Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold246
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: 1425817
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
File 3 of 8
Found at i:253063 original size:18 final size:19
Alignment explanation
Indices: 253042--253086 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
253032 TTTATATTAT
253042 ATTATATATTA-TTTTTAA
1 ATTATATATTATTTTTTAA
* *
253060 ATTATATTTTATTTTTTAT
1 ATTATATATTATTTTTTAA
253079 ATTATATA
1 ATTATATA
253087 ATCATATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTATATATTATTTTTTAA
Found at i:253068 original size:34 final size:34
Alignment explanation
Indices: 253004--253083 Score: 80
Period size: 34 Copynumber: 2.5 Consensus size: 34
252994 TATTAATAAT
* * *
253004 TTATATTATATA-AAATTTAAAATATTTATTTATA
1 TTATATTATATATTATTTTAAAATATATATTT-TA
*
253038 TTATATTATATATTATTTTTAAAT-TATATTTTA
1 TTATATTATATATTATTTTAAAATATATATTTTA
253071 TT-T-TT-TATATTAT
1 TTATATTATATATTAT
253084 ATAATCATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
30 8 0.20
31 2 0.05
32 1 0.02
33 4 0.10
34 18 0.44
35 8 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (34 bp):
TTATATTATATATTATTTTAAAATATATATTTTA
Found at i:253537 original size:21 final size:22
Alignment explanation
Indices: 253513--253555 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
253503 TTATTTGATT
253513 TATTAATAATATA-TAAATATA
1 TATTAATAATATATTAAATATA
* *
253534 TATTATTAATGTATTAAATATA
1 TATTAATAATATATTAAATATA
253556 AATTCAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TATTAATAATATATTAAATATA
Found at i:253539 original size:24 final size:22
Alignment explanation
Indices: 253512--253555 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
253502 ATTATTTGAT
253512 TTATTAATAATATATAAATATATA
1 TTATTAAT-ATAT-TAAATATATA
*
253536 TTATTAATGTATTAAATATA
1 TTATTAATATATTAAATATA
253556 AATTCAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 3 0.16
24 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TTATTAATATATTAAATATATA
Found at i:259269 original size:64 final size:63
Alignment explanation
Indices: 259169--259288 Score: 195
Period size: 64 Copynumber: 1.9 Consensus size: 63
259159 GAAATTTAAC
* *
259169 AAAAGAAATATATATTATATATGTAAATGTTTATATGAAAAATCATATCATACATCATTAGTG
1 AAAAGAAATATAGATTATATATGTAAATGTTTATATGAAAAATAATATCATACATCATTAGTG
* *
259232 AAAAGAAATATAGATTTATATATGTAGATGTTTATATGAAAAATAATATCATGCATC
1 AAAAGAAATATAGA-TTATATATGTAAATGTTTATATGAAAAATAATATCATACATC
259289 GAAATTTAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
63 13 0.25
64 39 0.75
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (63 bp):
AAAAGAAATATAGATTATATATGTAAATGTTTATATGAAAAATAATATCATACATCATTAGTG
Found at i:259540 original size:3 final size:3
Alignment explanation
Indices: 259532--259559 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
259522 TTAAAAGCAG
259532 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
259560 GAAATTAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:261465 original size:19 final size:19
Alignment explanation
Indices: 261399--261465 Score: 50
Period size: 19 Copynumber: 3.3 Consensus size: 19
261389 AATTATAATT
261399 ATTAATATAAAATATTTTTAA
1 ATTAATAT-AAAT-TTTTTAA
261420 TATT--T-TAATATTATTTTAA
1 -ATTAATATAA-ATT-TTTTAA
261439 ATAATAATATAAATTTTTTAA
1 AT--TAATATAAATTTTTTAA
261460 ATTAAT
1 ATTAAT
261466 TTGATCTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 17
0.69 0.00 0.31
Matches are distributed among these distances:
18 5 0.13
19 13 0.34
20 2 0.05
21 8 0.21
22 7 0.18
23 3 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTAATATAAATTTTTTAA
Found at i:262260 original size:2 final size:2
Alignment explanation
Indices: 262253--262282 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
262243 CAAGATTAAA
*
262253 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
262283 GTTATTCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:262897 original size:15 final size:15
Alignment explanation
Indices: 262852--262905 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
262842 ATTTGAATTA
*
262852 TTTTAAATTTTG-AT
1 TTTTAAAGTTTGAAT
*
262866 ATTTT-AA-TTTAAAT
1 -TTTTAAAGTTTGAAT
*
262880 TTTTCAAGTTTGAAT
1 TTTTAAAGTTTGAAT
262895 TTTTAAAGTTT
1 TTTTAAAGTTT
262906 TTTAATTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 7 0.21
14 6 0.18
15 20 0.61
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.59
Consensus pattern (15 bp):
TTTTAAAGTTTGAAT
Found at i:267237 original size:29 final size:29
Alignment explanation
Indices: 267171--267240 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
267161 TATATTAGTA
* *
267171 TTAATATTTTTTATATATCATTTTAAATT
1 TTAATATATTTTATATATCATTATAAATT
* *
267200 TATCA-ATATTTTATATAT-ATATATATATT
1 T-TAATATATTTTATATATCAT-TATAAATT
267229 TTAATATATTTT
1 TTAATATATTTT
267241 TAAGTTTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
28 4 0.12
29 27 0.82
30 2 0.06
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (29 bp):
TTAATATATTTTATATATCATTATAAATT
Found at i:268491 original size:11 final size:11
Alignment explanation
Indices: 268475--268508 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
268465 ATTAAATATT
268475 TATATTTAAAA
1 TATATTTAAAA
268486 TATATTT-AAA
1 TATATTTAAAA
*
268496 TATATATAAAA
1 TATATTTAAAA
268507 TA
1 TA
268509 AAAAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TATATTTAAAA
Found at i:268775 original size:2 final size:2
Alignment explanation
Indices: 268768--268795 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
268758 TTCAATGAAG
268768 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
268796 GATTTTTATT
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:269984 original size:13 final size:14
Alignment explanation
Indices: 269958--270003 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
269948 TTGAAAAAAA
*
269958 AATAAATGTTTTTT
1 AATAAATCTTTTTT
*
269972 AATATAT-TTTTTT
1 AATAAATCTTTTTT
*
269985 ATTAAATCTTTTTT
1 AATAAATCTTTTTT
269999 AATAA
1 AATAA
270004 TGATACTTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (14 bp):
AATAAATCTTTTTT
Found at i:270489 original size:30 final size:30
Alignment explanation
Indices: 270433--270524 Score: 71
Period size: 30 Copynumber: 2.9 Consensus size: 30
270423 TTATTCAAAT
270433 AATAA-AATATTACTTTCATTTAAATATAATTATA
1 AATAATAATA-TACTTT--TTT-AATATAATT-TA
** *
270467 AATTTTAATATA-TTTTTTAATATTATGTTA
1 AATAATAATATACTTTTTTAATATAAT-TTA
* *
270497 AATAATGATATACTTTTTTATTATAATT
1 AATAATAATATACTTTTTTAATATAATT
270525 GTAACGTACA
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
30 19 0.40
31 16 0.34
33 3 0.06
34 5 0.11
35 4 0.09
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.52
Consensus pattern (30 bp):
AATAATAATATACTTTTTTAATATAATTTA
Found at i:270636 original size:15 final size:14
Alignment explanation
Indices: 270605--270658 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 14
270595 CTGATCCTAA
*
270605 ATTAAATGTAATAAT
1 ATTAAATATAAT-AT
270620 ATTAAATATAA-AT
1 ATTAAATATAATAT
*
270633 ATATAATTATAATAT
1 AT-TAAATATAATAT
270648 ATTAAAATATA
1 ATT-AAATATA
270659 TAAATATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 4 0.12
14 9 0.27
15 20 0.61
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (14 bp):
ATTAAATATAATAT
Found at i:270646 original size:13 final size:13
Alignment explanation
Indices: 270615--270676 Score: 60
Period size: 13 Copynumber: 5.0 Consensus size: 13
270605 ATTAAATGTA
270615 ATAATAT-TAAAT
1 ATAATATATAAAT
*
270627 ATAAATATATAATT
1 AT-AATATATAAAT
270641 ATAATATAT---T
1 ATAATATATAAAT
*
270651 AAAATATATAAAT
1 ATAATATATAAAT
*
270664 ATAATATAAAAAT
1 ATAATATATAAAT
270677 CTGAATTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
10 9 0.22
12 2 0.05
13 24 0.59
14 6 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATAATATATAAAT
Found at i:270649 original size:21 final size:21
Alignment explanation
Indices: 270617--270676 Score: 68
Period size: 23 Copynumber: 2.8 Consensus size: 21
270607 TAAATGTAAT
270617 AATATTAA-ATATAAATATATA
1 AATA-TAATATATAAATATATA
*
270638 ATTATAATATATTAAAATATATA
1 AATATAATATA-T-AAATATATA
*
270661 AATATAATATAAAAAT
1 AATATAATATATAAAT
270677 CTGAATTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 3 0.09
21 10 0.30
22 1 0.03
23 19 0.58
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AATATAATATATAAATATATA
Found at i:270655 original size:29 final size:28
Alignment explanation
Indices: 270616--270672 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
270606 TTAAATGTAA
270616 TAATATTAAATATA-AATATATAATTATAA
1 TAATATTAAATATATAA-ATATAA-TATAA
270645 T-ATATTAAAATATATAAATATAATATAA
1 TAATATT-AAATATATAAATATAATATAA
270673 AAATCTGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
28 10 0.38
29 14 0.54
30 2 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
TAATATTAAATATATAAATATAATATAA
Found at i:271691 original size:2 final size:2
Alignment explanation
Indices: 271684--271715 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
271674 CAAATTCAGA
271684 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
271716 GAAAATGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:272186 original size:111 final size:112
Alignment explanation
Indices: 271991--272207 Score: 341
Period size: 111 Copynumber: 1.9 Consensus size: 112
271981 ACACCCACAA
271991 ATCACTGACATTTAAGGCCTTTCCTCCTGTAGGCTTTTATCCCCTCCTTCCACTCCTCTCTTTCA
1 ATCACTGACATTTAAGGCCTTTCCTCCTGTAGGCTTTTATCCCCTCCTTCCACTCCTCTCTTTCA
* *
272056 GATCGGCAACCTCAGTAATTAATATATCGAGTAATTTTGTATACCGG
66 AATCGGCAACCTCAGTAATTAATATAGCGAGTAATTTTGTATACCGG
* * *
272103 ATCACTGACGTTTAAGGCCTTTACC-CTTGTAGGCTTTTATCTCCT-CTTCCACT-CTACTCTTT
1 ATCACTGACATTTAAGGCCTTT-CCTCCTGTAGGCTTTTATCCCCTCCTTCCACTCCT-CTCTTT
*
272165 CAAATCGGCAACCTCAGTAATTAATATAGCTAGTAATTTTGTA
64 CAAATCGGCAACCTCAGTAATTAATATAGCGAGTAATTTTGTA
272208 GTACACAATA
Statistics
Matches: 97, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
110 2 0.02
111 54 0.56
112 39 0.40
113 2 0.02
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.37
Consensus pattern (112 bp):
ATCACTGACATTTAAGGCCTTTCCTCCTGTAGGCTTTTATCCCCTCCTTCCACTCCTCTCTTTCA
AATCGGCAACCTCAGTAATTAATATAGCGAGTAATTTTGTATACCGG
Found at i:272508 original size:18 final size:20
Alignment explanation
Indices: 272456--272508 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
272446 CGAGAATGAT
272456 ATATTAAAATTTAA-ATTTTA
1 ATATT-AAATTTAATATTTTA
* *
272476 ATATTATATTAAATA-TTTA
1 ATATTAAATTTAATATTTTA
272495 AT-TTAAATTTAATA
1 ATATTAAATTTAATA
272509 GAGAATAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 10 0.36
19 12 0.43
20 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATTAAATTTAATATTTTA
Found at i:273540 original size:22 final size:24
Alignment explanation
Indices: 273512--273560 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
273502 AGCACTAATA
*
273512 AAAAATAATTTTA-AAAAAT-TAT
1 AAAAATAATATTATAAAAATATAT
*
273534 AAAAATAATATTATATAAATATAT
1 AAAAATAATATTATAAAAATATAT
273558 AAA
1 AAA
273561 CATATAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 12 0.52
23 5 0.22
24 6 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
AAAAATAATATTATAAAAATATAT
Found at i:273648 original size:19 final size:19
Alignment explanation
Indices: 273624--273673 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
273614 ATATTATTTT
*
273624 AAATATAATTATAATATAA
1 AAATATAAATATAATATAA
*
273643 AAATATAAATATAATATCA
1 AAATATAAATATAATATAA
*
273662 ATATATAAATAT
1 AAATATAAATAT
273674 CAATCATACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATATAAATATAATATAA
Found at i:273652 original size:25 final size:25
Alignment explanation
Indices: 273623--273673 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
273613 AATATTATTT
273623 TAAATATAATTAT-AATATAAAAATA
1 TAAATATAA-TATCAATATAAAAATA
*
273648 TAAATATAATATCAATATATAAATA
1 TAAATATAATATCAATATAAAAATA
273673 T
1 T
273674 CAATCATACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (25 bp):
TAAATATAATATCAATATAAAAATA
Found at i:273655 original size:45 final size:43
Alignment explanation
Indices: 273509--273656 Score: 119
Period size: 45 Copynumber: 3.4 Consensus size: 43
273499 TTGAGCACTA
* * *
273509 ATAAAAA-ATAATTTTAAAAA-ATTATA-AAAATAA-TATTAT
1 ATAAAAATATAAATATAAAAATATTATATAAAATAATTATAAT
* * *
273548 ATAAATATATAAACATATAAAATTTTATATAAAATAATTTATTAAT
1 ATAAAAATATAAATATA-AAAATATTATATAAAATAA-TTA-TAAT
* *
273594 ATATTAAAAT-T-TATATAAAAATATTATTTTAAATATAATTATAAT
1 ATA--AAAATATAAATATAAAAATATTA-TATAAA-ATAATTATAAT
273639 ATAAAAATATAAATATAA
1 ATAAAAATATAAATATAA
273657 TATCAATATA
Statistics
Matches: 84, Mismatches: 12, Indels: 20
0.72 0.10 0.17
Matches are distributed among these distances:
39 6 0.07
40 6 0.07
41 4 0.05
42 5 0.06
43 12 0.14
44 1 0.01
45 23 0.27
46 18 0.21
47 5 0.06
48 4 0.05
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (43 bp):
ATAAAAATATAAATATAAAAATATTATATAAAATAATTATAAT
Found at i:273673 original size:6 final size:6
Alignment explanation
Indices: 273623--273673 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
273613 AATATTATTT
* *
273623 TAAATA TAATTA TAATATA AAAATA TAAATA T-AATA TCAATATA TAAATA
1 TAAATA TAAATA TAA-ATA TAAATA TAAATA TAAATA T-AA-ATA TAAATA
273673 T
1 T
273674 CAATCATACT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
5 5 0.14
6 21 0.57
7 7 0.19
8 4 0.11
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (6 bp):
TAAATA
Found at i:278826 original size:205 final size:205
Alignment explanation
Indices: 278474--278884 Score: 768
Period size: 205 Copynumber: 2.0 Consensus size: 205
278464 TATGATATCC
*
278474 TGCTATATTACTGGGATTCAAGCATAAGTGTTAGATACAAATACGTGATTCTGAGAATGCCATTT
1 TGCTATATTACTGGGATTCAAGCATAAGTGATAGATACAAATACGTGATTCTGAGAATGCCATTT
* *
278539 ATGTTTTTTCATGTATTTGGAGAGTTTTTAATAGATCATATCCTTATATATTCATGTCTTCATGC
66 ATGTTTTTTCATGTATTTGAAGAGTTTTTAATAGATCATATCCTTATATATTCATATCTTCATGC
278604 GTATCGGACATGAGTACTTCAAAAATATATATATAAAGAGTAAGAGCAATGTAGACATCTTGTTA
131 GTATCGGACATGAGTACTTCAAAAATATATATATAAAGAGTAAGAGCAATGTAGACATCTTGTTA
278669 AATCAAGTCT
196 AATCAAGTCT
*
278679 TGCTATATTACTTGGATTCAAGCATAAGTGATAGATACAAATACGTGATTCTGAGAATGCCATTT
1 TGCTATATTACTGGGATTCAAGCATAAGTGATAGATACAAATACGTGATTCTGAGAATGCCATTT
*
278744 ATGTTTTTTCATGTATTTGAAGAGTTTTTAATATATCATATCCTTATATATTCATATCTTCATGC
66 ATGTTTTTTCATGTATTTGAAGAGTTTTTAATAGATCATATCCTTATATATTCATATCTTCATGC
*
278809 GTATCGGACATGAGTACTTCAAAAATATATGTATAAAGAGTAAGAGCAATGTAGACATCTTGTTA
131 GTATCGGACATGAGTACTTCAAAAATATATATATAAAGAGTAAGAGCAATGTAGACATCTTGTTA
278874 AATCAAGTCT
196 AATCAAGTCT
278884 T
1 T
278885 AAGTCCATGT
Statistics
Matches: 200, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
205 200 1.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (205 bp):
TGCTATATTACTGGGATTCAAGCATAAGTGATAGATACAAATACGTGATTCTGAGAATGCCATTT
ATGTTTTTTCATGTATTTGAAGAGTTTTTAATAGATCATATCCTTATATATTCATATCTTCATGC
GTATCGGACATGAGTACTTCAAAAATATATATATAAAGAGTAAGAGCAATGTAGACATCTTGTTA
AATCAAGTCT
Found at i:279819 original size:11 final size:11
Alignment explanation
Indices: 279799--279841 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
279789 ATTAAATATT
*
279799 TTATTTTAAAA
1 TTATTATAAAA
279810 TTATTATAAAA
1 TTATTATAAAA
279821 -TATT-TAAAA
1 TTATTATAAAA
*
279830 ATATTATAAAA
1 TTATTATAAAA
279841 T
1 T
279842 ATATATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 5 0.18
10 8 0.29
11 15 0.54
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TTATTATAAAA
Found at i:279826 original size:20 final size:20
Alignment explanation
Indices: 279803--279843 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
279793 AATATTTTAT
*
279803 TTTAAAATTATTATAAAATA
1 TTTAAAAATATTATAAAATA
279823 TTTAAAAATATTATAAAATA
1 TTTAAAAATATTATAAAATA
279843 T
1 T
279844 ATATTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTAAAAATATTATAAAATA
Found at i:281073 original size:23 final size:23
Alignment explanation
Indices: 281027--281088 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
281017 TCATTGTTTA
*
281027 AATAATTAAAATATTAATAAATTTT
1 AATAATT--AATATTTATAAATTTT
** *
281052 TTTAATTAATATTTATATATTTT
1 AATAATTAATATTTATAAATTTT
281075 AATAATTAA-ATTTA
1 AATAATTAATATTTA
281089 AATAATAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
22 5 0.16
23 21 0.68
25 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATAATTAATATTTATAAATTTT
Found at i:290063 original size:15 final size:15
Alignment explanation
Indices: 290045--290077 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
290035 TCTTTTAATC
290045 TTGACGCTTT-TTTTT
1 TTGACG-TTTATTTTT
290060 TTGACGTTTATTTTT
1 TTGACGTTTATTTTT
290075 TTG
1 TTG
290078 TAAATATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.09, C:0.09, G:0.15, T:0.67
Consensus pattern (15 bp):
TTGACGTTTATTTTT
Found at i:290610 original size:37 final size:36
Alignment explanation
Indices: 290569--290645 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 36
290559 TTATTTTTAT
290569 ATTATTATTTACA-TATTTATAA-ATAAATTTAAATAAA
1 ATTATTATTTA-ATTA-TTA-AATATAAATTTAAATAAA
* * *
290606 ATTATTTTTTAATTATTAAATATTAATTTAAATCAA
1 ATTATTATTTAATTATTAAATATAAATTTAAATAAA
290642 ATTA
1 ATTA
290646 ACCAAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
35 2 0.06
36 21 0.60
37 12 0.34
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (36 bp):
ATTATTATTTAATTATTAAATATAAATTTAAATAAA
Found at i:294251 original size:23 final size:23
Alignment explanation
Indices: 294225--294268 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
294215 GATGCCTACA
294225 GTAATCTATTAAGATGATATATG
1 GTAATCTATTAAGATGATATATG
294248 GTAATCTATTAAGATGATATA
1 GTAATCTATTAAGATGATATA
294269 AAAGACTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.39
Consensus pattern (23 bp):
GTAATCTATTAAGATGATATATG
Found at i:298838 original size:20 final size:21
Alignment explanation
Indices: 298797--298870 Score: 61
Period size: 20 Copynumber: 3.7 Consensus size: 21
298787 GATATAAAAA
298797 TTAAATT--ATTTATGTTAA-T
1 TTAAATTAAATTTAT-TTAATT
298816 TT-AATTAAATTTATTTAATT
1 TTAAATTAAATTTATTTAATT
*
298836 TTAAATTTAA-TTATTT-ATGT
1 TTAAATTAAATTTATTTAAT-T
*
298856 TTGAATATAAATTTA
1 TTAAAT-TAAATTTA
298871 AGTTTAAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
18 4 0.09
19 8 0.18
20 21 0.47
21 9 0.20
22 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (21 bp):
TTAAATTAAATTTATTTAATT
Found at i:299488 original size:19 final size:23
Alignment explanation
Indices: 299465--299511 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
299455 AGTAATCTAA
299465 ATTAATT-ATTT-T-TAATTATT
1 ATTAATTAATTTATATAATTATT
299485 -TTAATTAATTTATATAATTATT
1 ATTAATTAATTTATATAATTATT
299507 ATTAA
1 ATTAA
299512 AAATAATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 6 0.26
20 4 0.17
21 1 0.04
22 8 0.35
23 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
ATTAATTAATTTATATAATTATT
Found at i:299824 original size:20 final size:21
Alignment explanation
Indices: 299789--299836 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
299779 AAATCGTAAC
*
299789 TAAAATATATAAAAATAATAA
1 TAAAATATAAAAAAATAATAA
*
299810 TAAAAT-TAAAAAAATTATAA
1 TAAAATATAAAAAAATAATAA
*
299830 TATAATA
1 TAAAATA
299837 AACATTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
TAAAATATAAAAAAATAATAA
Found at i:299995 original size:15 final size:16
Alignment explanation
Indices: 299972--300009 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
299962 AATATTTTTA
299972 TTTTAAA-ATTATATTT
1 TTTTAAATA-TATATTT
299988 TTTTAAATATATATTT
1 TTTTAAATATATATTT
300004 TTTTAA
1 TTTTAA
300010 TTTTAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 20 0.95
17 1 0.05
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTTAAATATATATTT
Found at i:300527 original size:30 final size:29
Alignment explanation
Indices: 300492--300556 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
300482 TAAAATTTTA
*
300492 AAAAATAAAATATAAAAATTTTTAAAATAT
1 AAAAATAAAATATAAAAATTTTAAAAAT-T
* ** *
300522 AAAAATTATCTTTAAAAATTTTAAAAATT
1 AAAAATAAAATATAAAAATTTTAAAAATT
300551 AAAAAT
1 AAAAAT
300557 TATCTTTAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 7 0.23
30 23 0.77
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (29 bp):
AAAAATAAAATATAAAAATTTTAAAAATT
Found at i:300538 original size:29 final size:29
Alignment explanation
Indices: 300506--300570 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 29
300496 ATAAAATATA
300506 AAAATTTTT-AAAATATAAAAATTATCTTT
1 AAAATTTTTAAAAAT-TAAAAATTATCTTT
*
300535 AAAAATTTTAAAAATTAAAAATTATCTTT
1 AAAATTTTTAAAAATTAAAAATTATCTTT
300564 AACAATT
1 AA-AATT
300571 ATTCTTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 24 0.75
30 8 0.25
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.42
Consensus pattern (29 bp):
AAAATTTTTAAAAATTAAAAATTATCTTT
Found at i:300539 original size:13 final size:13
Alignment explanation
Indices: 300521--300607 Score: 54
Period size: 13 Copynumber: 6.5 Consensus size: 13
300511 TTTTAAAATA
300521 TAAAAATTATCTT
1 TAAAAATTATCTT
***
300534 TAAAAATTTTAAAAAT
1 TAAAAA--TT-ATCTT
300550 TAAAAATTATCTT
1 TAAAAATTATCTT
*
300563 TAACAATTATTCTT
1 TAAAAATTA-TCTT
*
300577 T-AAAATTATATTT
1 TAAAAATTAT-CTT
*
300590 TTAAAATT-T-TT
1 TAAAAATTATCTT
300601 TAAAAAT
1 TAAAAAT
300608 AATATTTATT
Statistics
Matches: 58, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
11 8 0.14
12 1 0.02
13 26 0.45
14 13 0.22
15 2 0.03
16 8 0.14
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (13 bp):
TAAAAATTATCTT
Found at i:300578 original size:14 final size:13
Alignment explanation
Indices: 300552--300597 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
300542 TTAAAAATTA
300552 AAAATTA-TCTTT
1 AAAATTATTCTTT
300564 AACAATTATTCTTT
1 AA-AATTATTCTTT
*
300578 AAAATTATATTTTT
1 AAAATTAT-TCTTT
300592 AAAATT
1 AAAATT
300598 TTTTAAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 2 0.07
13 11 0.37
14 17 0.57
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (13 bp):
AAAATTATTCTTT
Found at i:300618 original size:29 final size:29
Alignment explanation
Indices: 300504--300640 Score: 88
Period size: 29 Copynumber: 4.8 Consensus size: 29
300494 AAATAAAATA
*
300504 TAAAAATTTTTAAAATATAAAAATTATCTT
1 TAAAATTTTTTAAAA-ATAAAAATTATCTT
*
300534 TAAAA-ATTTTAAAAATTAAAAATTATCTT
1 TAAAATTTTTTAAAAA-TAAAAATTATCTT
* * *
300563 TAACAATTATTCTTTAAAAT---TA-TATTTT
1 TAA-AATT-TT-TTAAAAATAAAAATTATCTT
* * *
300591 TAAAATTTTTTAAAAATAATATTTATTTT
1 TAAAATTTTTTAAAAATAAAAATTATCTT
* * *
300620 TAATA-TTATTAAAATTAAAAA
1 TAAAATTTTTTAAAAATAAAAA
300641 AAATTATAAT
Statistics
Matches: 85, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
25 7 0.08
26 2 0.02
27 4 0.05
28 21 0.25
29 35 0.41
30 7 0.08
32 3 0.04
33 6 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (29 bp):
TAAAATTTTTTAAAAATAAAAATTATCTT
Found at i:300905 original size:17 final size:15
Alignment explanation
Indices: 300873--300901 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
300863 AATACAAATA
300873 ATATATTTAATATTT
1 ATATATTTAATATTT
300888 ATATATTTAA-ATTT
1 ATATATTTAATATTT
300902 TTTAAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATATATTTAATATTT
Found at i:304800 original size:33 final size:34
Alignment explanation
Indices: 304758--304821 Score: 112
Period size: 33 Copynumber: 1.9 Consensus size: 34
304748 TCCATCTGCG
*
304758 AAGGTGAAATTGACCAGAGAGGGAAA-AGGGCAC
1 AAGGTGAAATTGAACAGAGAGGGAAAGAGGGCAC
304791 AAGGTGAAATTGAACAGAGAGGGAAAGAGGG
1 AAGGTGAAATTGAACAGAGAGGGAAAGAGGG
304822 TATGCACGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.44, C:0.08, G:0.39, T:0.09
Consensus pattern (34 bp):
AAGGTGAAATTGAACAGAGAGGGAAAGAGGGCAC
Found at i:304904 original size:25 final size:26
Alignment explanation
Indices: 304862--304910 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
304852 TTTAGTACTT
*
304862 AATTAATTATGATATTATTTATTATA
1 AATTAATTATGATATTATTAATTATA
* *
304888 AATT-ATTATTATTTTATTAATTA
1 AATTAATTATGATATTATTAATTA
304911 AGATATTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (26 bp):
AATTAATTATGATATTATTAATTATA
Found at i:304931 original size:22 final size:23
Alignment explanation
Indices: 304891--304938 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
304881 TATTATAAAT
* *
304891 TATTATTATTTTATTAATTAAGA
1 TATTATTATGTTATGAATTAAGA
*
304914 TATTATTA-GTTATGAATTAATA
1 TATTATTATGTTATGAATTAAGA
304936 TAT
1 TAT
304939 AATTTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (23 bp):
TATTATTATGTTATGAATTAAGA
Found at i:306372 original size:17 final size:16
Alignment explanation
Indices: 306346--306398 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 16
306336 GACAAGAACC
*
306346 TAAATATTTATATTTA
1 TAAATATTTAAATTTA
306362 TAAATTATTTAAATTTAA
1 TAAA-TATTTAAATTT-A
306380 TTAAAATAATTTAAATTTA
1 -T-AAAT-ATTTAAATTTA
306399 ATTTGATCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 4 0.13
17 10 0.32
18 1 0.03
19 3 0.10
20 13 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TAAATATTTAAATTTA
Found at i:306391 original size:20 final size:20
Alignment explanation
Indices: 306363--306401 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
306353 TTATATTTAT
*
306363 AAATTATTTAAATTTAATTA
1 AAATAATTTAAATTTAATTA
306383 AAATAATTTAAATTTAATT
1 AAATAATTTAAATTTAATT
306402 TGATCATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATAATTTAAATTTAATTA
Found at i:306471 original size:22 final size:23
Alignment explanation
Indices: 306426--306486 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
306416 TTAAATTTAA
*
306426 TAAATTTAAAT-TATTGAATGAAT
1 TAAATTTAAATAT-TTTAATGAAT
306449 TAAATTTAAATATTTTAAT-AAT
1 TAAATTTAAATATTTTAATGAAT
*
306471 T-AATTTAAATAATTTA
1 TAAATTTAAATATTTTA
306487 TAAATTTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.40
22 4 0.11
23 16 0.46
24 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (23 bp):
TAAATTTAAATATTTTAATGAAT
Found at i:306494 original size:17 final size:18
Alignment explanation
Indices: 306419--306502 Score: 62
Period size: 21 Copynumber: 4.3 Consensus size: 18
306409 TGACAAGTTA
306419 AATTTAATAAATTTAAAT
1 AATTTAATAAATTTAAAT
*
306437 TATTGAATGAATTAAATTTAAAT
1 AATT---T-AA-TAAATTTAAAT
*
306460 ATTTTAATAATTAATTTAAAT
1 AATTTAAT-A--AATTTAAAT
*
306481 AATTT-ATAAATTTAATT
1 AATTTAATAAATTTAAAT
306498 AATTT
1 AATTT
306503 TTTTATTTAA
Statistics
Matches: 53, Mismatches: 5, Indels: 17
0.71 0.07 0.23
Matches are distributed among these distances:
17 13 0.25
18 4 0.08
19 4 0.08
20 3 0.06
21 14 0.26
22 2 0.04
23 13 0.25
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
AATTTAATAAATTTAAAT
Found at i:306495 original size:22 final size:21
Alignment explanation
Indices: 306428--306497 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 21
306418 AAATTTAATA
* * *
306428 AATTTAAATTATTGAATGAATTA
1 AATTTAAA-TATT-TATAAATTT
*
306451 AATTTAAATATTT-TAATAATT
1 AATTTAAATATTTATAA-ATTT
306472 AATTTAAATAATTTATAAATTT
1 AATTTAAAT-ATTTATAAATTT
306494 AATT
1 AATT
306498 AATTTTTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
20 2 0.05
21 11 0.28
22 15 0.38
23 11 0.28
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (21 bp):
AATTTAAATATTTATAAATTT
Found at i:306499 original size:21 final size:21
Alignment explanation
Indices: 306423--306486 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
306413 AAGTTAAATT
* *
306423 TAATAAATTTAAAT-TATTGAA
1 TAATTAATTTAAATAT-TTTAA
306444 TGAATTAAATTTAAATATTTTAA
1 T-AATT-AATTTAAATATTTTAA
*
306467 TAATTAATTTAAATAATTTA
1 TAATTAATTTAAATATTTTA
306487 TAAATTTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
21 15 0.41
22 7 0.19
23 14 0.38
24 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (21 bp):
TAATTAATTTAAATATTTTAA
Found at i:306673 original size:10 final size:10
Alignment explanation
Indices: 306660--306689 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
306650 AATTTTAAAA
306660 AATTAAATTT
1 AATTAAATTT
306670 AATTAAATTT
1 AATTAAATTT
*
306680 AAATAAATTT
1 AATTAAATTT
306690 TAAATATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
AATTAAATTT
Found at i:306716 original size:24 final size:24
Alignment explanation
Indices: 306671--306717 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
306661 ATTAAATTTA
*
306671 ATTAAATTTAAATAAATTTTAAAT
1 ATTAAATTTAAATAAATGTTAAAT
*
306695 ATTAAATATTAAATTAA-GTTAAA
1 ATTAAAT-TTAAATAAATGTTAAA
306718 ACTTTCGACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
ATTAAATTTAAATAAATGTTAAAT
Found at i:306717 original size:35 final size:35
Alignment explanation
Indices: 306649--306717 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
306639 AATTAATCTC
*
306649 AAATTTTAAAAAATTAAATTTAATTAAATTTAAAT
1 AAATTTTAAAAAATTAAATTTAATTAAAGTTAAAT
*
306684 AAATTTT-AAATATTAAATATTAAATT-AAGTTAAA
1 AAATTTTAAAAAATTAAAT-TT-AATTAAAGTTAAA
306718 ACTTTCGACT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 10 0.33
35 16 0.53
36 4 0.13
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (35 bp):
AAATTTTAAAAAATTAAATTTAATTAAAGTTAAAT
Found at i:306978 original size:2 final size:2
Alignment explanation
Indices: 306971--306997 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
306961 TCTAGTCGGT
306971 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 T
306998 TCCTTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:308299 original size:14 final size:14
Alignment explanation
Indices: 308227--308299 Score: 50
Period size: 14 Copynumber: 5.4 Consensus size: 14
308217 TTTTTAATTT
308227 TTTAAAGTATTAATA
1 TTTAAA-TATTAATA
* *
308242 TTT-TATATTTATA
1 TTTAAATATTAATA
308255 TTTAACATA-T--T-
1 TTTAA-ATATTAATA
308266 TTTAAATATTAATA
1 TTTAAATATTAATA
*
308280 TATAAATA-TAATTA
1 TTTAAATATTAA-TA
308294 TTTAAA
1 TTTAAA
308300 AATCTTTTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 15
0.70 0.08 0.23
Matches are distributed among these distances:
10 3 0.07
11 6 0.13
12 1 0.02
13 14 0.30
14 16 0.35
15 6 0.13
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (14 bp):
TTTAAATATTAATA
Found at i:308556 original size:13 final size:13
Alignment explanation
Indices: 308538--308562 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
308528 ATTTTTTAAA
308538 ATATTTATATTTT
1 ATATTTATATTTT
308551 ATATTTATATTT
1 ATATTTATATTT
308563 GAGACATATA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATATTTATATTTT
Found at i:310463 original size:19 final size:20
Alignment explanation
Indices: 310439--310479 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
310429 CACAAATATA
*
310439 TTCAATCTTTT-TAAAGTTT
1 TTCAATCTTTTGAAAAGTTT
*
310458 TTCAATGTTTTGAAAAGTTT
1 TTCAATCTTTTGAAAAGTTT
310478 TT
1 TT
310480 GGAAGGTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.27, C:0.07, G:0.10, T:0.56
Consensus pattern (20 bp):
TTCAATCTTTTGAAAAGTTT
Found at i:313052 original size:22 final size:21
Alignment explanation
Indices: 313005--313053 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
312995 TATGTTAATT
*
313005 TATTTAAAAATATTTTTTATA
1 TATTTAAAAATATATTTTATA
313026 TATTTAAAATATCATATTTT-TA
1 TATTTAAAA-AT-ATATTTTATA
313048 TATTTA
1 TATTTA
313054 TATTTAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 9 0.36
22 10 0.40
23 6 0.24
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTAAAAATATATTTTATA
Found at i:321482 original size:23 final size:23
Alignment explanation
Indices: 321453--321518 Score: 77
Period size: 22 Copynumber: 2.9 Consensus size: 23
321443 TTAAATTATT
321453 ATTTAATA-AAATAATTTATTTAA
1 ATTTAATATAAA-AATTTATTTAA
321476 ATTTAATTATAAAAATTTA--TAA
1 ATTTAA-TATAAAAATTTATTTAA
321498 ATATTAATATAAAAA-TTATTT
1 AT-TTAATATAAAAATTTATTT
321519 TTTATTATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
21 3 0.08
22 13 0.34
23 11 0.29
24 8 0.21
25 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTTAATATAAAAATTTATTTAA
Found at i:321750 original size:29 final size:29
Alignment explanation
Indices: 321685--321751 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
321675 TTTTAAATGT
* * *
321685 TATAAATATATTTAAAATATTATATATTT
1 TATAAATTTATTTAAAACATTATATATTA
* *
321714 TATAAATTTATTTATAACATTTTATATTA
1 TATAAATTTATTTAAAACATTATATATTA
321743 TATAAATTT
1 TATAAATTT
321752 TAATTAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (29 bp):
TATAAATTTATTTAAAACATTATATATTA
Found at i:324388 original size:13 final size:13
Alignment explanation
Indices: 324370--324395 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
324360 TTTATGTGTC
324370 AAATATAAATATT
1 AAATATAAATATT
324383 AAATATAAATATT
1 AAATATAAATATT
324396 TAAAAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATATAAATATT
Found at i:324989 original size:2 final size:2
Alignment explanation
Indices: 324982--325010 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
324972 ATGAGCTGTG
324982 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
325011 GAAATGGGGG
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
Found at i:326723 original size:19 final size:21
Alignment explanation
Indices: 326685--326724 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
326675 TATATTTATA
*
326685 TAATATTTATATAATTACATT
1 TAATATTTATATAATAACATT
326706 TAATA-TTAT-TAATAACATT
1 TAATATTTATATAATAACATT
326725 ATTACTCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 4 0.22
21 5 0.28
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (21 bp):
TAATATTTATATAATAACATT
Found at i:327171 original size:22 final size:24
Alignment explanation
Indices: 327146--327190 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
327136 AATATATAAA
327146 TATTAA-TATAAA-AATAAATTTT
1 TATTAATTATAAATAATAAATTTT
327168 TATTAATTATAAATAATAAATTT
1 TATTAATTATAAATAATAAATTT
327191 ATGCTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.29
23 6 0.29
24 9 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TATTAATTATAAATAATAAATTTT
Found at i:327191 original size:22 final size:22
Alignment explanation
Indices: 327125--327192 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 22
327115 TTTTTTAATT
327125 TTAATTATAAAAATATATAAA--TA
1 TTAATTAT--AAATA-ATAAATTTA
327148 TTAA-TATAAA-AATAAATTTTTA
1 TTAATTATAAATAATAAA--TTTA
327170 TTAATTATAAATAATAAATTTA
1 TTAATTATAAATAATAAATTTA
327192 T
1 T
327193 GCTTTTAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
18 5 0.13
19 1 0.03
20 3 0.08
22 14 0.36
23 10 0.26
24 6 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TTAATTATAAATAATAAATTTA
Found at i:328180 original size:18 final size:18
Alignment explanation
Indices: 328149--328183 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
328139 ATCCTCTTTG
*
328149 ATAAAAAGAGAAAACAAA
1 ATAAAAAGACAAAACAAA
*
328167 ATAAAAAGCCAAAACAA
1 ATAAAAAGACAAAACAA
328184 GATCTTGATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.11, G:0.09, T:0.06
Consensus pattern (18 bp):
ATAAAAAGACAAAACAAA
Found at i:329278 original size:20 final size:21
Alignment explanation
Indices: 329255--329333 Score: 67
Period size: 21 Copynumber: 3.9 Consensus size: 21
329245 AAAATATTTT
329255 ATAA-TTAAATTTAAATAAAA
1 ATAATTTAAATTTAAATAAAA
**
329275 ATAATTTTTATTT-AATAAATA
1 ATAATTTAAATTTAAATAAA-A
* *
329296 ATAATTTAAA-TTCAATTAAA
1 ATAATTTAAATTTAAATAAAA
*
329316 TTAA-TTAAATATTAAATA
1 ATAATTTAAAT-TTAAATA
329334 TTTTATTTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
19 5 0.11
20 16 0.35
21 25 0.54
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (21 bp):
ATAATTTAAATTTAAATAAAA
Found at i:329315 original size:46 final size:46
Alignment explanation
Indices: 329225--329316 Score: 107
Period size: 46 Copynumber: 2.0 Consensus size: 46
329215 GTTAAATTTA
* * * *
329225 AAAAATATTTTTTATTATTTAAAATATTTTATAATTAAATTTAAAT
1 AAAAATAATTTTTATTAATAAAAATAATTTATAATTAAATTTAAAT
*
329271 AAAAATAATTTTTATTTAATAAATAATAATTTA-AATTCAA-TTAAAT
1 AAAAATAATTTTTA-TTAATAAA-AATAATTTATAATTAAATTTAAAT
329317 TAATTAAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
46 19 0.49
47 12 0.31
48 8 0.21
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (46 bp):
AAAAATAATTTTTATTAATAAAAATAATTTATAATTAAATTTAAAT
Found at i:330226 original size:16 final size:16
Alignment explanation
Indices: 330182--330226 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
330172 TATTTATTAT
*
330182 TTATTTTTTAAATATA
1 TTATTTTATAAATATA
* * *
330198 TTCTATTAAAAATATA
1 TTATTTTATAAATATA
330214 TTATTTTATAAAT
1 TTATTTTATAAAT
330227 TTTATTTATG
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATTTTATAAATATA
Found at i:332780 original size:16 final size:15
Alignment explanation
Indices: 332754--332813 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 15
332744 GAAATTTAAT
332754 TTAATTATTTATAAAA
1 TTAA-TATTTATAAAA
332770 TATAATATTTA-ATAAA
1 T-TAATATTTATA-AAA
* *
332786 TTTATAATTTA-AAAT
1 TTAAT-ATTTATAAAA
332801 TTAATATTTATAA
1 TTAATATTTATAA
332814 TTATTTTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 5 0.14
15 12 0.32
16 17 0.46
17 3 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAATATTTATAAAA
Found at i:332809 original size:14 final size:14
Alignment explanation
Indices: 332751--332815 Score: 51
Period size: 14 Copynumber: 4.3 Consensus size: 14
332741 TACGAAATTT
332751 AATTTAATTATTTATAA
1 AATTTAA-TA-TT-TAA
*
332768 AATATAATATTTAATA
1 AATTTAATATTT-A-A
332784 AATTT-ATAATTTAA
1 AATTTAAT-ATTTAA
*
332798 AATTTAATATTTAT
1 AATTTAATATTTAA
332812 AATT
1 AATT
332816 ATTTTTTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
14 16 0.39
15 8 0.20
16 11 0.27
17 6 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
AATTTAATATTTAA
Found at i:333192 original size:31 final size:32
Alignment explanation
Indices: 333157--333217 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
333147 ATTTGATAAT
* * *
333157 TTATATTTATATTTAATAT-TTATTTATTTTA
1 TTATAATTATATTTAAAATATTATATATTTTA
*
333188 TTATAATTATGTTTAAAATATTATATATTT
1 TTATAATTATATTTAAAATATTATATATTT
333218 ATATAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 16 0.64
32 9 0.36
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (32 bp):
TTATAATTATATTTAAAATATTATATATTTTA
Found at i:341526 original size:2 final size:2
Alignment explanation
Indices: 341519--341546 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
341509 AATTACTTGA
341519 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
341547 TCATATAAAT
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:347917 original size:19 final size:18
Alignment explanation
Indices: 347895--348037 Score: 84
Period size: 19 Copynumber: 7.8 Consensus size: 18
347885 TAGAATGAAA
*
347895 ATTTATGTATTTATATTAT
1 ATTTATATATTTATA-TAT
*
347914 ATTTATATATTTTTATAT
1 ATTTATATATTTATATAT
*
347932 ATTATAATTATATTTA-AAAT
1 ATT-T-A-TATATTTATATAT
347952 A-TTATATATTTATATGA-
1 ATTTATATATTTATAT-AT
*
347969 AGTTTGATATA-TT-TATGT
1 A-TTT-ATATATTTATATAT
347987 ATTTATAT-TTTATATTAT
1 ATTTATATATTTATA-TAT
* * *
348005 ATTTTTAATTATTTTTATTT
1 ATTTAT-A-TATTTATATAT
348025 A-TTATATATTTAT
1 ATTTATATATTTAT
348038 TATGTTTAAA
Statistics
Matches: 97, Mismatches: 12, Indels: 32
0.69 0.09 0.23
Matches are distributed among these distances:
16 14 0.14
17 14 0.14
18 20 0.21
19 23 0.24
20 14 0.14
21 12 0.12
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
ATTTATATATTTATATAT
Found at i:347922 original size:8 final size:8
Alignment explanation
Indices: 347911--348001 Score: 66
Period size: 8 Copynumber: 11.4 Consensus size: 8
347901 GTATTTATAT
347911 TATATTTA
1 TATATTTA
*
347919 TATATTTT
1 TATATTTA
347927 TATATATTA
1 TATAT-TTA
347936 TA-A-TTA
1 TATATTTA
*
347942 TAT-TTAA
1 TATATTTA
*
347949 AATA-TTA
1 TATATTTA
347956 TATATTTA
1 TATATTTA
347964 TATGAAGTTTGA
1 TAT--A-TTT-A
347976 TATATTTA
1 TATATTTA
*
347984 TGTATTTA
1 TATATTTA
347992 TAT-TTTA
1 TATATTTA
347999 TAT
1 TAT
348002 TATATTTTTA
Statistics
Matches: 66, Mismatches: 8, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
6 5 0.08
7 16 0.24
8 29 0.44
9 7 0.11
10 2 0.03
11 3 0.05
12 4 0.06
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.58
Consensus pattern (8 bp):
TATATTTA
Found at i:347937 original size:28 final size:29
Alignment explanation
Indices: 347896--348040 Score: 103
Period size: 28 Copynumber: 5.2 Consensus size: 29
347886 AGAATGAAAA
*
347896 TTTATGTATTTATATTATATTTATATATT
1 TTTATATATTTATATTATATTTATATATT
*
347925 TTTATATA-TTATAATTATATTTA-A-AAT
1 TTTATATATTTAT-ATTATATTTATATATT
* *
347952 ATTATATATTTATATGA-AGTTTGATATA--
1 TTTATATATTTATATTATA-TTT-ATATATT
* * *
347980 TTTATGTATTTATATTTTATAT-TATATT
1 TTTATATATTTATATTATATTTATATATT
*
348008 TTTA-ATTATTTTTATT-TA-TTATATATT
1 TTTATA-TATTTATATTATATTTATATATT
348035 TATTAT
1 T-TTAT
348041 GTTTAAAATT
Statistics
Matches: 91, Mismatches: 12, Indels: 26
0.71 0.09 0.20
Matches are distributed among these distances:
26 6 0.07
27 24 0.26
28 41 0.45
29 19 0.21
30 1 0.01
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (29 bp):
TTTATATATTTATATTATATTTATATATT
Found at i:347993 original size:56 final size:56
Alignment explanation
Indices: 347892--348002 Score: 129
Period size: 56 Copynumber: 2.0 Consensus size: 56
347882 GTATAGAATG
* * *
347892 AAAATTTATGTATTTATATTATATTTATATATTTTTATATATTATA-ATTATATTT
1 AAAATTTATATATTTATATGATATTTATATATTTATATATATTATATATTATATTT
* *
347947 AAAATATTATATATTTATATGA-AGTTTGATATATTTATGTAT-TTATATTTTATATT
1 AAAAT-TTATATATTTATATGATA-TTT-ATATATTTATATATATTATATATTATATT
348003 ATATTTTTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
55 6 0.13
56 22 0.47
57 19 0.40
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.58
Consensus pattern (56 bp):
AAAATTTATATATTTATATGATATTTATATATTTATATATATTATATATTATATTT
Found at i:348011 original size:20 final size:20
Alignment explanation
Indices: 347904--348011 Score: 51
Period size: 21 Copynumber: 4.8 Consensus size: 20
347894 AATTTATGTA
*
347904 TTTATATTATATTTATATAT
1 TTTATATTATATTTTTATAT
347924 TTT-TA-TATATTATAATTATAT
1 TTTATATTATATT-T--TTATAT
*
347945 TTAAAATATTATATATTTATATGAAGT
1 TT--TATATTATAT-TTT-TAT--A-T
347972 TTGATATATT-TATGTATTTATAT
1 TT--TATATTATAT-T-TTTATAT
347995 TTTATATTATATTTTTA
1 TTTATATTATATTTTTA
348012 ATTATTTTTA
Statistics
Matches: 69, Mismatches: 5, Indels: 28
0.68 0.05 0.27
Matches are distributed among these distances:
18 6 0.09
19 3 0.04
20 7 0.10
21 14 0.20
22 3 0.04
23 4 0.06
24 6 0.09
25 6 0.09
26 9 0.13
27 11 0.16
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTATATTATATTTTTATAT
Found at i:348036 original size:25 final size:24
Alignment explanation
Indices: 347951--348045 Score: 72
Period size: 24 Copynumber: 3.9 Consensus size: 24
347941 ATATTTAAAA
* *
347951 TATTATATATTTATATGAAGTTTGATA
1 TATTATATATTTAT-T-ATGTTT-ATT
*
347978 TATTTATGTATTTA-TAT-TTTA--
1 TA-TTATATATTTATTATGTTTATT
* *
347999 TATTATATTTTTAATTATTTTTATT
1 TATTATATATTT-ATTATGTTTATT
348024 TATTATATATTTATTATGTTTA
1 TATTATATATTTATTATGTTTA
348046 AAATTATCAG
Statistics
Matches: 56, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
20 8 0.14
21 3 0.05
22 3 0.05
23 5 0.09
24 12 0.21
25 12 0.21
26 1 0.02
27 2 0.04
28 10 0.18
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (24 bp):
TATTATATATTTATTATGTTTATT
Found at i:351770 original size:2 final size:2
Alignment explanation
Indices: 351763--351787 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
351753 TCTCTTTAAT
351763 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
351788 GAAAATTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:354825 original size:2 final size:2
Alignment explanation
Indices: 354818--354844 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
354808 TAAAACTATC
354818 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 T
354845 GCGTGTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:354852 original size:2 final size:2
Alignment explanation
Indices: 354847--354871 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
354837 ATATATATGC
354847 GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT G
354872 GATCTTCTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:363357 original size:33 final size:34
Alignment explanation
Indices: 363299--363369 Score: 108
Period size: 33 Copynumber: 2.1 Consensus size: 34
363289 ATATGAATCA
*
363299 ATAATTAAATTTAAAAAATTATAAATACTGATTT
1 ATAAATAAATTTAAAAAATTATAAATACTGATTT
* *
363333 ATAAATAAA-TTAAGAAATTGTAAATACTGATTT
1 ATAAATAAATTTAAAAAATTATAAATACTGATTT
363366 ATAA
1 ATAA
363370 TTATAAAGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 26 0.76
34 8 0.24
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.38
Consensus pattern (34 bp):
ATAAATAAATTTAAAAAATTATAAATACTGATTT
Found at i:365597 original size:49 final size:49
Alignment explanation
Indices: 365540--365638 Score: 144
Period size: 49 Copynumber: 2.0 Consensus size: 49
365530 AAGAAAAGAA
* * *
365540 AATAATTAAAGGCTTTTGATAGCTAGTAAGGGTTTCCTTCACTACGACT
1 AATAATTAAAGGCTTTAGATAGCTAGTAAGGGTTACATTCACTACGACT
* * *
365589 AATAATTAATGGCTTTAGTTAGCTAGTAAGGGTTACATTCAGTACGACT
1 AATAATTAAAGGCTTTAGATAGCTAGTAAGGGTTACATTCACTACGACT
365638 A
1 A
365639 GACCAACGTC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.34
Consensus pattern (49 bp):
AATAATTAAAGGCTTTAGATAGCTAGTAAGGGTTACATTCACTACGACT
Found at i:366553 original size:15 final size:15
Alignment explanation
Indices: 366533--366563 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
366523 ATTTGGTAGT
366533 TTTAATAAAATTAAA
1 TTTAATAAAATTAAA
*
366548 TTTAATAATATTAAA
1 TTTAATAAAATTAAA
366563 T
1 T
366564 ATGATCATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTAATAAAATTAAA
Found at i:367089 original size:13 final size:12
Alignment explanation
Indices: 367067--367193 Score: 53
Period size: 11 Copynumber: 10.8 Consensus size: 12
367057 AAAAAATAAT
367067 TAATATAAATTA
1 TAATATAAATTA
367079 TAATATGAAATTA
1 TAATAT-AAATTA
367092 T-ATATAAA--A
1 TAATATAAATTA
* *
367101 -AATTTATA-TA
1 TAATATAAATTA
*
367111 TAACATAAATTA
1 TAATATAAATTA
367123 TTAATATATTAAATT-
1 -T-A-ATA-TAAATTA
367138 T-ATATAAATATA
1 TAATATAAAT-TA
367150 TAATATTTTAAA-TA
1 TAATA---TAAATTA
367164 TAATA-AAA--A
1 TAATATAAATTA
367173 TAATATAAA-TA
1 TAATATAAATTA
*
367184 TAAAATAAAT
1 TAATATAAAT
367194 AACAGGTTAT
Statistics
Matches: 90, Mismatches: 7, Indels: 36
0.68 0.05 0.27
Matches are distributed among these distances:
9 12 0.13
10 12 0.13
11 21 0.23
12 13 0.14
13 11 0.12
14 9 0.10
15 2 0.02
16 10 0.11
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (12 bp):
TAATATAAATTA
Found at i:367110 original size:37 final size:34
Alignment explanation
Indices: 367094--367191 Score: 60
Period size: 33 Copynumber: 2.9 Consensus size: 34
367084 TGAAATTATA
* *
367094 TATAAAAAATTTATATATAA-CATAA-ATTATTAA
1 TATAAAAAATTTATATA-AATTATAATATAATTAA
** *
367127 TATATTAAATTTATATAAATATATAATAT-TTTAAA
1 TATAAAAAATTTATATAAAT-TATAATATAATT-AA
* * *
367162 TATAATAAAAATAATATAAA-TATAAAATAA
1 TATAA-AAAATTTATATAAATTATAATATAA
367192 ATAACAGGTT
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
32 2 0.04
33 15 0.31
34 13 0.27
35 8 0.16
36 11 0.22
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (34 bp):
TATAAAAAATTTATATAAATTATAATATAATTAA
Found at i:367153 original size:26 final size:25
Alignment explanation
Indices: 367115--367179 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 25
367105 TATATATAAC
*
367115 ATAAAT-TATTAATATATTAAATTTA
1 ATAAATATA-TAATATATTAAATATA
*
367140 TATAAATATATAATATTTTAAATATA
1 -ATAAATATATAATATATTAAATATA
367166 ATAAA-A-ATAATATA
1 ATAAATATATAATATA
367180 AATATAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 7 0.20
24 1 0.03
25 5 0.14
26 20 0.57
27 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
ATAAATATATAATATATTAAATATA
Found at i:367193 original size:20 final size:20
Alignment explanation
Indices: 367139--367195 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
367129 TATTAAATTT
* *
367139 ATATAAATATATAATATTTTAA
1 ATATAAA-ATA-AATAATATAA
367161 ATATAATAA-AAATAATATAA
1 ATATAA-AATAAATAATATAA
367181 ATATAAAATAAATAA
1 ATATAAAATAAATAA
367196 CAGGTTATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 2 0.06
20 20 0.65
21 1 0.03
22 7 0.23
23 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
ATATAAAATAAATAATATAA
Found at i:370995 original size:29 final size:29
Alignment explanation
Indices: 370959--371040 Score: 91
Period size: 28 Copynumber: 2.9 Consensus size: 29
370949 TATTTGAATA
* *
370959 AATA-TTTAATTAATAAAAATTATTTTATT
1 AATATTTTAATTAATAAAAATAAATTT-TT
*
370988 TA-ATTTTAATT-ATAAAAATAAATTTTT
1 AATATTTTAATTAATAAAAATAAATTTTT
*
371015 AATATTTTAAATAAT-AAAATAAATTT
1 AATATTTTAATTAATAAAAATAAATTT
371041 ATAAGTCGGA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
27 3 0.07
28 32 0.71
29 10 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
AATATTTTAATTAATAAAAATAAATTTTT
Found at i:376925 original size:20 final size:20
Alignment explanation
Indices: 376884--376926 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
376874 ATTGTCCATT
* *
376884 TATTTTAATCATTTTTATTA
1 TATTTTAATCATATATATTA
376904 TATTTTAAT-ATATATATATA
1 TATTTTAATCATATATAT-TA
376924 TAT
1 TAT
376927 GGAGATCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTTTAATCATATATATTA
Found at i:378489 original size:25 final size:24
Alignment explanation
Indices: 378461--378507 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
378451 TAATTTATTT
378461 TTATAAATTTTTAAAAAATAATTAA
1 TTAT-AATTTTTAAAAAATAATTAA
* *
378486 TTATATTTTTTAAAATATAATT
1 TTATAATTTTTAAAAAATAATT
378508 TTAATTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTATAATTTTTAAAAAATAATTAA
Found at i:384108 original size:2 final size:2
Alignment explanation
Indices: 384101--384128 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
384091 TTGATAACAA
384101 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
384129 TAATAGGATT
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:384625 original size:2 final size:2
Alignment explanation
Indices: 384618--384651 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
384608 CCAATCTACA
384618 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
384652 TTCTTTTAAC
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:389380 original size:21 final size:21
Alignment explanation
Indices: 389356--389429 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 21
389346 ATAAATTTTG
389356 ATAAATATTTAATAAAATTAT
1 ATAAATATTTAATAAAATTAT
*
389377 ATAAATA--TAATATAAA-AAT
1 ATAAATATTTAATA-AAATTAT
* *
389396 ATAAATATTT-TTAAATTTAT
1 ATAAATATTTAATAAAATTAT
389416 ATAAAT-TATTAATA
1 ATAAATAT-TTAATA
389430 TATCGATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
19 17 0.40
20 15 0.36
21 10 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATAAATATTTAATAAAATTAT
Found at i:389905 original size:29 final size:30
Alignment explanation
Indices: 389846--389906 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
389836 AGCTAATGAA
* *
389846 TTTTATTATTTTTAAAATAATTATTATATT
1 TTTTATTATATTTAAAATAAATATTATATT
389876 TTTTATTATATTT-AAATAAATA-TATCATT
1 TTTTATTATATTTAAAATAAATATTAT-ATT
389905 TT
1 TT
389907 ATTAAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 3 0.11
29 13 0.46
30 12 0.43
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (30 bp):
TTTTATTATATTTAAAATAAATATTATATT
Found at i:390104 original size:21 final size:19
Alignment explanation
Indices: 390066--390106 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
390056 TAATCAAAAT
*
390066 AAATTTATATTTATATTTA
1 AAATTTATATTTAAATTTA
390085 AAATATTATATTTTAAATTTA
1 AAAT-TTATA-TTTAAATTTA
390106 A
1 A
390107 TTTTTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 5 0.26
21 10 0.53
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AAATTTATATTTAAATTTA
Found at i:390151 original size:3 final size:3
Alignment explanation
Indices: 390145--390169 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
390135 TATCATCATC
390145 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
390170 GACTAGTACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:390527 original size:24 final size:24
Alignment explanation
Indices: 390500--390547 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
390490 TAAATTATTA
390500 TTAAA-TTAATAAAAATATTTTTAT
1 TTAAATTTAAT-AAAATATTTTTAT
*
390524 TTAAATTTAATTAAATATTTTTAT
1 TTAAATTTAATAAAATATTTTTAT
390548 ATTTTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TTAAATTTAATAAAATATTTTTAT
Found at i:391088 original size:18 final size:20
Alignment explanation
Indices: 391052--391090 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
391042 TGTAATAGTA
*
391052 TATATAAAATATTTTATATT
1 TATATAAAATATTTAATATT
391072 TATAT-AAAT-TTTAATATT
1 TATATAAAATATTTAATATT
391090 T
1 T
391091 TAATAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 4 0.22
20 5 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATATAAAATATTTAATATT
Found at i:391096 original size:18 final size:17
Alignment explanation
Indices: 391062--391140 Score: 56
Period size: 18 Copynumber: 4.4 Consensus size: 17
391052 TATATAAAAT
391062 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
391079 ATTTTAATATTT-TAATAA
1 ATTTT-ATATTTAT-ATAA
*
391097 ATATATATAATTTA-A-AA
1 AT-TTTAT-ATTTATATAA
*
391114 TATTTATGTATTTATATAA
1 -ATTT-TATATTTATATAA
391133 TATTTTAT
1 -ATTTTAT
391141 TTTTTAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 17
0.70 0.06 0.24
Matches are distributed among these distances:
17 14 0.29
18 22 0.45
19 13 0.27
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:391110 original size:26 final size:25
Alignment explanation
Indices: 391059--391152 Score: 66
Period size: 28 Copynumber: 3.6 Consensus size: 25
391049 GTATATATAA
**
391059 AATATTTTATATTTATATAAATTTT
1 AATATTTTATAAATATATAAATTTT
*
391084 AATATTTTAATAAATATATATAATTTAA
1 AATATTTT-ATAAATATATA-AATTT-T
* **
391112 AATATTTATGTATTTATATAATATTTT
1 AATATTT-TATAAATATATAA-ATTTT
*
391139 -ATTTTTTA-AAATAT
1 AATATTTTATAAATAT
391153 TATAGTAGTA
Statistics
Matches: 53, Mismatches: 11, Indels: 11
0.71 0.15 0.15
Matches are distributed among these distances:
24 4 0.08
25 9 0.17
26 14 0.26
27 6 0.11
28 19 0.36
29 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (25 bp):
AATATTTTATAAATATATAAATTTT
Found at i:391115 original size:28 final size:26
Alignment explanation
Indices: 391056--391118 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
391046 ATAGTATATA
**
391056 TAAAATATTTTATATTTATATAAATT
1 TAAAATATTTTATAAATATATAAATT
*
391082 T-TAATATTTTAATAAATATATATAATT
1 TAAAATATTTT-ATAAATATATA-AATT
391109 TAAAATATTT
1 TAAAATATTT
391119 ATGTATTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
25 8 0.27
26 10 0.33
27 5 0.17
28 7 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TAAAATATTTTATAAATATATAAATT
Found at i:391129 original size:28 final size:26
Alignment explanation
Indices: 391056--391137 Score: 85
Period size: 28 Copynumber: 3.0 Consensus size: 26
391046 ATAGTATATA
391056 TAAAATATTTTATATTTATATAAATT
1 TAAAATATTTTATATTTATATAAATT
* **
391082 T-TAATATTTTAATAAATATATATAATT
1 TAAAATATTTT-ATATTTATATA-AATT
*
391109 TAAAATATTTATGTATTTATATAATATT
1 TAAAATATTT-TATATTTATATAA-ATT
391137 T
1 T
391138 TATTTTTTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
25 8 0.18
26 10 0.23
27 6 0.14
28 19 0.43
29 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (26 bp):
TAAAATATTTTATATTTATATAAATT
Found at i:391153 original size:17 final size:19
Alignment explanation
Indices: 391107--391153 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
391097 ATATATATAA
391107 TTTAAAATA-TTTATGTAT
1 TTTAAAATATTTTATGTAT
*
391125 TTATATAATATTTTAT-T-T
1 TT-TAAAATATTTTATGTAT
391143 TTTAAAATATT
1 TTTAAAATATT
391154 ATAGTAGTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 8 0.32
18 5 0.20
19 7 0.28
20 5 0.20
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTAAAATATTTTATGTAT
Found at i:394307 original size:31 final size:31
Alignment explanation
Indices: 394248--394330 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 31
394238 CGGTTCAATC
* * *
394248 TATTTATATTATTATTTATTATTTTAAAAA-AA
1 TATTT-TAATATTATTT-TAATTATAAAAATAA
*
394280 TATTTTAATTTTAATTTTAATTATAAAAATAA
1 TATTTTAATATT-ATTTTAATTATAAAAATAA
394312 TATTTTAATATTATTTTAA
1 TATTTTAATATTATTTTAA
394331 ATAATTATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
31 22 0.50
32 22 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (31 bp):
TATTTTAATATTATTTTAATTATAAAAATAA
Found at i:394938 original size:6 final size:6
Alignment explanation
Indices: 394927--394968 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
394917 ATTTGGTCAC
394927 ATGCAG ATGCAG ATGCAG ATGCAG ATGCAG ATGCAG ATGCAG
1 ATGCAG ATGCAG ATGCAG ATGCAG ATGCAG ATGCAG ATGCAG
394969 GGCAGGCCCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.33, C:0.17, G:0.33, T:0.17
Consensus pattern (6 bp):
ATGCAG
Found at i:395150 original size:20 final size:21
Alignment explanation
Indices: 395125--395164 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
395115 TAAATATTTT
395125 ATTAATTTAA-ATTAAATTAA
1 ATTAATTTAATATTAAATTAA
*
395145 ATTAATTTAATATTTAATTA
1 ATTAATTTAATATTAAATTA
395165 TTATTATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTAATTTAATATTAAATTAA
Found at i:395760 original size:30 final size:28
Alignment explanation
Indices: 395726--395841 Score: 108
Period size: 30 Copynumber: 3.9 Consensus size: 28
395716 TAATTTTATA
* *
395726 TTTTACTTGTATTTAAATAAACTTTTTAAT
1 TTTTAATT-TATTTAAATAAA-TATTTAAT
* *
395756 TTTTAATTTAAGTTAAATAAATCTTTAAT
1 TTTTAATTT-ATTTAAATAAATATTTAAT
*
395785 TTTTAATTTATATTCAAATAAATACTTAAT
1 TTTTAATTTAT-TT-AAATAAATATTTAAT
*
395815 TTTTAATCTATGTCTAAATAAA-ATTTA
1 TTTTAATTTAT-T-TAAATAAATATTTA
395842 TAAATCTAAT
Statistics
Matches: 73, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
28 1 0.01
29 23 0.32
30 48 0.66
31 1 0.01
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.52
Consensus pattern (28 bp):
TTTTAATTTATTTAAATAAATATTTAAT
Found at i:395782 original size:29 final size:29
Alignment explanation
Indices: 395738--395836 Score: 112
Period size: 30 Copynumber: 3.3 Consensus size: 29
395728 TTACTTGTAT
*
395738 TTAAATAAACTTTTTAATTTTTAATTTAAG
1 TTAAATAAA-TCTTTAATTTTTAATTTAAG
395768 TTAAATAAATCTTTAATTTTTAATTTATA-
1 TTAAATAAATCTTTAATTTTTAATTTA-AG
* *
395797 TTCAAATAAATAC-TTAATTTTTAATCTATG
1 TT-AAATAAAT-CTTTAATTTTTAATTTAAG
395827 TCTAAATAAA
1 T-TAAATAAA
395837 ATTTATAAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
29 19 0.31
30 40 0.66
31 2 0.03
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.49
Consensus pattern (29 bp):
TTAAATAAATCTTTAATTTTTAATTTAAG
Found at i:396316 original size:21 final size:20
Alignment explanation
Indices: 396290--396331 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
396280 TAAATATTAT
396290 TTTTAAAAAATAATAAATAAA
1 TTTTAAAAAAT-ATAAATAAA
**
396311 TTTTAATTAATATAAATAAA
1 TTTTAAAAAATATAAATAAA
396331 T
1 T
396332 AACCTTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TTTTAAAAAATATAAATAAA
Found at i:397173 original size:20 final size:20
Alignment explanation
Indices: 397134--397174 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
397124 AAATAATTTT
** *
397134 TAATAATTTAATTTTTTAAA
1 TAATAATTTAAAATTATAAA
397154 TAATAATTTAAAATTATAAA
1 TAATAATTTAAAATTATAAA
397174 T
1 T
397175 TAAATTAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAATAATTTAAAATTATAAA
Found at i:397429 original size:2 final size:2
Alignment explanation
Indices: 397422--397449 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
397412 AGGAGGGAGG
397422 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
397450 TAAATGTAAT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:397936 original size:27 final size:28
Alignment explanation
Indices: 397906--397966 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
397896 TTTTAATTAC
*
397906 ATTTAAAATATATT-ATTATTTATATAA
1 ATTTAAAATATATTAATAATTTATATAA
* *
397933 ATTT-TAATATATTAATAATTTATATTA
1 ATTTAAAATATATTAATAATTTATATAA
*
397960 TTTTAAA
1 ATTTAAA
397967 TACTTATTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
26 8 0.30
27 18 0.67
28 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
ATTTAAAATATATTAATAATTTATATAA
Found at i:397959 original size:36 final size:35
Alignment explanation
Indices: 397880--397962 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 35
397870 TCTAGTGTAG
*
397880 TTATAATATTTATATATTTTAATTACATTTAAAAT
1 TTATATTATTTATATATTTTAATTACATTTAAAAT
* *
397915 ATATTATTATTTATATAAATTTTAA-TATA-TTAATAAT
1 TTA-TATTATTTATAT--ATTTTAATTACATTTAA-AAT
397952 TTATATTATTT
1 TTATATTATTT
397963 TAAATACTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
35 2 0.05
36 23 0.57
37 8 0.20
38 7 0.17
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (35 bp):
TTATATTATTTATATATTTTAATTACATTTAAAAT
Found at i:397962 original size:26 final size:26
Alignment explanation
Indices: 397912--397973 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
397902 TTACATTTAA
*
397912 AATATATTATTATTTATATAAATTTT
1 AATATATTATAATTTATATAAATTTT
*
397938 AATATATTAATAATTTATAT-TATTTT
1 AATATATT-ATAATTTATATAAATTTT
397964 AA-ATACTTAT
1 AATATA-TTAT
397974 TTATATTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 5 0.16
26 17 0.53
27 10 0.31
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (26 bp):
AATATATTATAATTTATATAAATTTT
Found at i:398405 original size:20 final size:23
Alignment explanation
Indices: 398376--398424 Score: 68
Period size: 20 Copynumber: 2.3 Consensus size: 23
398366 TTTCATCGAC
*
398376 TTTAAGAAATTTT-T-TTT-AAT
1 TTTAATAAATTTTATATTTAAAT
398396 TTTAATAAATTTTATATTTAAAT
1 TTTAATAAATTTTATATTTAAAT
398419 TTTAAT
1 TTTAAT
398425 CTTTTATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 12 0.48
21 1 0.04
22 3 0.12
23 9 0.36
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
TTTAATAAATTTTATATTTAAAT
Found at i:399399 original size:2 final size:2
Alignment explanation
Indices: 399392--399417 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
399382 CCTGGAAAAC
399392 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
399418 TGATTTTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.