGCTGCTTCTCAACCAGTAGATATTAC
270602 GAATCAAATTCCTGACGGTA
324 GAATCAAATTCCTGACGGTA
270622 TTA
1 TTA
270625 ACAGTACTTC
Statistics
Matches: 330, Mismatches: 11, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
340 239 0.72
344 42 0.13
345 1 0.00
346 15 0.05
347 33 0.10
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (343 bp):
TTATAATAAAAAGAGTCACCAATCACCCATAATTTTTTACAAATAAAAATTTATCTTTTTTTTGA
CATTAATAAAAATGATTTTTATTGATTAAAGAGAGCCCACTACAGTTTCCTCCCAACCTGACTGC
CTGAGTTTTTAACTTCATTAAGGAGTAGGTTGAAAAAGATAGGCCGTGGAGTTAGCAGTGGTGGT
GGACAGAGCTCATTGGGCTATCTGTTTCGGAGTGGAGAAGCTCCAAAATCAGCCATAAACAATTC
CCAAGCTGCTCCAACCGAAGAACCAGCTGCCTCCAAAGCTGCTTCTCAACCAGTAGATATTACGA
ATCAAATTCCTGACGGTA
Found at i:271532 original size:11 final size:11
Alignment explanation
Indices: 271516--271562 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
271506 ATATTTAATT
271516 ATATAAATATA
1 ATATAAATATA
271527 ATATAAA-ATA
1 ATATAAATATA
271537 AT-TAAAATATA
1 ATAT-AAATATA
*
271548 ATATATATAT-
1 ATATAAATATA
271558 ATATA
1 ATATA
271563 TGATTAGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
9 1 0.03
10 13 0.41
11 17 0.53
12 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
ATATAAATATA
Found at i:271635 original size:15 final size:17
Alignment explanation
Indices: 271615--271647 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
271605 TTTAGTGATT
271615 AAGAT-AATTTAT-TAA
1 AAGATAAATTTATATAA
271630 AAGATAAATTTATATAA
1 AAGATAAATTTATATAA
271647 A
1 A
271648 GTAATCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 7 0.44
17 4 0.25
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (17 bp):
AAGATAAATTTATATAA
Found at i:272213 original size:24 final size:25
Alignment explanation
Indices: 272185--272238 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
272175 ATTAATATTT
272185 AATATTTATCTATAT-AAT-TATAAA
1 AATATTTAT-TATATAAATATATAAA
*
272209 AATA-TTATTATTTAAATATATAAA
1 AATATTTATTATATAAATATATAAA
272233 AATATT
1 AATATT
272239 AAATATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 4 0.15
23 7 0.27
24 14 0.54
25 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
AATATTTATTATATAAATATATAAA
Found at i:272260 original size:22 final size:24
Alignment explanation
Indices: 272232--272278 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
272222 AAATATATAA
272232 AAATATTAAATATATT-TAT-TTT
1 AAATATTAAATATATTCTATATTT
* *
272254 AAATATTTATTATATTCTATATTT
1 AAATATTAAATATATTCTATATTT
272278 A
1 A
272279 TAGTCAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 3 0.14
24 4 0.19
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
AAATATTAAATATATTCTATATTT
Found at i:275753 original size:2 final size:2
Alignment explanation
Indices: 275746--275795 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
275736 CATTTTAACC
275746 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
275788 AT AT AT AT
1 AT AT AT AT
275796 CAATTATCAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:276349 original size:21 final size:19
Alignment explanation
Indices: 276307--276347 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
276297 TATAAATGAC
276307 ATAATTTGAATAAAAATAT
1 ATAATTTGAATAAAAATAT
*
276326 ATAATTTGAATAAAATTAT
1 ATAATTTGAATAAAAATAT
276345 ATA
1 ATA
276348 TATACTAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (19 bp):
ATAATTTGAATAAAAATAT
Found at i:277111 original size:2 final size:2
Alignment explanation
Indices: 277104--277139 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
277094 GTCCATCGTC
277104 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
277140 CAATTAATTT
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:277271 original size:16 final size:16
Alignment explanation
Indices: 277250--277280 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
277240 CGTTTTCATA
277250 AGGTTGGGAATGATAG
1 AGGTTGGGAATGATAG
277266 AGGTTGGGAATGATA
1 AGGTTGGGAATGATA
277281 AATCATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.42, T:0.26
Consensus pattern (16 bp):
AGGTTGGGAATGATAG
Found at i:282586 original size:15 final size:15
Alignment explanation
Indices: 282551--282587 Score: 60
Period size: 13 Copynumber: 2.6 Consensus size: 15
282541 ATGTTGTCTT
282551 AAAATATTTATATTC
1 AAAATATTTATATTC
282566 --AATATTTATATTC
1 AAAATATTTATATTC
282579 AAAATATTT
1 AAAATATTT
282588 TTAGATATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 13 0.65
15 7 0.35
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (15 bp):
AAAATATTTATATTC
Found at i:284881 original size:13 final size:13
Alignment explanation
Indices: 284863--284891 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
284853 CCTGAAACTT
284863 GTATTGAACACAA
1 GTATTGAACACAA
284876 GTATTGAACACAA
1 GTATTGAACACAA
284889 GTA
1 GTA
284892 CTTTAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (13 bp):
GTATTGAACACAA
Found at i:286607 original size:14 final size:14
Alignment explanation
Indices: 286587--286624 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
286577 ATTCGTATTT
286587 AATATATATTTAAA
1 AATATATATTTAAA
* *
286601 TATATATATATAAA
1 AATATATATTTAAA
286615 AATATA-ATTT
1 AATATATATTT
286625 TTTAAAAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
13 3 0.15
14 17 0.85
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AATATATATTTAAA
Found at i:292994 original size:14 final size:15
Alignment explanation
Indices: 292943--292987 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
292933 ATTTATTAGA
* *
292943 TTTAT-ATTAAAAAA
1 TTTATAATTTAAAAT
292957 TTTA-AA-TTAAAAT
1 TTTATAATTTAAAAT
292970 TTTATAATTTAAAAT
1 TTTATAATTTAAAAT
292985 TTT
1 TTT
292988 TGATTTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 9 0.35
14 7 0.27
15 10 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTTATAATTTAAAAT
Found at i:293066 original size:28 final size:28
Alignment explanation
Indices: 293002--293097 Score: 72
Period size: 28 Copynumber: 3.4 Consensus size: 28
292992 TTATTTGATT
*
293002 TATTATTT-ATATATTAAAAATTATTTT-A
1 TATTATTTAAT-TA-TAAATATTATTTTAA
293030 T-TTAAATTTAATTATAAATATTATTTTAA
1 TATT--ATTTAATTATAAATATTATTTTAA
* * *
293059 TATTATTTAAATATTAATATGAATTTTAA
1 TATTATTTAATTATAAATAT-TATTTTAA
* *
293088 AATTACTTAA
1 TATTATTTAA
293098 ATTTAAACAA
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
27 2 0.04
28 27 0.48
29 23 0.41
30 4 0.07
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (28 bp):
TATTATTTAATTATAAATATTATTTTAA
Found at i:293092 original size:29 final size:28
Alignment explanation
Indices: 293035--293103 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
293025 TTTTATTTAA
* * * *
293035 ATTTAATTATAAATATTATTTTAATATT
1 ATTTAAATATTAATATAATTTTAAAATT
293063 ATTTAAATATTAATATGAATTTTAAAATT
1 ATTTAAATATTAATAT-AATTTTAAAATT
*
293092 ACTTAAAT-TTAA
1 ATTTAAATATTAA
293104 ACAAAAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 18 0.51
29 17 0.49
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (28 bp):
ATTTAAATATTAATATAATTTTAAAATT
Found at i:293239 original size:25 final size:25
Alignment explanation
Indices: 293211--293260 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
293201 ATTATCTCAC
293211 TAAAAAATTAAAAAAATTTAAAATA
1 TAAAAAATTAAAAAAATTTAAAATA
* * * *
293236 TAAATATTTTAAAAAATTTTAAATA
1 TAAAAAATTAAAAAAATTTAAAATA
293261 ATGTAATCCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
TAAAAAATTAAAAAAATTTAAAATA
Found at i:293576 original size:14 final size:14
Alignment explanation
Indices: 293511--293569 Score: 54
Period size: 14 Copynumber: 4.5 Consensus size: 14
293501 ATTTTTTAAA
293511 TAATATAATATATT
1 TAATATAATATATT
293525 TAATA-AATATA--
1 TAATATAATATATT
* * *
293536 -AAAATAATAAAAT
1 TAATATAATATATT
*
293549 AAATATAATATATT
1 TAATATAATATATT
293563 TAATATA
1 TAATATA
293570 TATTATTATA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
10 3 0.09
11 5 0.14
13 6 0.17
14 21 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATATAATATATT
Found at i:293621 original size:19 final size:19
Alignment explanation
Indices: 293558--293623 Score: 56
Period size: 19 Copynumber: 3.7 Consensus size: 19
293548 TAAATATAAT
293558 ATATTTAATATATATT-ATT-
1 ATATTT-AT-TATATTAATTA
293577 ATATTTA-TAT-TTAA--A
1 ATATTTATTATATTAATTA
*
293592 AT-TTTAATATATTAATTA
1 ATATTTATTATATTAATTA
293610 ATATTTATTATATT
1 ATATTTATTATATT
293624 TATATTTGTA
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
14 4 0.10
15 7 0.18
16 8 0.21
18 4 0.10
19 16 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATATTTATTATATTAATTA
Found at i:294584 original size:14 final size:14
Alignment explanation
Indices: 294539--294603 Score: 76
Period size: 14 Copynumber: 4.6 Consensus size: 14
294529 ATTTAATAAA
294539 AAAATTAATAATTT
1 AAAATTAATAATTT
* * **
294553 AAAATCAATCATAA
1 AAAATTAATAATTT
294567 AAAATTAATAATTT
1 AAAATTAATAATTT
294581 AAAATTAATCAATTT
1 AAAATTAAT-AATTT
*
294596 AAATTTAA
1 AAAATTAA
294604 AAATAATTTT
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
14 29 0.71
15 12 0.29
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAATTAATAATTT
Found at i:294600 original size:28 final size:28
Alignment explanation
Indices: 294537--294591 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
294527 TAATTTAATA
294537 AAAAAATTAATAATTTAAAATCAATCAT
1 AAAAAATTAATAATTTAAAATCAATCAT
*
294565 AAAAAATTAATAATTTAAAATTAATCA
1 AAAAAATTAATAATTTAAAATCAATCA
294592 ATTTAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (28 bp):
AAAAAATTAATAATTTAAAATCAATCAT
Found at i:294635 original size:17 final size:16
Alignment explanation
Indices: 294573--294631 Score: 68
Period size: 16 Copynumber: 3.7 Consensus size: 16
294563 ATAAAAAATT
*
294573 AATAATTTAAAATT--
1 AATAATTTAAATTTAA
294587 AATCAATTTAAATTTAAA
1 AAT-AATTTAAATTT-AA
*
294605 AATAATTTTAATTTAA
1 AATAATTTAAATTTAA
294621 AATAATTTAAA
1 AATAATTTAAA
294632 ATTTCTTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
14 3 0.08
15 10 0.26
16 12 0.32
17 10 0.26
18 3 0.08
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAATTTAAATTTAA
Found at i:294676 original size:22 final size:21
Alignment explanation
Indices: 294628--294676 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
294618 TAAAATAATT
* *
294628 TAAAATTTCTTAATTTAAATA
1 TAAAATTTATTAACTTAAATA
* *
294649 TTAAATTTGATTAACTTAAATC
1 TAAAATTT-ATTAACTTAAATA
294671 TAAAAT
1 TAAAAT
294677 GATATAAATT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (21 bp):
TAAAATTTATTAACTTAAATA
Found at i:296514 original size:16 final size:16
Alignment explanation
Indices: 296488--296537 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
296478 ATTTTGACAC
*
296488 TTAATAATTTATGTTA
1 TTAATATTTTATGTTA
296504 TATAA-ATTTTAATG-TA
1 T-TAATATTTT-ATGTTA
*
296520 TTAATATTTTATATTA
1 TTAATATTTTATGTTA
296536 TT
1 TT
296538 TTTATATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 5 0.18
16 17 0.61
17 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (16 bp):
TTAATATTTTATGTTA
Found at i:296542 original size:11 final size:11
Alignment explanation
Indices: 296526--296574 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
296516 TGTATTAATA
296526 TTTTATATTAT
1 TTTTATATTAT
296537 TTTTATATTA-
1 TTTTATATTAT
*
296547 TTATATA-T-T
1 TTTTATATTAT
296556 TTTTATATTAT
1 TTTTATATTAT
*
296567 ATTTATAT
1 TTTTATAT
296575 CATATAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
9 7 0.22
10 7 0.22
11 18 0.56
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTATATTAT
Found at i:296547 original size:16 final size:17
Alignment explanation
Indices: 296528--296569 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 17
296518 TATTAATATT
296528 TTATATTA-TTTTTATA
1 TTATATTATTTTTTATA
296544 TTATTATATATTTTTTATA
1 TTA-TAT-TATTTTTTATA
296563 TTATATT
1 TTATATT
296570 TATATCATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 3 0.13
17 4 0.17
18 5 0.22
19 11 0.48
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTATATTATTTTTTATA
Found at i:296552 original size:19 final size:19
Alignment explanation
Indices: 296523--296569 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
296513 TAATGTATTA
296523 ATATT-TTATATTATTTTT
1 ATATTATTATATTATTTTT
296541 ATATTATTATA-TATTTTT
1 ATATTATTATATTATTTTT
296559 -TA-TATTATATT
1 ATATTATTATATT
296570 TATATCATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 7 0.26
17 3 0.11
18 12 0.44
19 5 0.19
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
ATATTATTATATTATTTTT
Found at i:296579 original size:16 final size:15
Alignment explanation
Indices: 296529--296579 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
296519 ATTAATATTT
*
296529 TATATTATTTTTATA
1 TATATTATATTTATA
* *
296544 T-TATTATATATTTTT
1 TATATTATAT-TTATA
296559 TATATTATATTTATA
1 TATATTATATTTATA
296574 TCATAT
1 T-ATAT
296580 AATTATATGG
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
14 7 0.25
15 9 0.32
16 12 0.43
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (15 bp):
TATATTATATTTATA
Found at i:298147 original size:27 final size:26
Alignment explanation
Indices: 298087--298147 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 26
298077 TATTATAAAA
298087 ATATATA-AAGCTAAATTAATTTTAT
1 ATATATATAAGCTAAATTAATTTTAT
* * *
298112 ACATGTATAAG-TAAATCTTATTTATAT
1 ATATATATAAGCTAAAT-TAATTT-TAT
298139 ATATATATA
1 ATATATATA
298148 TATATTGCAG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
25 10 0.36
26 8 0.29
27 10 0.36
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (26 bp):
ATATATATAAGCTAAATTAATTTTAT
Found at i:298285 original size:38 final size:38
Alignment explanation
Indices: 298243--298322 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
298233 ATTCTTCCCA
* * *
298243 TTATAGTTGCCATTATATCGAAATAAAACGCTTATATT
1 TTATAATTACCATTATATCGAAATAAAACACTTATATT
* *
298281 TTATAATTATCATTATATCGAAATAAAATACTTATATT
1 TTATAATTACCATTATATCGAAATAAAACACTTATATT
298319 TTAT
1 TTAT
298323 GTTATTTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (38 bp):
TTATAATTACCATTATATCGAAATAAAACACTTATATT
Found at i:307552 original size:2 final size:2
Alignment explanation
Indices: 307545--307572 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
307535 CATTCGGTAA
307545 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
307573 TTAATTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:308518 original size:12 final size:12
Alignment explanation
Indices: 308501--308536 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
308491 ATATAATATT
308501 TATATTTAAATA
1 TATATTTAAATA
308513 TATA-TTAAATA
1 TATATTTAAATA
*
308524 TAAATTTAAATA
1 TATATTTAAATA
308536 T
1 T
308537 TTTAAAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TATATTTAAATA
Found at i:309835 original size:13 final size:14
Alignment explanation
Indices: 309817--309846 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
309807 TTATGTTTTG
309817 ATTATTTTTAAT-T
1 ATTATTTTTAATAT
309830 ATTATTTTTAATAT
1 ATTATTTTTAATAT
309844 ATT
1 ATT
309847 CTAACATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTATTTTTAATAT
Found at i:309946 original size:18 final size:19
Alignment explanation
Indices: 309925--309963 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
309915 TTTTTAACAA
309925 TAAAAAATTAATTAA-ATT
1 TAAAAAATTAATTAATATT
**
309943 TAAAATTTTAATTAATATT
1 TAAAAAATTAATTAATATT
309962 TA
1 TA
309964 TAATCATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TAAAAAATTAATTAATATT
Found at i:310264 original size:22 final size:22
Alignment explanation
Indices: 310215--310264 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
310205 AAATTTAGTA
*
310215 ATATATATTTTTATATTATATTT
1 ATAT-TATTTTTATATTATAATT
* *
310238 GTATTATTTTTATTTTATAATT
1 ATATTATTTTTATATTATAATT
310260 ATATT
1 ATATT
310265 TAAAATATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (22 bp):
ATATTATTTTTATATTATAATT
Found at i:310378 original size:5 final size:5
Alignment explanation
Indices: 310343--310393 Score: 51
Period size: 5 Copynumber: 11.4 Consensus size: 5
310333 TATATTTTAC
*
310343 ATTAT ATT-T AAT-T ATTA- ATTAT ATTAT -TTAT ATTAT A-TA- ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
310387 ATTAT AT
1 ATTAT AT
310394 ATCAAATTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
3 1 0.03
4 18 0.46
5 20 0.51
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:310383 original size:22 final size:20
Alignment explanation
Indices: 310347--310391 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 20
310337 TTTTACATTA
310347 TATTTAATTATTAATTATAT
1 TATTTAATTATTAATTATAT
310367 TATTTATATTATATAATTATAT
1 TATTTA-ATTAT-TAATTATAT
310389 TAT
1 TAT
310392 ATATCAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 6 0.26
21 5 0.22
22 12 0.52
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTTAATTATTAATTATAT
Found at i:310388 original size:13 final size:13
Alignment explanation
Indices: 310343--310394 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
310333 TATATTTTAC
*
310343 ATTATATT-TAATT
1 ATTATATTAT-ATA
310356 ATTA-ATTATATTA
1 ATTATATTATA-TA
*
310369 TTTATATTATATA
1 ATTATATTATATA
310382 ATTATATTATATA
1 ATTATATTATATA
310395 TCAAATTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
12 4 0.12
13 23 0.70
14 6 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
ATTATATTATATA
Found at i:310394 original size:29 final size:29
Alignment explanation
Indices: 310305--310395 Score: 71
Period size: 29 Copynumber: 3.0 Consensus size: 29
310295 TATGTTAATA
310305 ATTTATATTATATAAATTAAAATATTGATATA-T
1 ATTTATATTATAT-AATT---ATATT-ATATATT
* *
310338 -TTTACATTATATTTAATTAT-TAATTATATT
1 ATTTATATTATA--TAATTATATTA-TATATT
310368 ATTTATATTATATAATTATATTATATAT
1 ATTTATATTATATAATTATATTATATAT
310396 CAAATTTATT
Statistics
Matches: 48, Mismatches: 4, Indels: 16
0.71 0.06 0.24
Matches are distributed among these distances:
28 1 0.02
29 17 0.35
30 5 0.10
31 10 0.21
32 10 0.21
33 4 0.08
34 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (29 bp):
ATTTATATTATATAATTATATTATATATT
Found at i:310803 original size:10 final size:10
Alignment explanation
Indices: 310788--310819 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
310778 TAATTTTTTT
310788 ATTTAAATTA
1 ATTTAAATTA
*
310798 ATTTAATTTA
1 ATTTAAATTA
310808 ATTTAAATTA
1 ATTTAAATTA
310818 AT
1 AT
310820 ATTTAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
ATTTAAATTA
Found at i:310829 original size:20 final size:20
Alignment explanation
Indices: 310788--310853 Score: 70
Period size: 19 Copynumber: 3.5 Consensus size: 20
310778 TAATTTTTTT
310788 ATTTAAATT-A-ATTTAATTTA
1 ATTTAAATTAATATTTAA--TA
310808 ATTTAAATTAATATTTAATA
1 ATTTAAATTAATATTTAATA
*
310828 A-TTAAAATAATATTT--TA
1 ATTTAAATTAATATTTAATA
310845 ATTTAAATT
1 ATTTAAATT
310854 TAATTATAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
17 3 0.07
18 6 0.15
19 13 0.32
20 12 0.29
21 1 0.02
22 6 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTTAAATTAATATTTAATA
Found at i:310857 original size:19 final size:17
Alignment explanation
Indices: 310788--310853 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 17
310778 TAATTTTTTT
310788 ATTTAAATTAATTTAATTTA
1 ATTTAAATTAA--T-ATTTA
310808 ATTTAAATTAATATTTA
1 ATTTAAATTAATATTTA
*
310825 ATAATTAAAATAATATTTTA
1 AT--TTAAATTAATA-TTTA
310845 ATTTAAATT
1 ATTTAAATT
310854 TAATTATAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
17 7 0.17
18 7 0.17
19 10 0.24
20 17 0.41
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTTAAATTAATATTTA
Found at i:310886 original size:38 final size:37
Alignment explanation
Indices: 310804--310882 Score: 101
Period size: 37 Copynumber: 2.1 Consensus size: 37
310794 ATTAATTTAA
*
310804 TTTAATTTAAATTAATATTTAATAATTAAAATAATAT
1 TTTAATTTAAATTAATATATAATAATTAAAATAATAT
310841 TTTAATTTAAATTTAAT-TATAA-AATATAAAAATAA-AT
1 TTTAATTTAAA-TTAATATATAATAAT-T-AAAATAATAT
310878 TTTAA
1 TTTAA
310883 ATTTTTTTGT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
36 3 0.08
37 23 0.61
38 12 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (37 bp):
TTTAATTTAAATTAATATATAATAATTAAAATAATAT
Found at i:317074 original size:69 final size:69
Alignment explanation
Indices: 316959--317103 Score: 254
Period size: 69 Copynumber: 2.1 Consensus size: 69
316949 CTTCTTGCTT
*
316959 ATATCAGATAAAGGAAGTTCATTATTCATAATTGTTTTCCAATGATTGCCTCGAAGTTTCCTGTT
1 ATATCAGATAAAGGAACTTCATTATTCATAATTGTTTTCCAATGATTGCCTCGAAGTTTCCTGTT
317024 TATA
66 TATA
** *
317028 ATATCAGATAAAGGAACTTCATTATTCATAATTGTTTTCCTGTGATTGCCTCGAAGTTTCTTGTT
1 ATATCAGATAAAGGAACTTCATTATTCATAATTGTTTTCCAATGATTGCCTCGAAGTTTCCTGTT
317093 TATA
66 TATA
317097 ATATCAG
1 ATATCAG
317104 CTGATATGCA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 72 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.41
Consensus pattern (69 bp):
ATATCAGATAAAGGAACTTCATTATTCATAATTGTTTTCCAATGATTGCCTCGAAGTTTCCTGTT
TATA
Found at i:321097 original size:15 final size:15
Alignment explanation
Indices: 321064--321100 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
321054 TAAATATTAA
321064 ATTTAAAAAATAAAT
1 ATTTAAAAAATAAAT
*
321079 -TTTAAAAAATATAT
1 ATTTAAAAAATAAAT
321093 ATTTAAAA
1 ATTTAAAA
321101 TTTAAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTTAAAAAATAAAT
Found at i:321231 original size:8 final size:9
Alignment explanation
Indices: 321182--321236 Score: 53
Period size: 8 Copynumber: 6.4 Consensus size: 9
321172 TTTTTATATT
*
321182 TATATATAT
1 TATATATAA
*
321191 TATATGTAA
1 TATATATAA
*
321200 T-TATATCA
1 TATATATAA
*
321208 TATA-AAAA
1 TATATATAA
321216 TATATATAA
1 TATATATAA
321225 TAT-TATAA
1 TATATATAA
321233 TATA
1 TATA
321237 AATATAAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
8 20 0.56
9 16 0.44
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (9 bp):
TATATATAA
Found at i:321333 original size:11 final size:10
Alignment explanation
Indices: 321302--321330 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
321292 TAAAATTTAA
321302 ATTTAAAAAT
1 ATTTAAAAAT
321312 ATTTAAAAAT
1 ATTTAAAAAT
321322 ATTTAAAAA
1 ATTTAAAAA
321331 ATAAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
ATTTAAAAAT
Found at i:321528 original size:2 final size:2
Alignment explanation
Indices: 321523--321552 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
321513 AAAACAAATA
321523 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
321553 TTAGAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:321885 original size:2 final size:2
Alignment explanation
Indices: 321880--321919 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
321870 ACACACACAC
321880 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
321920 TTCAAAAGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:322868 original size:2 final size:2
Alignment explanation
Indices: 322856--322898 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
322846 AAGAACCAAA
322856 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
322897 AT
1 AT
322899 GGCTATGGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:323449 original size:2 final size:2
Alignment explanation
Indices: 323442--323474 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
323432 GCTTTTAAGT
323442 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
323475 GTGTGTGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:324171 original size:17 final size:17
Alignment explanation
Indices: 324151--324185 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
324141 TAAAAATTAA
324151 ATTTTATATTAATAAAT
1 ATTTTATATTAATAAAT
* *
324168 ATTTTTTATTAATTAAT
1 ATTTTATATTAATAAAT
324185 A
1 A
324186 ATAAATTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTTATATTAATAAAT
Found at i:324561 original size:15 final size:16
Alignment explanation
Indices: 324541--324571 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
324531 GATAAATATT
324541 AATTATAAAA-AATAA
1 AATTATAAAATAATAA
324556 AATTATAAAATAATAA
1 AATTATAAAATAATAA
324572 TTCTGTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AATTATAAAATAATAA
Found at i:328597 original size:2 final size:2
Alignment explanation
Indices: 328590--328625 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
328580 AACAATTGCA
328590 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
328626 TGGGTAAAGG
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:330485 original size:24 final size:21
Alignment explanation
Indices: 330456--330509 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 21
330446 TATTAAAAAA
330456 TATATTTAATATATATATTATATT
1 TATATTTAATATAT-T-TT-TATT
330480 TATATTTAA-A-ATTTTTATT
1 TATATTTAATATATTTTTATT
330499 TAT-TTTAATAT
1 TATATTTAATAT
330510 GATTAAATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
18 5 0.18
19 8 0.29
20 2 0.07
21 1 0.04
22 2 0.07
23 1 0.04
24 9 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TATATTTAATATATTTTTATT
Found at i:331200 original size:28 final size:28
Alignment explanation
Indices: 331155--331217 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
331145 TAAAATGATC
* *
331155 AATATTAATAAAAAATAAAATATGATATA
1 AATA-TAATAAAAAATAAAAAATAATATA
*
331184 AATATAATAAAATATAAAAAATAATATA
1 AATATAATAAAAAATAAAAAATAATATA
*
331212 AGTATA
1 AATATA
331218 TTATAAACGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (28 bp):
AATATAATAAAAAATAAAAAATAATATA
Found at i:331204 original size:9 final size:10
Alignment explanation
Indices: 331168--331206 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
331158 ATTAATAAAA
331168 AATAAAATAT
1 AATAAAATAT
*
331178 GATATAAATAT
1 AATA-AAATAT
331189 AATAAAATAT
1 AATAAAATAT
331199 AA-AAAATA
1 AATAAAATA
331207 ATATAAGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
9 6 0.23
10 11 0.42
11 9 0.35
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (10 bp):
AATAAAATAT
Found at i:331606 original size:19 final size:19
Alignment explanation
Indices: 331582--331626 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
331572 TTCAAGGCTC
*
331582 AATTTAATCTGATTTATTA
1 AATTTAATCTGATTCATTA
*
331601 AATTTAATTTGATTCATTA
1 AATTTAATCTGATTCATTA
*
331620 GATTTAA
1 AATTTAA
331627 ATTAAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (19 bp):
AATTTAATCTGATTCATTA
Found at i:331660 original size:20 final size:20
Alignment explanation
Indices: 331622--331660 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
331612 ATTCATTAGA
*
331622 TTTAAATTAAAATATTTTAT
1 TTTAAATTAAAATAATTTAT
* *
331642 TTTAAATTGATATAATTTA
1 TTTAAATTAAAATAATTTA
331661 AATTAAATTT
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:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
TTTAAATTAAAATAATTTAT
Found at i:333013 original size:18 final size:18
Alignment explanation
Indices: 332990--333024 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
332980 TCTAACATAG
332990 ATGAAAATTGCATTCCAC
1 ATGAAAATTGCATTCCAC
333008 ATGAAAATTGCATTCCA
1 ATGAAAATTGCATTCCA
333025 ACCATTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (18 bp):
ATGAAAATTGCATTCCAC
Found at i:333859 original size:19 final size:20
Alignment explanation
Indices: 333823--333860 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
333813 ATATATATAT
*
333823 AACTTGTTTTATATCAATTA
1 AACTTGTTTTATACCAATTA
*
333843 AACTT-TTTTTTACCAATT
1 AACTTGTTTTATACCAATT
333861 TGAGAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.32, C:0.13, G:0.03, T:0.53
Consensus pattern (20 bp):
AACTTGTTTTATACCAATTA
Found at i:335295 original size:22 final size:21
Alignment explanation
Indices: 335247--335299 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
335237 TTTTAAAAAT
*
335247 TATTTTATATTAATATTTATA
1 TATTTTATATTAATATTTAAA
335268 TATTTTATAATTAA-ATTTAAA
1 TATTTTAT-ATTAATATTTAAA
335289 TATTTT-TATTA
1 TATTTTATATTA
335300 GTTAAACAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 4 0.13
20 1 0.03
21 20 0.67
22 5 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATATTAATATTTAAA
Found at i:335481 original size:28 final size:28
Alignment explanation
Indices: 335430--335505 Score: 91
Period size: 28 Copynumber: 2.7 Consensus size: 28
335420 AAAAAAAATA
*
335430 AAAAATAAATA-ATAAAAAAATTATATGTT
1 AAAAATAAATACAT--AAATATTATATGTT
* *
335459 AAAAATAATTACATAAATATTATATTTT
1 AAAAATAAATACATAAATATTATATGTT
*
335487 AAAAATAAATATATAAATA
1 AAAAATAAATACATAAATA
335506 AATAGAGTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 29 0.71
29 10 0.24
30 2 0.05
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (28 bp):
AAAAATAAATACATAAATATTATATGTT
Found at i:335516 original size:28 final size:26
Alignment explanation
Indices: 335430--335518 Score: 70
Period size: 28 Copynumber: 3.2 Consensus size: 26
335420 AAAAAAAATA
*
335430 AAAAATAAATAATAAAAAAATTATATGTT
1 AAAAATAAATAATAAATAAA-TA-A-GTT
* * **
335459 AAAAATAATTACATAAATATTATATTTT
1 AAAAATAAATA-ATAAATA-AATAAGTT
335487 AAAAATAAATATATAAATAAATAGAGTT
1 AAAAATAAATA-ATAAATAAATA-AGTT
335515 AAAA
1 AAAA
335519 TCAATTCCCC
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
27 3 0.06
28 25 0.53
29 10 0.21
30 8 0.17
31 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (26 bp):
AAAAATAAATAATAAATAAATAAGTT
Found at i:335979 original size:16 final size:14
Alignment explanation
Indices: 335947--335992 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 14
335937 TATCATCTGT
335947 ATTTAATTTAATAA
1 ATTTAATTTAATAA
335961 ATTTAATTTATATTAA
1 ATTTAATTTA-A-TAA
*
335977 ATTAAATTTAAATAA
1 ATTTAATTT-AATAA
335992 A
1 A
335993 ATATTTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 10 0.36
15 5 0.18
16 12 0.43
17 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTTAATTTAATAA
Found at i:337201 original size:292 final size:294
Alignment explanation
Indices: 336637--337226 Score: 1166
Period size: 292 Copynumber: 2.0 Consensus size: 294
336627 GTTATATTAT
336637 CCTGTCTGTTGTTCAGATTTTTATTTTTTTATTTATTTATATTCAAAATATTTTTAAAAATAAAT
1 CCTGTCTGTTGTTCAGATTTTTATTTTTTTATTTATTTATATTCAAAATATTTTTAAAAATAAAT
336702 ATATAAATATAATTTTTAAATATATAAAAATTTAAAAAAAATTAAATATATAATTATATATAATA
66 ATATAAATATAATTTTTAAATATATAAAAATTTAAAAAAAATTAAATATATAATTATATATAATA
336767 TTTATATTTAAATTCGAATAAAATAAGAAAAAAAAAAAACTATTCTGTTATCCTGAGACATAATT
131 TTTATATTTAAATTCGAATAAAATAAGAAAAAAAAAAAACTATTCTGTTATCCTGAGACATAATT
336832 TTGAAAGCTAAAAAGTCAGTCCAGCATGGTGGATTCAGGTTCCTTTTCAAAGTCTGTTCTATTTG
196 TTGAAAGCTAAAAAGTCAGTCCAGCATGGTGGATTCAGGTTCCTTTTCAAAGTCTGTTCTATTTG
336897 CCCAGTTCTTCTAATCCAACTGTGTCTCCACTCA
261 CCCAGTTCTTCTAATCCAACTGTGTCTCCACTCA
336931 CCTGTCTGTTGTTCAGATTTTTATTTTTTTATTTATTTATATTCAAAATATTTTTAAAAATAAAT
1 CCTGTCTGTTGTTCAGATTTTTATTTTTTTATTTATTTATATTCAAAATATTTTTAAAAATAAAT
336996 ATATAAATATAATTTTTAAATATATAAAAATTT-AAAAAAATTAAATATATAATTATATATAATA
66 ATATAAATATAATTTTTAAATATATAAAAATTTAAAAAAAATTAAATATATAATTATATATAATA
337060 TTTATATTTAAATTCGAATAAAATAAG-AAAAAAAAAAACTATTCTGTTATCCTGAGACATAATT
131 TTTATATTTAAATTCGAATAAAATAAGAAAAAAAAAAAACTATTCTGTTATCCTGAGACATAATT
337124 TTGAAAGCTAAAAAGTCAGTCCAGCATGGTGGATTCAGGTTCCTTTTCAAAGTCTGTTCTATTTG
196 TTGAAAGCTAAAAAGTCAGTCCAGCATGGTGGATTCAGGTTCCTTTTCAAAGTCTGTTCTATTTG
337189 CCCAGTTCTTCTAATCCAACTGTGTCTCCACTCA
261 CCCAGTTCTTCTAATCCAACTGTGTCTCCACTCA
337223 CCTG
1 CCTG
337227 CTTCATAATT
Statistics
Matches: 296, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
292 140 0.47
293 58 0.20
294 98 0.33
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (294 bp):
CCTGTCTGTTGTTCAGATTTTTATTTTTTTATTTATTTATATTCAAAATATTTTTAAAAATAAAT
ATATAAATATAATTTTTAAATATATAAAAATTTAAAAAAAATTAAATATATAATTATATATAATA
TTTATATTTAAATTCGAATAAAATAAGAAAAAAAAAAAACTATTCTGTTATCCTGAGACATAATT
TTGAAAGCTAAAAAGTCAGTCCAGCATGGTGGATTCAGGTTCCTTTTCAAAGTCTGTTCTATTTG
CCCAGTTCTTCTAATCCAACTGTGTCTCCACTCA
Done.