Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1769
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: 283831
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
File 2 of 2
Found at i:161080 original size:11 final size:11
Alignment explanation
Indices: 161049--161080 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
161039 AATAATTTAA
161049 AATTAATTTTT
1 AATTAATTTTT
161060 AATTAATTTTT
1 AATTAATTTTT
161071 AATTAATTTT
1 AATTAATTTT
161081 AAGTAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
AATTAATTTTT
Found at i:161126 original size:21 final size:21
Alignment explanation
Indices: 161104--161144 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
161094 CTATCTATTT
*
161104 AATAAAATATTAATTTTAATTA
1 AATAAAA-ATTAAGTTTAATTA
*
161126 AATCAAAATTAAGTTTAAT
1 AATAAAAATTAAGTTTAAT
161145 CATCTTTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
AATAAAAATTAAGTTTAATTA
Found at i:161419 original size:16 final size:17
Alignment explanation
Indices: 161387--161427 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
161377 ATTTTGAAGG
*
161387 TTATAAA-TAAATTTAT
1 TTATAAATTAAATATAT
161403 TTATAAATTAAA-ATAT
1 TTATAAATTAAATATAT
*
161419 TTATCAATT
1 TTATAAATT
161428 TGTTTTGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
TTATAAATTAAATATAT
Found at i:162663 original size:2 final size:2
Alignment explanation
Indices: 162656--162686 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
162646 TGACACAATT
162656 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 T
162687 GTGCGTGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:170611 original size:22 final size:24
Alignment explanation
Indices: 170559--170611 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 24
170549 AAAAAAAAAA
*
170559 TTTAATAATATTAAAATTTTAAAT
1 TTTAATAATATTAAAATATTAAAT
* **
170583 TTAAATAA-ATT-AAATATTATTT
1 TTTAATAATATTAAAATATTAAAT
170605 TTTAATA
1 TTTAATA
170612 TTAATTATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
22 14 0.58
23 3 0.12
24 7 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTTAATAATATTAAAATATTAAAT
Found at i:172277 original size:28 final size:27
Alignment explanation
Indices: 172225--172321 Score: 72
Period size: 28 Copynumber: 3.3 Consensus size: 27
172215 ATTATAATTG
* *
172225 TATTTAATATATTTATATAAATTTTAATA
1 TATTT-ATATA-TTATATTATTTTTAATA
172254 TATTTATATATTCATATTATTTTT--TA
1 TATTTATATATT-ATATTATTTTTAATA
*
172280 TATTATATAATATTTTAATTATTTTTTATATCA
1 TATT-TAT-ATATTAT-ATTA-TTTTTA-AT-A
172313 TATTTATAT
1 TATTTATAT
172322 CGTATTTAAG
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
26 6 0.11
27 6 0.11
28 23 0.41
29 10 0.18
31 2 0.04
32 4 0.07
33 5 0.09
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (27 bp):
TATTTATATATTATATTATTTTTAATA
Found at i:172295 original size:19 final size:20
Alignment explanation
Indices: 172249--172296 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
172239 ATATAAATTT
172249 TAATATATTTATATATTCATA
1 TAATAT-TTTATATATTCATA
*
172270 T--TATTTTTTATATT-ATA
1 TAATATTTTATATATTCATA
172287 TAATATTTTA
1 TAATATTTTA
172297 ATTATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
17 4 0.17
18 9 0.39
19 9 0.39
21 1 0.04
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
TAATATTTTATATATTCATA
Found at i:172821 original size:2 final size:2
Alignment explanation
Indices: 172816--172843 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
172806 ATACTTTCTT
172816 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
172844 CAATTACTCC
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):
TA
Found at i:172946 original size:27 final size:29
Alignment explanation
Indices: 172893--172961 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
172883 AATTTTTAAA
172893 ATATAAAAATTAAAACACTAAATTTAATT
1 ATATAAAAATTAAAACACTAAATTTAATT
* * *
172922 ATAT-AAAATTAAAATATTTAA-TTAATT
1 ATATAAAAATTAAAACACTAAATTTAATT
172949 ATAGTATAAAATT
1 ATA-TA-AAAATT
172962 TACTAATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 9 0.26
28 15 0.44
29 4 0.12
30 6 0.18
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (29 bp):
ATATAAAAATTAAAACACTAAATTTAATT
Found at i:173698 original size:34 final size:33
Alignment explanation
Indices: 173655--173749 Score: 104
Period size: 33 Copynumber: 2.8 Consensus size: 33
173645 TGAGAAAGAA
173655 AAAAAATTATATATTTGTAT-TATTTTTTATATAT
1 AAAAAATTATAT-TTT-TATATATTTTTTATATAT
*
173689 AAAATATTATATTTTTATATATTTTTTATATAT
1 AAAAAATTATATTTTTATATATTTTTTATATAT
* * *
173722 TAATAATT-TATTTTATTTTATATTTTTT
1 AAAAAATTATA-TTT-TTATATATTTTTT
173750 TATGTACATG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
32 5 0.09
33 25 0.47
34 23 0.43
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (33 bp):
AAAAAATTATATTTTTATATATTTTTTATATAT
Found at i:174285 original size:17 final size:18
Alignment explanation
Indices: 174255--174288 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
174245 AAAATTCATA
174255 TTTATATCATATTCATGT
1 TTTATATCATATTCATGT
*
174273 TTTATTTCA-ATTCATG
1 TTTATATCATATTCATG
174289 AATATTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTATATCATATTCATGT
Found at i:174827 original size:21 final size:20
Alignment explanation
Indices: 174803--174889 Score: 59
Period size: 21 Copynumber: 4.2 Consensus size: 20
174793 TAATATTATC
* *
174803 TTTATATTATATCTTAATTT
1 TTTATATTATATATAAATTT
*
174823 ATTTATATTTTATATAAATTT
1 -TTTATATTATATATAAATTT
* **
174844 TTATATATTAAATATTTATTT
1 TT-TATATTATATATAAATTT
* *
174865 TTAAT-TTATTTATTAAATATT
1 TTTATATTATATA-TAAAT-TT
174886 TTTA
1 TTTA
174890 AATAAATTTT
Statistics
Matches: 50, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
19 5 0.10
20 7 0.14
21 38 0.76
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTATATTATATATAAATTT
Found at i:174835 original size:23 final size:24
Alignment explanation
Indices: 174792--174837 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
174782 AAATTATTTT
174792 TTAATATTATCTTTATATTATATC
1 TTAATATTATCTTTATATTATATC
*
174816 TTAAT-TTAT-TTATATTTTATAT
1 TTAATATTATCTT-TATATTATAT
174838 AAATTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 2 0.10
23 13 0.65
24 5 0.25
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (24 bp):
TTAATATTATCTTTATATTATATC
Found at i:174861 original size:15 final size:15
Alignment explanation
Indices: 174827--174886 Score: 51
Period size: 15 Copynumber: 4.4 Consensus size: 15
174817 TAATTTATTT
174827 ATATTT-TATA-TAA
1 ATATTTATATATTAA
*
174840 ATTTTTATATATTAA
1 ATATTTATATATTAA
*
174855 ATATTTAT-T-TT-T
1 ATATTTATATATTAA
*
174867 A-ATTTATTTATTAA
1 ATATTTATATATTAA
174881 ATATTT
1 ATATTT
174887 TTAAATAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
11 6 0.16
12 2 0.05
13 9 0.24
14 6 0.16
15 14 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATATTTATATATTAA
Found at i:174931 original size:54 final size:55
Alignment explanation
Indices: 174830--174934 Score: 126
Period size: 54 Copynumber: 1.9 Consensus size: 55
174820 TTTATTTATA
* * * *
174830 TTTTATATAAATTTTTATATATTAAATATTTATTTTTAATTTATTTATTAAATAT
1 TTTTAAATAAATTTTTATATAATAAATATTAAATTTTAATTTATTTATTAAATAT
*
174885 TTTTAAATAAA-TTTTAT-TAATAAA-ATTAAATTTTATATTATTTTTATTAA
1 TTTTAAATAAATTTTTATATAATAAATATTAAATTTTA-ATT-TATTTATTAA
174935 TAATTAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
52 9 0.21
53 9 0.21
54 15 0.35
55 10 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (55 bp):
TTTTAAATAAATTTTTATATAATAAATATTAAATTTTAATTTATTTATTAAATAT
Found at i:176931 original size:17 final size:18
Alignment explanation
Indices: 176900--176972 Score: 77
Period size: 17 Copynumber: 4.4 Consensus size: 18
176890 AGTATCAGTC
176900 ATTT-TTTAAATATTTAA
1 ATTTATTTAAATATTTAA
176917 ATTTATTTAAA-ATTTAA
1 ATTTATTTAAATATTTAA
* * *
176934 ATTTAATT--AT-TATAT
1 ATTTATTTAAATATTTAA
176949 ATTTA-TTAAATATTTAA
1 ATTTATTTAAATATTTAA
176966 ATTTATT
1 ATTTATT
176973 ATTTATTATG
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
14 2 0.04
15 9 0.20
16 2 0.04
17 25 0.56
18 7 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTATTTAAATATTTAA
Found at i:176957 original size:24 final size:23
Alignment explanation
Indices: 176930--176980 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 23
176920 TATTTAAAAT
*
176930 TTAA-ATTTAATTATTATATATTTA
1 TTAATATTTAAAT-TTAT-TATTTA
176954 TTAAATATTTAAATTTATTATTTA
1 TTAA-TATTTAAATTTATTATTTA
176978 TTA
1 TTA
176981 TGAATAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 13 0.54
25 4 0.17
26 7 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TTAATATTTAAATTTATTATTTA
Found at i:177008 original size:31 final size:31
Alignment explanation
Indices: 176925--177010 Score: 84
Period size: 32 Copynumber: 2.7 Consensus size: 31
176915 AAATTTATTT
* ** *
176925 AAAATTTAAATTTAATTATTATATATTTATTA
1 AAAATTTAAATTTAAAT-TTATATATGAATAA
* *
176957 AATATTTAAATTTATTATTTAT-TATGAATAA
1 AAAATTTAAATTTA-AATTTATATATGAATAA
176988 AAAATTTAATATTTAAATTTATA
1 AAAATTTAA-ATTTAAATTTATA
177011 AAAATTAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
31 20 0.47
32 22 0.51
33 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (31 bp):
AAAATTTAAATTTAAATTTATATATGAATAA
Found at i:177461 original size:12 final size:12
Alignment explanation
Indices: 177423--177463 Score: 50
Period size: 11 Copynumber: 3.4 Consensus size: 12
177413 ATACAGTTTT
177423 AATA-AATATAA
1 AATATAATATAA
177434 AA-ATAATATAATA
1 AATATAATAT-A-A
177447 AATATAATATAA
1 AATATAATATAA
177459 AATAT
1 AATAT
177464 TTAAAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
10 1 0.04
11 7 0.27
12 7 0.27
13 4 0.15
14 7 0.27
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AATATAATATAA
Found at i:178235 original size:28 final size:25
Alignment explanation
Indices: 178174--178235 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 25
178164 CCATTGGATT
*
178174 TCATTATCATTTATTTATAATTTTTA
1 TCATTAT-ATATATTTATAATTTTTA
*
178200 T-ATGATATATATTTATACAATATTTTA
1 TCATTATATATATTTAT--AAT-TTTTA
178227 TCATTATAT
1 TCATTATAT
178236 TTCATCTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
24 9 0.31
25 4 0.14
26 4 0.14
27 6 0.21
28 6 0.21
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.56
Consensus pattern (25 bp):
TCATTATATATATTTATAATTTTTA
Found at i:179840 original size:3 final size:3
Alignment explanation
Indices: 179832--179884 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
179822 GCCTATTTCA
179832 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
179880 AAT AA
1 AAT AA
179885 GAATGATAGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:181935 original size:25 final size:27
Alignment explanation
Indices: 181896--181947 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
181886 TACATGTGTC
*
181896 AACATTTAAACATAAATAA-AAATTTT
1 AACATTTAAAAATAAATAATAAATTTT
*
181922 AACA-TTAAAAATAATTAATAAATTTT
1 AACATTTAAAAATAAATAATAAATTTT
181948 TCTAAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.37
Consensus pattern (27 bp):
AACATTTAAAAATAAATAATAAATTTT
Found at i:189243 original size:10 final size:10
Alignment explanation
Indices: 189228--189258 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
189218 ATTTTATATA
189228 AATATTTAAT
1 AATATTTAAT
189238 AATATTTAAT
1 AATATTTAAT
189248 AATAATTTAAT
1 AAT-ATTTAAT
189259 TTTTAGTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 13 0.65
11 7 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
AATATTTAAT
Found at i:189316 original size:35 final size:35
Alignment explanation
Indices: 189275--189350 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
189265 TTCTTAATAC
* *
189275 ATATTTTATTATTTAATATAAATATAATTTTATTT
1 ATATTTTATTATCTAATATAAATATAATTTTAATT
* *
189310 ATATTTTATTATCTAATGTTAATATAATTTTAATT
1 ATATTTTATTATCTAATATAAATATAATTTTAATT
189345 AT-TTTT
1 ATATTTT
189351 CATACATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 4 0.11
35 33 0.89
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (35 bp):
ATATTTTATTATCTAATATAAATATAATTTTAATT
Found at i:190008 original size:2 final size:2
Alignment explanation
Indices: 189992--190037 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
189982 TTCTGAATCT
* *
189992 TA TA TA CA TA CA 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
190034 TA TA
1 TA TA
190038 GCTTGATAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:190765 original size:12 final size:12
Alignment explanation
Indices: 190748--190774 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
190738 ACTAAAGATT
190748 TTTATTTTTATA
1 TTTATTTTTATA
190760 TTTATTTTTATA
1 TTTATTTTTATA
190772 TTT
1 TTT
190775 TTAATATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTATTTTTATA
Found at i:193409 original size:18 final size:17
Alignment explanation
Indices: 193385--193457 Score: 66
Period size: 17 Copynumber: 4.4 Consensus size: 17
193375 GTTTTGAAGT
193385 ATTTTATAATTATATAA
1 ATTTTATAATTATATAA
*
193402 ATTTTTATATGTTA-AT-A
1 A-TTTTATA-ATTATATAA
193419 A-TTTAT-ATTATATAA
1 ATTTTATAATTATATAA
*
193434 ATTTTA-AAATATATCAA
1 ATTTTATAATTATAT-AA
193451 ATTTTAT
1 ATTTTAT
193458 TATATTTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 15
0.71 0.05 0.24
Matches are distributed among these distances:
13 3 0.07
14 2 0.04
15 7 0.16
16 10 0.22
17 11 0.24
18 9 0.20
19 3 0.07
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (17 bp):
ATTTTATAATTATATAA
Found at i:193454 original size:32 final size:32
Alignment explanation
Indices: 193387--193462 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 32
193377 TTTGAAGTAT
* * *
193387 TTTATAATTATATAAATTTTTATATGTTAATAA
1 TTTAT-ATTATATAAATTTTAAAATATTAATAA
*
193420 TTTATATTATATAAATTTTAAAATATATCA-AA
1 TTTATATTATATAAATTTTAAAATAT-TAATAA
193452 TTT-TATTATAT
1 TTTATATTATAT
193463 TTTTATAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
31 8 0.21
32 23 0.61
33 7 0.18
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (32 bp):
TTTATATTATATAAATTTTAAAATATTAATAA
Found at i:193486 original size:48 final size:50
Alignment explanation
Indices: 193384--193487 Score: 112
Period size: 48 Copynumber: 2.1 Consensus size: 50
193374 AGTTTTGAAG
*
193384 TATTTTATAATTATATAAATTTTTATATGTTAATAATTTATATTATATAA
1 TATTTTATAAATATATAAATTTTTATATGTTAATAATTTATATTATATAA
* *
193434 -ATTTTA-AAATATATCAAATTTTATTATATTTTTATAA-TTAT-TT-T-TAA
1 TATTTTATAAATATAT-AAA-TTT-TTATATGTTAATAATTTATATTATATAA
193481 TATTTTA
1 TATTTTA
193488 CCAAATTGAC
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
47 3 0.06
48 14 0.30
49 11 0.23
50 7 0.15
51 12 0.26
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (50 bp):
TATTTTATAAATATATAAATTTTTATATGTTAATAATTTATATTATATAA
Found at i:193824 original size:36 final size:40
Alignment explanation
Indices: 193740--193838 Score: 129
Period size: 43 Copynumber: 2.5 Consensus size: 40
193730 TGGCAAAAGC
193740 TTTAATTTGAAGCTTCAATATTGCTAACTACCTTGGTCAATAA
1 TTTAATTTGAAGCTTCAATATTG---ACTACCTTGGTCAATAA
193783 TTTAATTTGAAGCTTCAATATTG-CTA-CTT-GTCAAT-A
1 TTTAATTTGAAGCTTCAATATTGACTACCTTGGTCAATAA
193819 TTTAATTT-AAGCTT-AATATT
1 TTTAATTTGAAGCTTCAATATT
193839 ATATTTATAT
Statistics
Matches: 56, Mismatches: 0, Indels: 9
0.86 0.00 0.14
Matches are distributed among these distances:
34 6 0.11
35 6 0.11
36 9 0.16
37 6 0.11
38 3 0.05
39 3 0.05
43 23 0.41
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.44
Consensus pattern (40 bp):
TTTAATTTGAAGCTTCAATATTGACTACCTTGGTCAATAA
Found at i:194194 original size:25 final size:20
Alignment explanation
Indices: 194147--194201 Score: 92
Period size: 20 Copynumber: 2.7 Consensus size: 20
194137 ATAATTTTAT
194147 AATTATTTTAATTACTATCA
1 AATTATTTTAATTACTATCA
194167 AATTATTTTAATTACTATCA
1 AATTATTTTAATTACTATCA
*
194187 AATTAAATTTAATTA
1 AATT-ATTTTAATTA
194202 AATTATCATT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 24 0.73
21 9 0.27
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTATTTTAATTACTATCA
Found at i:194363 original size:21 final size:22
Alignment explanation
Indices: 194338--194388 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
194328 ATAAATAGGT
*
194338 TAAATTATATA-TTGTTAATAA
1 TAAATTATATATTTGATAATAA
194359 TAAATT-TATATTTGATAATAA
1 TAAATTATATATTTGATAATAA
194380 TAAA-TATAT
1 TAAATTATAT
194389 TAAAAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 5 0.19
21 22 0.81
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
TAAATTATATATTTGATAATAA
Found at i:195408 original size:23 final size:23
Alignment explanation
Indices: 195381--195426 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
195371 AAAATATTTT
195381 TATATAAAT-TTAATTATAAAAAA
1 TATATAAATATTAA-TATAAAAAA
195404 TATATAAATATTAATATAAAAAA
1 TATATAAATATTAATATAAAAAA
195427 ATTATTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
TATATAAATATTAATATAAAAAA
Found at i:195414 original size:29 final size:28
Alignment explanation
Indices: 195360--195414 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 28
195350 TTAAATTATT
* **
195360 ATTTAATAATAAAAATATTTTTATATAA
1 ATTTAATAATAAAAATATATAAATATAA
*
195388 ATTTAATTATAAAAAATATATAAATAT
1 ATTTAATAAT-AAAAATATATAAATAT
195415 TAATATAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 9 0.41
29 13 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
ATTTAATAATAAAAATATATAAATATAA
Found at i:195804 original size:68 final size:68
Alignment explanation
Indices: 195677--195806 Score: 165
Period size: 69 Copynumber: 1.9 Consensus size: 68
195667 TTATAAATTA
* * * *
195677 ATTAAATTTAATAAATTTAATAAATAATAATATATTAATTATTATTTTGTAATTAAAAAATATAT
1 ATTAAATTTAAAAAATTTAATAAACAATAAAATATTAATTATTATTTTGTAAATAAAAAATATAT
195742 TTT
66 TTT
* *
195745 ATTAACTTTAAAAAATTTACATTAACAATTAAAATATTAATTATT-TTTT-TAAAATAAAAAAT
1 ATTAAATTTAAAAAATTTA-ATAAACAA-TAAAATATTAATTATTATTTTGT-AAATAAAAAAT
195807 TAAAATAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
68 18 0.34
69 20 0.38
70 15 0.28
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (68 bp):
ATTAAATTTAAAAAATTTAATAAACAATAAAATATTAATTATTATTTTGTAAATAAAAAATATAT
TTT
Found at i:195859 original size:23 final size:22
Alignment explanation
Indices: 195833--195890 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 22
195823 ATTATTATTA
195833 TAAAATTTAAAATAATATTTA-AT
1 TAAAATTTAAAATAA-A-TTACAT
195856 T-AAATTTAAAA-AAATTACAT
1 TAAAATTTAAAATAAATTACAT
*
195876 TAACAAATTAAAATA
1 TAA-AATTTAAAATA
195891 TTAATTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
19 3 0.10
20 4 0.13
21 3 0.10
22 18 0.60
23 2 0.07
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (22 bp):
TAAAATTTAAAATAAATTACAT
Found at i:195914 original size:109 final size:109
Alignment explanation
Indices: 195714--196002 Score: 290
Period size: 109 Copynumber: 2.6 Consensus size: 109
195704 TAATATATTA
* * * * *
195714 ATTATTATTTTGTAAT-TA-AAAAAT-ATATTTTATTAACTTTAAAAAATTTACATTAAC-AATT
1 ATTATTATTTTATAATAAATAAAAATAATATTTAATTAAATTTAAAAAAATTACATTAACAAATT
*
195775 AAAATATTAATTATTTTTTTAAAATAAAAAATTAAAA-TA-AAAGG
66 AAAATATTAATTATTTTTTT-AAATAAAAAATAAAAAGTATAAA-G
* *
195819 AGTTATTATTATTATAA-AATTTAAAATAATATTTAATTAAATTTAAAAAAATTACATTAACAAA
1 A-TTATTATT-TTATAATAAATAAAAATAATATTTAATTAAATTTAAAAAAATTACATTAACAAA
* ** *
195883 TTAAAATATTAATTATTATGTTTT-TAT-AAAAATAAAAAGTATTTAT
64 TTAAAATATTAATTATT-T-TTTTAAATAAAAAATAAAAAGTATAAAG
* *
195929 ATTATTATTTTTTAATAAATAAAAATAATATTTAATTAATTAAATTTTTAAAAAATTACATTAAC
1 ATTATTATTTTATAATAAATAAAAATAATA--T--TTAATTAAA-TTTAAAAAAATTACATTAAC
195994 AAATTAAAA
61 AAATTAAAA
196003 ATAATATTTA
Statistics
Matches: 152, Mismatches: 16, Indels: 23
0.80 0.08 0.12
Matches are distributed among these distances:
105 1 0.01
106 8 0.05
107 5 0.03
108 10 0.07
109 60 0.39
110 24 0.16
111 3 0.02
112 4 0.03
113 9 0.06
114 28 0.18
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (109 bp):
ATTATTATTTTATAATAAATAAAAATAATATTTAATTAAATTTAAAAAAATTACATTAACAAATT
AAAATATTAATTATTTTTTTAAATAAAAAATAAAAAGTATAAAG
Found at i:195961 original size:35 final size:34
Alignment explanation
Indices: 195885--195984 Score: 100
Period size: 35 Copynumber: 2.9 Consensus size: 34
195875 TTAACAAATT
195885 AAAATA-TTAATTATTATGTTTTT-ATAAA-AATA
1 AAAATATTTAATTATTAT-TTTTTAATAAATAATA
195917 AAAAGTATTTATATTATTATTTTTTAATAAATAA-A
1 AAAA-TATTTA-ATTATTATTTTTTAATAAATAATA
* *
195952 AATAATATTTAATTAATTAAATTTTTAAAAAAT
1 AA-AATATTTAATT-ATT-ATTTTTTAATAAAT
195985 TACATTAACA
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
32 4 0.07
33 2 0.03
34 11 0.19
35 25 0.43
36 16 0.28
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (34 bp):
AAAATATTTAATTATTATTTTTTAATAAATAATA
Found at i:196000 original size:21 final size:20
Alignment explanation
Indices: 195976--196027 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
195966 AATTAAATTT
*
195976 TTAAAAAATTACATTAACAAA
1 TTAAAAAAATA-ATTAACAAA
* *
195997 TTAAAAATAATATTTAAGAAA
1 TTAAAAA-AATAATTAACAAA
196018 TTAAAAAAAT
1 TTAAAAAAAT
196028 TTATCATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.11
21 21 0.78
22 3 0.11
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (20 bp):
TTAAAAAAATAATTAACAAA
Found at i:196440 original size:121 final size:123
Alignment explanation
Indices: 196309--196663 Score: 390
Period size: 121 Copynumber: 2.9 Consensus size: 123
196299 AAAAAATATT
**
196309 ATTATAATAAAAATTTTTTTTCAATTTAAAATTTTTATTTTAAAAAACATAATAATTAATATTTT
1 ATTATAATAAAAATTTTTTTT-AATTTAATTTTTTTATTTTAAAAAACATAATAATTAATATTTT
* * *
196374 AA-TTGTTAATGAAAATTTTTT-AACTTAATTAAACATTATTTTTTATTTTATT-AAAA
65 AATTTGTTAATGATAATTTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAA
** * *
196430 ATTATAATAAAAAACATTTTTTATTTTTATTTTTTTATTTTTATAAAAACATAATAATTAATATT
1 ATTATAAT-AAAAATTTTTTTTAATTTAATTTTTTTA-TTTTA-AAAAACATAATAATTAATATT
* * *
196495 TTAATTTGTTAATG-TAGTTTTTTAAACTTAATTAAATATTAATATTAATTTTATTAAAAA
63 TTAATTTGTTAATGATAATTTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAA
* ** *
196555 ATAATAATAAACTCTTTTTTATTTTTTATTTAATTTTTTTATTTT----AA-A-AATAATTAATA
1 ATTATAATAAA----AATTT-TTTTTAATTTAATTTTTTTATTTTAAAAAACATAATAATTAATA
*
196614 TTTTAATTTGTTAAT-ATAATTTTTGTAAAGTTAATTAAATATTATTTTTA
61 TTTTAATTTGTTAATGATAATTTTT-TAAACTTAATTAAATATTATTTTTA
196664 TTAAAAATAA
Statistics
Matches: 197, Mismatches: 24, Indels: 25
0.80 0.10 0.10
Matches are distributed among these distances:
121 52 0.26
122 39 0.20
123 34 0.17
124 39 0.20
125 11 0.06
128 5 0.03
129 17 0.09
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (123 bp):
ATTATAATAAAAATTTTTTTTAATTTAATTTTTTTATTTTAAAAAACATAATAATTAATATTTTA
ATTTGTTAATGATAATTTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAA
Found at i:196449 original size:124 final size:125
Alignment explanation
Indices: 196301--196663 Score: 398
Period size: 124 Copynumber: 2.9 Consensus size: 125
196291 AAAAATTAAA
* **
196301 AAAATATTATTATAATAAAA-ATTTTTTTTCAATTTAAAATTTTTATTTTAAAAAACATAATAAT
1 AAAA-ATTATAATAATAAAACATTTTTTTT--ATTTAATTTTTTTATTTTAAAAAACATAATAAT
* * *
196365 TAATATTTTAA-TTGTTAATGAAAATTTTTT-AACTTAATTAAACATTATTTTTTATTTTATT
63 TAATATTTTAATTTGTTAATGATAATTTTTTAAACTTAATTAAATATTATTTTTAATTTTATT
196426 AAAAATTATAATAA-AAAACATTTTTTATT-TTT-ATTTTTTTATTTTTATAAAAACATAATAAT
1 AAAAATTATAATAATAAAACATTTTTT-TTATTTAATTTTTTTA-TTTTA-AAAAACATAATAAT
* * *
196488 TAATATTTTAATTTGTTAATG-TAGTTTTTTAAACTTAATTAAATATTAATATTAATTTTATT
63 TAATATTTTAATTTGTTAATGATAATTTTTTAAACTTAATTAAATATTATTTTTAATTTTATT
* *
196550 AAAAA--ATAATAATAAACTCTTTTTTATTTTTTATTTAATTTTTTTATTTT----AA-A-AATA
1 AAAAATTATAATAATAAA-AC---ATT-TTTTTTATTTAATTTTTTTATTTTAAAAAACATAATA
*
196607 ATTAATATTTTAATTTGTTAAT-ATAATTTTTGTAAAGTTAATTAAATATTATTTTTA
61 ATTAATATTTTAATTTGTTAATGATAATTTTT-TAAACTTAATTAAATATTATTTTTA
196664 TTAAAAATAA
Statistics
Matches: 207, Mismatches: 15, Indels: 35
0.81 0.06 0.14
Matches are distributed among these distances:
121 40 0.19
122 38 0.18
123 41 0.20
124 58 0.28
125 6 0.03
127 4 0.02
128 11 0.05
129 9 0.04
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (125 bp):
AAAAATTATAATAATAAAACATTTTTTTTATTTAATTTTTTTATTTTAAAAAACATAATAATTAA
TATTTTAATTTGTTAATGATAATTTTTTAAACTTAATTAAATATTATTTTTAATTTTATT
Found at i:196465 original size:14 final size:14
Alignment explanation
Indices: 196446--196473 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
196436 ATAAAAAACA
196446 TTTTTTATTTTTAT
1 TTTTTTATTTTTAT
196460 TTTTTTATTTTTAT
1 TTTTTTATTTTTAT
196474 AAAAACATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTTATTTTTAT
Found at i:196490 original size:123 final size:125
Alignment explanation
Indices: 196340--196663 Score: 418
Period size: 124 Copynumber: 2.7 Consensus size: 125
196330 CAATTTAAAA
*
196340 TTTTTA-TTTTA-AAAAACATAATAATTAATATTTTAA-TTGTTAATGAAAATTTTTT-AACTTA
1 TTTTTATTTTTATAAAAACATAATAATTAATATTTTAATTTGTTAATGATAATTTTTTAAACTTA
* *
196401 ATTAAACATTATTTTTTATTTTATTAAAAATTATAATAAAAAAC-ATTTTTTA-TTTTTATT
66 ATTAAATATTATTTTTAATTTTATTAAAAA--ATAATAAAAAACTATTTTTTATTTTTTATT
*
196461 TTTTTATTTTTATAAAAACATAATAATTAATATTTTAATTTGTTAATG-TAGTTTTTTAAACTTA
1 TTTTTATTTTTATAAAAACATAATAATTAATATTTTAATTTGTTAATGATAATTTTTTAAACTTA
* * * *
196525 ATTAAATATTAATATTAATTTTATTAAAAAATAATAATAAACTCTTTTTTATTTTTTATT
66 ATTAAATATTATTTTTAATTTTATTAAAAAATAATAAAAAACTATTTTTTATTTTTTATT
** *** *
196585 TAATT-TTTTTATTTTAA-A-AATAATTAATATTTTAATTTGTTAAT-ATAATTTTTGTAAAGTT
1 TTTTTATTTTTATAAAAACATAATAATTAATATTTTAATTTGTTAATGATAATTTTT-TAAACTT
196646 AATTAAATATTATTTTTA
65 AATTAAATATTATTTTTA
196664 TTAAAAATAA
Statistics
Matches: 178, Mismatches: 17, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
121 39 0.22
122 39 0.22
123 48 0.27
124 52 0.29
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (125 bp):
TTTTTATTTTTATAAAAACATAATAATTAATATTTTAATTTGTTAATGATAATTTTTTAAACTTA
ATTAAATATTATTTTTAATTTTATTAAAAAATAATAAAAAACTATTTTTTATTTTTTATT
Found at i:196711 original size:121 final size:121
Alignment explanation
Indices: 196359--196733 Score: 300
Period size: 123 Copynumber: 3.1 Consensus size: 121
196349 TAAAAAACAT
* * *
196359 AATAATTAATATTTTAA-TTGTTAATGAAAATTTTTT-AACTTAATTAAACATTATTTTTTATTT
1 AATAATTAATATTTTAATTTGTTAAT-ATAATTTTTTAAACTTAATTAAATATTA--TATTATTT
* * * * *
196422 TATTAAAAATTATAATAAAAAAC-ATTTTTTATT-TTTATT--TTTTTATT--TTTATAAAAACA
63 TATTAAAAA--ATAATAATAAACTCTTTTTTATTATTTATTAAATTTAATTAATTTGT---AA-A
* *
196481 TAATAATTAATATTTTAATTTGTTAATGTAGTTTTTTAAACTTAATTAAATATTAATATTAATTT
1 -AATAATTAATATTTTAATTTGTTAATATAATTTTTTAAACTTAATTAAATATT-ATATT-ATTT
* * * *
196546 TATTAAAAAATAATAATAAACTCTTTTTTATTTTTTATTTAATTT-TTTTATTT-TAAA
63 TATTAAAAAATAATAATAAACTCTTTTTTATTATTTATTAAATTTAATTAATTTGTAAA
*
196603 AATAATTAATATTTTAATTTGTTAATATAATTTTTGTAAAGTTAATTAAATA-T-TA-T-TTTTA
1 AATAATTAATATTTTAATTTGTTAATATAATTTTT-TAAACTTAATTAAATATTATATTATTTTA
196664 TT-AAAAATAATAAATAATACAT-TATTATTTATTAAAATTT-TTAAATTTAATTAATTTGTAAA
65 TTAAAAAATAAT-AATAA-AC-TCT-TT-TTTATT---ATTTATTAAATTTAATTAATTTGTAAA
196726 AA-AATTAA
1 AATAATTAA
196734 ACAATTGAAA
Statistics
Matches: 215, Mismatches: 16, Indels: 43
0.78 0.06 0.16
Matches are distributed among these distances:
115 9 0.04
116 12 0.06
117 3 0.01
118 4 0.02
119 8 0.04
121 41 0.19
122 42 0.20
123 44 0.20
124 42 0.20
125 3 0.01
126 4 0.02
127 3 0.01
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (121 bp):
AATAATTAATATTTTAATTTGTTAATATAATTTTTTAAACTTAATTAAATATTATATTATTTTAT
TAAAAAATAATAATAAACTCTTTTTTATTATTTATTAAATTTAATTAATTTGTAAA
Found at i:197146 original size:18 final size:18
Alignment explanation
Indices: 197123--197166 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
197113 ATAAATGCAT
197123 AGATTCTTAATGGGAATC
1 AGATTCTTAATGGGAATC
*
197141 AGATTCTTAATGGGAATT
1 AGATTCTTAATGGGAATC
197159 AGATTCTT
1 AGATTCTT
197167 TTTGATAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (18 bp):
AGATTCTTAATGGGAATC
Found at i:197742 original size:93 final size:92
Alignment explanation
Indices: 197295--198155 Score: 924
Period size: 93 Copynumber: 9.5 Consensus size: 92
197285 AATAAATGTG
* * *
197295 ATTATATCTGAAAAT-AGA--CTTTTTTATAGAAAAAGA-AAAG-TTGATTGATTGTAAATGTCA
1 ATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAAAAGAAAGACTGATTGATTGTAAATGTCA
* *
197355 GACTGCAAGAATTAGACTAATGTATGA
66 GACTGCAAGGATTAGACTAATGCATGA
* * * *
197382 ATTATATCTGAGAATCGGATT-TTTTGTTAT-G-AAAAAA-AAAG-TTGATTGATTATAAATGTT
1 ATTATATCTGAGAATCAGATTCTTTT-TTATAGAAAAAAAGAAAGACTGATTGATTGTAAATGTC
**
197442 AGACTGCAAGGATTAGACTAATATATGA
65 AGACTGCAAGGATTAGACTAATGCATGA
** * * *
197470 ATTATATCTGAGAATTGGATTATTTGTTATAG-AAAAAAGAAA-AGTTGATTGATTGTAAATG-C
1 ATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAAAAGAAAGA-CTGATTGATTGTAAATGTC
* * *
197532 TAGACTGCAAGAATTAGACTAGTGCATAA
65 -AGACTGCAAGGATTAGACTAATGCATGA
* * * * *
197561 ATTATATCTAAGAATC-GA------ATTATAGAAAAAAAGAAA-AGTTGATTGATTGTGAATATC
1 ATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAAAAGAAAGA-CTGATTGATTGTAAATGTC
*
197618 AGACTGCAAGGATTAAACTAATGCATGA
65 AGACTGCAAGGATTAGACTAATGCATGA
* *
197646 ATTATATCTGAGAATCAGATTCTTTTTTATATAAAAAAATGAAAGACTAATTGATTGTAAATGTC
1 ATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAAAA-GAAAGACTGATTGATTGTAAATGTC
* * **
197711 AAACTGAAAGGATTAGACTAATGCACAA
65 AGACTGCAAGGATTAGACTAATGCATGA
* * * * * * *
197739 ATTATATCTAAGAATTATATTCTTTTTTATAGATAAAAAGAAA-AGTTAACTGATTGTAAATGTC
1 ATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAAAAGAAAGA-CTGATTGATTGTAAATGTC
** *
197803 AGACTATAAGGATTAGACTAATGCATAA
65 AGACTGCAAGGATTAGACTAATGCATGA
* * * * *
197831 ATTATATATGAGAATTAGA-TCATTTTTTATAGAAAAAAAAGAAAAACTGATTGATTATAATTGT
1 ATTATATCTGAGAATCAGATTC-TTTTTTATAG-AAAAAAAGAAAGACTGATTGATTGTAAATGT
*
197895 CAGACTGCAAGGATTAGACTAATGCATAA
64 CAGACTGCAAGGATTAGACTAATGCATGA
* * * * * *
197924 ATTATATCTAAGAATCAGATTCTTTTTTATTGGAAAAAAAGAAAAACTAATTGATTATAATTGTC
1 ATTATATCTGAGAATCAGATTCTTTTTTA-TAGAAAAAAAGAAAGACTGATTGATTGTAAATGTC
* ** *
197989 AGATTATAAAGATTAGACTAATGCATGA
65 AGACTGCAAGGATTAGACTAATGCATGA
* * *
198017 ATCATATTTGAGAATCATATTCTTTTTTATAGAAAAAAAGAAAGACTGATTGATTGTAAATGTCA
1 ATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAAAAGAAAGACTGATTGATTGTAAATGTCA
198082 GACTGCAAGGATTAGACTAATGCATGA
66 GACTGCAAGGATTAGACTAATGCATGA
*
198109 ATTATATTTGAGAATCAGATTCTTTTTTATA-AAAAAAAGAAAGACTG
1 ATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAAAAGAAAGACTG
198156 CAAGGATTAG
Statistics
Matches: 663, Mismatches: 84, Indels: 50
0.83 0.11 0.06
Matches are distributed among these distances:
84 6 0.01
85 66 0.10
86 3 0.00
87 14 0.02
88 78 0.12
89 15 0.02
90 9 0.01
91 72 0.11
92 166 0.25
93 228 0.34
94 6 0.01
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.33
Consensus pattern (92 bp):
ATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAAAAGAAAGACTGATTGATTGTAAATGTCA
GACTGCAAGGATTAGACTAATGCATGA
Found at i:197816 original size:185 final size:184
Alignment explanation
Indices: 197295--198150 Score: 982
Period size: 185 Copynumber: 4.7 Consensus size: 184
197285 AATAAATGTG
* * *
197295 ATTATATCTGAAAAT-AGA--CTTTTTTATAGAAAAAGA-AAAG-TTGATTGATTGTAAATGTCA
1 ATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAAAAGAAAGACTGATTGATTGTAAATGTCA
* * * * *
197355 GACTGCAAGAATTAGACTAATGTATGAATTATATCTGAGAATCGGATT-TTTTGTTAT-G--AAA
66 GACTGCAAGGATTAGACTAATGCATAAATTATATCTAAGAATCAGATTCTTTT-TTATAGAAAAA
* * * **
197416 AA-AAAAGTTGATTGATTATAAATGTTAGACTGCAAGGATTAGACTAATATATGA
130 AAGAAAAGTTAATTGATTATAAATGTCAGACTACAAGGATTAGACTAATGCATGA
** * * *
197470 ATTATATCTGAGAATTGGATTATTTGTTATAG-AAAAAAGAAA-AGTTGATTGATTGTAAATG-C
1 ATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAAAAGAAAGA-CTGATTGATTGTAAATGTC
* * *
197532 TAGACTGCAAGAATTAGACTAGTGCATAAATTATATCTAAGAATC-GA------ATTATAGAAAA
65 -AGACTGCAAGGATTAGACTAATGCATAAATTATATCTAAGAATCAGATTCTTTTTTATAGAAAA
* * * * * *
197590 AAAGAAAAGTTGATTGATTGTGAATATCAGACTGCAAGGATTAAACTAATGCATGA
129 AAAGAAAAGTTAATTGATTATAAATGTCAGACTACAAGGATTAGACTAATGCATGA
* *
197646 ATTATATCTGAGAATCAGATTCTTTTTTATATAAAAAAATGAAAGACTAATTGATTGTAAATGTC
1 ATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAAAA-GAAAGACTGATTGATTGTAAATGTC
* * * * * *
197711 AAACTGAAAGGATTAGACTAATGCACAAATTATATCTAAGAATTATATTCTTTTTTATAGATAAA
65 AGACTGCAAGGATTAGACTAATGCATAAATTATATCTAAGAATCAGATTCTTTTTTATAGAAAAA
* * * *
197776 AAGAAAAGTTAACTGATTGTAAATGTCAGACTATAAGGATTAGACTAATGCATAA
130 AAGAAAAGTTAATTGATTATAAATGTCAGACTACAAGGATTAGACTAATGCATGA
* * * * *
197831 ATTATATATGAGAATTAGA-TCATTTTTTATAGAAAAAAAAGAAAAACTGATTGATTATAATTGT
1 ATTATATCTGAGAATCAGATTC-TTTTTTATAG-AAAAAAAGAAAGACTGATTGATTGTAAATGT
*
197895 CAGACTGCAAGGATTAGACTAATGCATAAATTATATCTAAGAATCAGATTCTTTTTTATTGGAAA
64 CAGACTGCAAGGATTAGACTAATGCATAAATTATATCTAAGAATCAGATTCTTTTTTA-TAGAAA
** * * * *
197960 AAAAGAAAAACTAATTGATTATAATTGTCAGATTATAAAGATTAGACTAATGCATGA
128 AAAAGAAAAGTTAATTGATTATAAATGTCAGACTACAAGGATTAGACTAATGCATGA
* * *
198017 ATCATATTTGAGAATCATATTCTTTTTTATAGAAAAAAAGAAAGACTGATTGATTGTAAATGTCA
1 ATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAAAAGAAAGACTGATTGATTGTAAATGTCA
* * *
198082 GACTGCAAGGATTAGACTAATGCATGAATTATATTTGAGAATCAGATTCTTTTTTATA-AAAAAA
66 GACTGCAAGGATTAGACTAATGCATAAATTATATCTAAGAATCAGATTCTTTTTTATAGAAAAAA
198146 AGAAA
131 AGAAA
198151 GACTGCAAGG
Statistics
Matches: 581, Mismatches: 74, Indels: 44
0.83 0.11 0.06
Matches are distributed among these distances:
172 4 0.01
173 1 0.00
175 19 0.03
176 74 0.13
177 11 0.02
178 72 0.12
179 60 0.10
183 11 0.02
184 3 0.01
185 239 0.41
186 85 0.15
187 2 0.00
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.34
Consensus pattern (184 bp):
ATTATATCTGAGAATCAGATTCTTTTTTATAGAAAAAAAGAAAGACTGATTGATTGTAAATGTCA
GACTGCAAGGATTAGACTAATGCATAAATTATATCTAAGAATCAGATTCTTTTTTATAGAAAAAA
AGAAAAGTTAATTGATTATAAATGTCAGACTACAAGGATTAGACTAATGCATGA
Found at i:197921 original size:278 final size:275
Alignment explanation
Indices: 197324--198155 Score: 973
Period size: 278 Copynumber: 3.1 Consensus size: 275
197314 TTTTTTATAG
** * *
197324 AAAAAGAAAAGTTGATTGATTGTAAATGTCAGACTGCAAGAATTAGACTAATGTATGAATTATAT
1 AAAAAGAAAAACTGATTGATTGT-AATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATAT
* * * * * * *
197389 CTGAGAATCGGATT-TTTTGT-TATGAAAAAA-AAAG-TTGATTGATTATAAATGTTAGACTGCA
65 CTGAGAATCAGATTCTTTTTTATATAAAAAAAGAAAGACTAATTGATTATAAATGTCAGACTGAA
** ** * *
197450 AGGATTAGACTAATATATGAATTATATCTGAGAATTGGATTATTTGTTATAGAAAAAAGAAAAGT
130 AGGATTAGACTAATGCATGAATTATATCTGAGAATTATATTCTTTTTTATAGAAAAAAGAAAAGT
* * * * *
197515 TGATTGATTGTAAATG-CTAGACTGCAAGAATTAGACTAGTGCATAAATTATATCTAAGAA-TCG
195 TGATTGATTGTAAATGTC-AGACTGCAAGGATTAGACTAATGCATAAATTATATATGAGAATTAG
197578 A--A----TTATAG-AA
259 ATCATTTTTTATAGAAA
** * *
197588 AAAAAGAAAAGTTGATTGATTGTGAATATCAGACTGCAAGGATTAAACTAATGCATGAATTATAT
1 AAAAAGAAAAACTGATTGATTGT-AATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATAT
* *
197653 CTGAGAATCAGATTCTTTTTTATATAAAAAAATGAAAGACTAATTGATTGTAAATGTCAAACTGA
65 CTGAGAATCAGATTCTTTTTTATATAAAAAAA-GAAAGACTAATTGATTATAAATGTCAGACTGA
** *
197718 AAGGATTAGACTAATGCACAAATTATATCTAAGAATTATATTCTTTTTTATAGATAAAAAGAAAA
129 AAGGATTAGACTAATGCATGAATTATATCTGAGAATTATATTCTTTTTTATAGA-AAAAAGAAAA
* * **
197783 GTTAACTGATTGTAAATGTCAGACTATAAGGATTAGACTAATGCATAAATTATATATGAGAATTA
193 GTTGATTGATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATAAATTATATATGAGAATTA
197848 GATCATTTTTTATAGAAA
258 GATCATTTTTTATAGAAA
* *
197866 AAAAAGAAAAACTGATTGATTATAATTGTCAGACTGCAAGGATTAGACTAATGCATAAATTATAT
1 AAAAAGAAAAACTGATTGATTGTAA-TGTCAGACTGCAAGGATTAGACTAATGCATGAATTATAT
* * * *
197931 CTAAGAATCAGATTCTTTTTTAT-TGGAAAAAAAGAAAAACTAATTGATTATAATTGTCAGA-TT
65 CTGAGAATCAGATTCTTTTTTATAT--AAAAAAAGAAAGACTAATTGATTATAAATGTCAGACTG
* * * *
197994 ATAAAGATTAGACTAATGCATGAATCATATTTGAGAATCATATTCTTTTTTATAGAAAAAA-AGA
128 A-AAGGATTAGACTAATGCATGAATTATATCTGAGAATTATATTCTTTTTTATAGAAAAAAGA-A
* * *
198058 AAGACTGATTGATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATTTGAGAA
191 AAG-TTGATTGATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATAAATTATATATGAGAA
*
198123 TCAGATTC-TTTTTTAT--AAA
255 TTAGA-TCATTTTTTATAGAAA
*
198142 AAAAAGAAAGACTG
1 AAAAAGAAAAACTG
198156 CAAGGATTAG
Statistics
Matches: 486, Mismatches: 60, Indels: 32
0.84 0.10 0.06
Matches are distributed among these distances:
264 73 0.15
265 5 0.01
266 9 0.02
268 4 0.01
269 65 0.13
270 62 0.13
271 4 0.01
273 1 0.00
276 17 0.03
277 20 0.04
278 217 0.45
279 9 0.02
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.33
Consensus pattern (275 bp):
AAAAAGAAAAACTGATTGATTGTAATGTCAGACTGCAAGGATTAGACTAATGCATGAATTATATC
TGAGAATCAGATTCTTTTTTATATAAAAAAAGAAAGACTAATTGATTATAAATGTCAGACTGAAA
GGATTAGACTAATGCATGAATTATATCTGAGAATTATATTCTTTTTTATAGAAAAAAGAAAAGTT
GATTGATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATAAATTATATATGAGAATTAGAT
CATTTTTTATAGAAA
Found at i:198211 original size:69 final size:71
Alignment explanation
Indices: 198081--198221 Score: 182
Period size: 69 Copynumber: 2.0 Consensus size: 71
198071 TGTAAATGTC
** *
198081 AGACTGCAAGGATTAGACTAATGCATGAATTATATTTGAGAATCAGATTCTTTTTTAT-AAAA-A
1 AGACTGCAAGGATTAGACTAATGCATGAATTATACATGAGAATCAGATTCTTTTTGATAAAAATA
198144 AAAGAA
66 AAAGAA
* * *
198150 AGACTGCAAGGATTAGACTAATGCATGAATTGTACATGAGAAT-TGAATT-TCTTTTGGTAAAAA
1 AGACTGCAAGGATTAGACTAATGCATGAATTATACATGAGAATCAG-ATTCT-TTTTGATAAAAA
198213 TAAAAGAA
64 TAAAAGAA
198221 A
1 A
198222 AGTTGGTTGA
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
68 2 0.03
69 48 0.77
70 4 0.06
71 8 0.13
ACGTcount: A:0.43, C:0.09, G:0.18, T:0.30
Consensus pattern (71 bp):
AGACTGCAAGGATTAGACTAATGCATGAATTATACATGAGAATCAGATTCTTTTTGATAAAAATA
AAAGAA
Found at i:202407 original size:11 final size:11
Alignment explanation
Indices: 202372--202421 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
202362 ATTTTAATAA
202372 AAATAAATT-T
1 AAATAAATTAT
* *
202382 ATATAATTTAT
1 AAATAAATTAT
*
202393 AAATAAATTAA
1 AAATAAATTAT
*
202404 AAATAATTTAT
1 AAATAAATTAT
202415 AAATAAA
1 AAATAAA
202422 AAGTAATAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
10 7 0.23
11 24 0.77
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAATAAATTAT
Found at i:202456 original size:298 final size:298
Alignment explanation
Indices: 201888--203737 Score: 3010
Period size: 298 Copynumber: 6.2 Consensus size: 298
201878 TTGAGAAAAT
* *
201888 TTTTTTCTTAGTCATTTTACAGATAAA-AAAA-CTCGTATTTAAGTCGTTACCGAAAAATAAAAT
1 TTTTTTCTTGGTCATTTTACAGATAAAGAAAAGCTCGTATTTAAGTCATTACCGAAAAATAAAAT
* * *
201951 GTGTGCGTCTATAAATCCAAAATGAGTCGTTATCGAAAAAAGTAATTTATTGTTGGCTAACATAA
66 GTGTGCGTCTATAAATCTAAAATAAGTCGTTATCAAAAAAAGTAATTTATTGTTGGCTAACATAA
*
202016 ATTTAAGTTCTATCAATTATAAAAATAATACATGTAGAATATTAATTAATTTTAATAAAAATAAA
131 ATTTAAGTTCTATCAATTATAAAAATAATACATGTACAATATTAATTAATTTTAATAAAAATAAA
*
202081 TTTGTATAATTTATAAATAAATTAAAAATAATTTATAAATAAAAAGTAATAATGCATGTACAATA
196 TTTGTATAATTTATAAATAAATTAAAAATAATTTATAAATAAAAAGTAATAATACATGTACAATA
202146 TTAATTAATTTTAATAAAAATAATATATGTACAATAAA
261 TTAATTAATTTTAATAAAAATAATATATGTACAATAAA
* * * * * *
202184 CTTTTTCTTGATCATTTTACAAATAAAGGAAAGTTCGTATTTAAGTCATTACCGAAAAATGAAAT
1 TTTTTTCTTGGTCATTTTACAGATAAAGAAAAGCTCGTATTTAAGTCATTACCGAAAAATAAAAT
* *
202249 GTGTGCTTCTGTAAATCTAAAATAAGTCGTTATCAAAAAAAGTAATTTATTGTTGGCTAACATAA
66 GTGTGCGTCTATAAATCTAAAATAAGTCGTTATCAAAAAAAGTAATTTATTGTTGGCTAACATAA
202314 ATTTAAGTTCTATCAATTATAAAAATAATACATGTACAATATTAATTAATTTTAATAAAAATAAA
131 ATTTAAGTTCTATCAATTATAAAAATAATACATGTACAATATTAATTAATTTTAATAAAAATAAA
* *
202379 TTTATATAATTTATAAATAAATTAAAAATAATTTATAAATAAAAAGTAATAATGCATGTACAATA
196 TTTGTATAATTTATAAATAAATTAAAAATAATTTATAAATAAAAAGTAATAATACATGTACAATA
*
202444 TTAATTAATTTTAATAAAAATAATATATGTACAACAAA
261 TTAATTAATTTTAATAAAAATAATATATGTACAATAAA
* *
202482 TTTTTTCTTGGTCATTTTACAGATAAAGGAAAGCTCGTATTTAAGTCATTACCGAAAAATGAAAT
1 TTTTTTCTTGGTCATTTTACAGATAAAGAAAAGCTCGTATTTAAGTCATTACCGAAAAATAAAAT
* * * *
202547 GTGTGCGTCTATAAATTTGAAATAAGTCGTTATCGAAAAAAGTAATTTATTGTTAGCTAACATAA
66 GTGTGCGTCTATAAATCTAAAATAAGTCGTTATCAAAAAAAGTAATTTATTGTTGGCTAACATAA
* *
202612 ATTTAAGTTCTATTAATTATAAAAATAATACATGTACAATATTAGTTAATTTTAATAAAAATAAA
131 ATTTAAGTTCTATCAATTATAAAAATAATACATGTACAATATTAATTAATTTTAATAAAAATAAA
* *
202677 TTTGTATAATTTATAAATAAATTAAAAATAATTTATAAATAAAAAGTAATAATGCATGCACAATA
196 TTTGTATAATTTATAAATAAATTAAAAATAATTTATAAATAAAAAGTAATAATACATGTACAATA
*
202742 TTAATTAATTTTAATAAAAATAATATATATACAATAAA
261 TTAATTAATTTTAATAAAAATAATATATGTACAATAAA
* * *
202780 TTTTTTCTTGATCATTTTACAAATAAAGAAAAGCTCGTATTTAAGTCATTACCGAAAAATGAAAT
1 TTTTTTCTTGGTCATTTTACAGATAAAGAAAAGCTCGTATTTAAGTCATTACCGAAAAATAAAAT
* * * * * *
202845 GTGTGCTTATGTAAATATAAAATAAGTCATTATCAAAAAAAGTAATTTATTGTTGGCTAAAATAA
66 GTGTGCGTCTATAAATCTAAAATAAGTCGTTATCAAAAAAAGTAATTTATTGTTGGCTAACATAA
*
202910 ATTTAAGTTCTATCAATTATAAAAATAATATATGTACAATATTAATTAATTTTAATAAAAATAAA
131 ATTTAAGTTCTATCAATTATAAAAATAATACATGTACAATATTAATTAATTTTAATAAAAATAAA
* *
202975 TTTGTATAGTTTATAAATAAATTAAAAATAATTTATAAATAAAAAGTAATAATACATGTATAATA
196 TTTGTATAATTTATAAATAAATTAAAAATAATTTATAAATAAAAAGTAATAATACATGTACAATA
*
203040 TTAATTAATTTTAATAAAAATAATATATGTATAATAAA
261 TTAATTAATTTTAATAAAAATAATATATGTACAATAAA
* *
203078 TTTTTTCTTGGTCATTTTACAGATAAAAGAAAA-ATCGTATTTAAATCATTACCGAAAAATAAAA
1 TTTTTTCTTGGTCATTTTACAGAT-AAAGAAAAGCTCGTATTTAAGTCATTACCGAAAAATAAAA
* * * * *
203142 TGTGTGCGTCTATAAATTTGAAATAAATTGTTATCGAAAAAAGTAATTTATTGTTGGCTAACATA
65 TGTGTGCGTCTATAAATCTAAAATAAGTCGTTATCAAAAAAAGTAATTTATTGTTGGCTAACATA
*
203207 AATTTAAGTTCTATCAATTATAAAAATAATACATTTACAATATTAATTAATTTTAATAAAAATAA
130 AATTTAAGTTCTATCAATTATAAAAATAATACATGTACAATATTAATTAATTTTAATAAAAATAA
* *
203272 ATTTGTATAATTTATAAATAAGTTAAAAATAATTTATAAATAAAAAGTAATAATACATGCACAAT
195 ATTTGTATAATTTATAAATAAATTAAAAATAATTTATAAATAAAAAGTAATAATACATGTACAAT
* *
203337 ATTAATTAATTTTAATAAAAATAAGACATGTACAATAAA
260 ATTAATTAATTTTAATAAAAATAATATATGTACAATAAA
* * *
203376 TTTTTTCTTGGTCATTTTATAGATAAA-AAAAGCTCATATTTAAGTCATTACAGAAAAATAAAAT
1 TTTTTTCTTGGTCATTTTACAGATAAAGAAAAGCTCGTATTTAAGTCATTACCGAAAAATAAAAT
* *
203440 GTGTGCTTCTATAAAT-TCGAAATAAGTCGTTATCAAAAAAAGTAATTTATTGTTGGCTAACATA
66 GTGTGCGTCTATAAATCT-AAAATAAGTCGTTATCAAAAAAAGTAATTTATTGTTGGCTAACATA
* *
203504 AATTTAAGTTCTATCAATTATAAAAATAATATATGTATAATATTAATTAATTTTAATAAAAATAA
130 AATTTAAGTTCTATCAATTATAAAAATAATACATGTACAATATTAATTAATTTTAATAAAAATAA
*
203569 ATTTGTATAATTTATAAATAAATTAAAAATAATTTATAAATAAAATA-TAATAATACATGTATAA
195 ATTTGTATAATTTATAAATAAATTAAAAATAATTTATAAATAAAA-AGTAATAATACATGTACAA
* *
203633 TATTAATTAATTTTAATAAAAATAATACATATACAATAAA
259 TATTAATTAATTTTAATAAAAATAATATATGTACAATAAA
* * * * *
203673 ATTTTTCTTGGTTATTTTACAGATAAAGAAAAGCTCGTATTTAAGTCGTTATCAAAAAATAAAAT
1 TTTTTTCTTGGTCATTTTACAGATAAAGAAAAGCTCGTATTTAAGTCATTACCGAAAAATAAAAT
203738 ATGTAAAAAT
Statistics
Matches: 1445, Mismatches: 102, Indels: 12
0.93 0.07 0.01
Matches are distributed among these distances:
296 28 0.02
297 275 0.19
298 1134 0.78
299 8 0.01
ACGTcount: A:0.47, C:0.07, G:0.08, T:0.38
Consensus pattern (298 bp):
TTTTTTCTTGGTCATTTTACAGATAAAGAAAAGCTCGTATTTAAGTCATTACCGAAAAATAAAAT
GTGTGCGTCTATAAATCTAAAATAAGTCGTTATCAAAAAAAGTAATTTATTGTTGGCTAACATAA
ATTTAAGTTCTATCAATTATAAAAATAATACATGTACAATATTAATTAATTTTAATAAAAATAAA
TTTGTATAATTTATAAATAAATTAAAAATAATTTATAAATAAAAAGTAATAATACATGTACAATA
TTAATTAATTTTAATAAAAATAATATATGTACAATAAA
Found at i:203617 original size:11 final size:11
Alignment explanation
Indices: 203575--203618 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
203565 ATAAATTTGT
*
203575 ATAATTTATAA
1 ATAAATTATAA
*
203586 ATAAATTAAAA
1 ATAAATTATAA
*
203597 ATAATTTATAA
1 ATAAATTATAA
*
203608 ATAAAATATAA
1 ATAAATTATAA
203619 TAATACATGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAAATTATAA
Found at i:203769 original size:14 final size:14
Alignment explanation
Indices: 203727--203769 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
203717 GTCGTTATCA
* *
203727 AAAAATAAAATATGT
1 AAAAATAAATTA-AT
203742 AAAAATAAATTTAAT
1 AAAAATAAA-TTAAT
203757 AAAAATAAATTAA
1 AAAAATAAATTAA
203770 ATTAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 4 0.16
15 19 0.76
16 2 0.08
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (14 bp):
AAAAATAAATTAAT
Found at i:204373 original size:2 final size:2
Alignment explanation
Indices: 204366--204394 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
204356 AATGCTCAAC
204366 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
204395 AACAAATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:206201 original size:15 final size:15
Alignment explanation
Indices: 206181--206215 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
206171 TTAGTTTCAT
*
206181 AATAACAATTATAAC
1 AATAACAATAATAAC
*
206196 AATAACAATAATAAT
1 AATAACAATAATAAC
206211 AATAA
1 AATAA
206216 TATCAGTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.26
Consensus pattern (15 bp):
AATAACAATAATAAC
Found at i:211805 original size:21 final size:22
Alignment explanation
Indices: 211776--211821 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
211766 TGTTCAGACA
** *
211776 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
211798 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
211819 AGT
1 AGT
211822 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:213312 original size:28 final size:27
Alignment explanation
Indices: 213257--213327 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
213247 GCCACCTGTT
213257 TGTTTGTCAAAAATGGTGATTATTTTG
1 TGTTTGTCAAAAATGGTGATTATTTTG
*
213284 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGATTAT--TTTG
*
213312 TGTTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
213328 AGGCTTATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.50
28 19 0.47
ACGTcount: A:0.23, C:0.07, G:0.24, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGATTATTTTG
Found at i:222288 original size:22 final size:22
Alignment explanation
Indices: 222223--222289 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
222213 TTGCTTGAAA
*
222223 TTATTTATTAAT-AAATAAAAT
1 TTATTTATTAATAAAATAATAT
* * *
222244 TATATTTTTTAA-AAATTTTATAT
1 T-TATTTATTAATAAA-ATAATAT
222267 TTATTTATTAATAAAATAATAT
1 TTATTTATTAATAAAATAATAT
222289 T
1 T
222290 ATATAATTTG
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
21 1 0.03
22 26 0.74
23 8 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTATTTATTAATAAAATAATAT
Found at i:224218 original size:8 final size:8
Alignment explanation
Indices: 224195--224235 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
224185 TTACATATAC
*
224195 ATACATAC
1 ATACATAT
224203 ATACATAT
1 ATACATAT
224211 ATACATAT
1 ATACATAT
*
224219 ATATATAT
1 ATACATAT
224227 ATATCATAT
1 ATA-CATAT
224236 TCACCATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
8 25 0.86
9 4 0.14
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (8 bp):
ATACATAT
Found at i:224222 original size:12 final size:12
Alignment explanation
Indices: 224191--224235 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
224181 GGCTTTACAT
*
224191 ATACATACATAC
1 ATACATATATAC
224203 ATACATATATAC
1 ATACATATATAC
* *
224215 ATATATATATAT
1 ATACATATATAC
224227 ATATCATAT
1 ATA-CATAT
224236 TCACCATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 24 0.86
13 4 0.14
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (12 bp):
ATACATATATAC
Found at i:228332 original size:26 final size:24
Alignment explanation
Indices: 228277--228325 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
228267 TTATTTAGAT
*
228277 AATACTATTTATATAATATTAAAC
1 AATATTATTTATATAATATTAAAC
228301 AATATTATTTAATAGTAATATTAAA
1 AATATTATTT-ATA-TAATATTAAA
228326 TTTTATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.41
25 3 0.14
26 10 0.45
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (24 bp):
AATATTATTTATATAATATTAAAC
Found at i:228339 original size:26 final size:27
Alignment explanation
Indices: 228310--228367 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
228300 CAATATTATT
* *
228310 TAATAGTA-ATATTAAATTTTATTT-AA
1 TAATAGTACAAATT-AATTTGATTTAAA
*
228336 TAATATTACAAATTAATTTGATTTAAA
1 TAATAGTACAAATTAATTTGATTTAAA
228363 TAATA
1 TAATA
228368 TTATAATTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (27 bp):
TAATAGTACAAATTAATTTGATTTAAA
Found at i:228980 original size:3 final size:3
Alignment explanation
Indices: 228972--229008 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
228962 ACGTGTGTTT
228972 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
229009 GTTAAAATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:231367 original size:2 final size:2
Alignment explanation
Indices: 231355--231385 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
231345 AAAATGAAGT
*
231355 TA TA TA CA 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 T
231386 TTAAAAGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:233664 original size:3 final size:3
Alignment explanation
Indices: 233604--233649 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
233594 AAGTATTGAA
233604 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
233650 CTTGGAATTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:236198 original size:2 final size:2
Alignment explanation
Indices: 236191--236222 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
236181 ACATACATAC
236191 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
236223 CTCATATTCA
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:238094 original size:31 final size:30
Alignment explanation
Indices: 238058--238121 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 30
238048 CAAACCATTC
*
238058 AAAATTAAAATTGAGTGATAAAATTTAATCA
1 AAAATTAAAATTGAGTGACAAAATTTAAT-A
*
238089 AAAATTAAAATTTAGTGACAAAATTTAATA
1 AAAATTAAAATTGAGTGACAAAATTTAATA
238119 AAA
1 AAA
238122 TAAATGTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.31
Consensus pattern (30 bp):
AAAATTAAAATTGAGTGACAAAATTTAATA
Found at i:240230 original size:23 final size:22
Alignment explanation
Indices: 240198--240268 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 22
240188 TTATTTAAAT
*
240198 AATACTATTTATATAATATTAA
1 AATATTATTTATATAATATTAA
240220 ACATATTATTTAATAGTAATATT-A
1 A-ATATTATTT-ATA-TAATATTAA
*
240244 AATTTTATTTA-ATAATATTACA
1 AATATTATTTATATAATATTA-A
240266 AAT
1 AAT
240269 TAATTTGATT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
20 7 0.17
21 1 0.02
22 6 0.14
23 16 0.38
24 5 0.12
25 7 0.17
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.46
Consensus pattern (22 bp):
AATATTATTTATATAATATTAA
Found at i:240259 original size:26 final size:27
Alignment explanation
Indices: 240230--240287 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
240220 ACATATTATT
* *
240230 TAATAGTA-ATATTAAATTTTATTTA-A
1 TAATAGTACAAATT-AATTTGATTTACA
*
240256 TAATATTACAAATTAATTTGATTTACA
1 TAATAGTACAAATTAATTTGATTTACA
240283 TAATA
1 TAATA
240288 TTATAATTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 17 0.63
27 10 0.37
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (27 bp):
TAATAGTACAAATTAATTTGATTTACA
Found at i:240902 original size:3 final size:3
Alignment explanation
Indices: 240894--240937 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
240884 GTGTTTTTTC
240894 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
240938 GAAACTGATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:246182 original size:3 final size:3
Alignment explanation
Indices: 246162--246204 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
246152 CTTTGTCAAG
*
246162 TAT TGAT TAT TAT AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
246205 CGTTGCAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:248843 original size:2 final size:2
Alignment explanation
Indices: 248836--248895 Score: 84
Period size: 2 Copynumber: 29.0 Consensus size: 2
248826 ATAGACATAC
* *
248836 AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT AC ACC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT A-T AT AT AT AT
248880 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
248896 GTCATATTCA
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
2 50 0.93
3 4 0.07
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:248876 original size:36 final size:36
Alignment explanation
Indices: 248835--248909 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
248825 CATAGACATA
248835 CATATATATATATATATATATATATATCATATACAC
1 CATATATATATATATATATATATATATCATATACAC
* *
248871 CATATATATATATATATATATATATGTCATATTCAC
1 CATATATATATATATATATATATATATCATATACAC
248907 CAT
1 CAT
248910 TATCGCTCAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.44, C:0.12, G:0.01, T:0.43
Consensus pattern (36 bp):
CATATATATATATATATATATATATATCATATACAC
Found at i:251528 original size:21 final size:22
Alignment explanation
Indices: 251490--251535 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
251480 ATCTGTTAAA
* **
251490 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
251511 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
251533 ACT
1 ACT
251536 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:254173 original size:27 final size:28
Alignment explanation
Indices: 254109--254179 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 28
254099 AAACAAGCCT
* *
254109 CCATATTTGACAAATC-CAAAAGAAATCA
1 CCATTTTTGACAAA-CACAAAAGAAACCA
*
254137 CCATTTTTGACAAACACAAAA-TAACCA
1 CCATTTTTGACAAACACAAAAGAAACCA
254164 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
254180 TATGAGTGGC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 21 0.54
28 18 0.46
ACGTcount: A:0.46, C:0.24, G:0.06, T:0.24
Consensus pattern (28 bp):
CCATTTTTGACAAACACAAAAGAAACCA
Found at i:255892 original size:31 final size:29
Alignment explanation
Indices: 255812--255896 Score: 82
Period size: 31 Copynumber: 2.9 Consensus size: 29
255802 AAATTGGTGA
* * *
255812 TAAAAAAT-GTATAATGACAAATATCAAT
1 TAAAATATAGTATAATGACAAATTTAAAT
* *
255840 TAAAATATAATATAATAACAAATTTAAAT
1 TAAAATATAGTATAATGACAAATTTAAAT
* *
255869 ATCTAACTATAGTATAATGACAAATTTA
1 -T-AAAATATAGTATAATGACAAATTTA
255897 TTCTTCAACC
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
28 7 0.16
29 16 0.36
30 1 0.02
31 21 0.47
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAAATATAGTATAATGACAAATTTAAAT
Found at i:257882 original size:19 final size:17
Alignment explanation
Indices: 257842--257882 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
257832 AAAAATATTT
257842 TATTTA-TTAAAAAAAC
1 TATTTATTTAAAAAAAC
257858 TA-TTATTTAAATAAATAC
1 TATTTATTTAAA-AAA-AC
257876 TATTTAT
1 TATTTAT
257883 CTAATGTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.14
16 7 0.33
17 3 0.14
18 4 0.19
19 4 0.19
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (17 bp):
TATTTATTTAAAAAAAC
Found at i:258412 original size:30 final size:30
Alignment explanation
Indices: 258376--258437 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
258366 GGTTTTATTC
258376 AATCCTTTGTTATATCAAAACCAAGATCCT
1 AATCCTTTGTTATATCAAAACCAAGATCCT
258406 AATCCTTTGTTATATCAAAACCAAGATCCT
1 AATCCTTTGTTATATCAAAACCAAGATCCT
258436 AA
1 AA
258438 CACTCATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.39, C:0.23, G:0.06, T:0.32
Consensus pattern (30 bp):
AATCCTTTGTTATATCAAAACCAAGATCCT
Found at i:260354 original size:23 final size:23
Alignment explanation
Indices: 260307--260382 Score: 82
Period size: 23 Copynumber: 3.2 Consensus size: 23
260297 AAAATTTTTT
*
260307 TATTGAAATAATATTATTTACATAA
1 TATT-AAATAATATT-TTTAAATAA
260332 TATTAAATAATATTTTTAAATAA
1 TATTAAATAATATTTTTAAATAA
* * *
260355 T-TTCAATATTATCATTTAAATAA
1 TATTAAATAATAT-TTTTAAATAA
260378 TATTA
1 TATTA
260383 TAATTAAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
22 9 0.20
23 19 0.43
24 12 0.27
25 4 0.09
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (23 bp):
TATTAAATAATATTTTTAAATAA
Found at i:263462 original size:59 final size:60
Alignment explanation
Indices: 263360--263476 Score: 182
Period size: 59 Copynumber: 2.0 Consensus size: 60
263350 AAAATAGTGA
* *
263360 ACAAGAATGGTAAAATGCGAAGAAAATGAAGTTATATACATATACATATATAT-ATATAT
1 ACAAGAATGGTAAAATGAGAAGAAAATGAAGTTATACACATATACATATATATCATATAT
* * *
263419 ACAAGAATGGTAAAATGAGAAGAAAATGAAGTTTTACATATATATATATATATCATAT
1 ACAAGAATGGTAAAATGAGAAGAAAATGAAGTTATACACATATACATATATATCATAT
263477 TAAAGATTTC
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
59 48 0.92
60 4 0.08
ACGTcount: A:0.50, C:0.06, G:0.14, T:0.30
Consensus pattern (60 bp):
ACAAGAATGGTAAAATGAGAAGAAAATGAAGTTATACACATATACATATATATCATATAT
Found at i:267473 original size:20 final size:20
Alignment explanation
Indices: 267448--267501 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
267438 CTTGTGTCTA
**
267448 TTTTTATTTATTTTTTACAT
1 TTTTTATTTATTTTACACAT
*
267468 TTTTTATATATTTTACACAT
1 TTTTTATTTATTTTACACAT
*
267488 ATTTTA-TTATTTTA
1 TTTTTATTTATTTTA
267502 TAATCGCAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 7 0.24
20 22 0.76
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTTATTTATTTTACACAT
Found at i:273717 original size:3 final size:3
Alignment explanation
Indices: 273672--273702 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
273662 AAGTATTGAA
273672 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
273703 CTTGGAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:280310 original size:19 final size:17
Alignment explanation
Indices: 280270--280310 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
280260 AAAAATATTA
280270 TATTTA-TTAAAAAAAC
1 TATTTATTTAAAAAAAC
280286 TA-TTATTTAAATAAATAC
1 TATTTATTTAAA-AAA-AC
280304 TATTTAT
1 TATTTAT
280311 CTAATGTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.14
16 7 0.33
17 3 0.14
18 4 0.19
19 4 0.19
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (17 bp):
TATTTATTTAAAAAAAC
Found at i:280628 original size:89 final size:90
Alignment explanation
Indices: 280491--280671 Score: 328
Period size: 89 Copynumber: 2.0 Consensus size: 90
280481 TAAACTAATA
280491 AATTTTAATTATAAATTTTTCTATGAAAATATATAATATTAATTTATTACAAAGATATTATTCAC
1 AATTTTAATTATAAATTTTTCTATGAAAATATATAATATTAATTTATTACAAAGATATTATTCAC
*
280556 TTAAAATTAAGTAGTATGAGAAAGG
66 TTAAAATTAAGTAGTATCAGAAAGG
*
280581 AATTTTAATTATAAATTTTTCTATG-AAATATATAATATTAATTTATTACAAAGTTATTATTCAC
1 AATTTTAATTATAAATTTTTCTATGAAAATATATAATATTAATTTATTACAAAGATATTATTCAC
*
280645 TTATAATTAAGTAGTATCAGAAAGG
66 TTAAAATTAAGTAGTATCAGAAAGG
280670 AA
1 AA
280672 ACAATTTTTC
Statistics
Matches: 88, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
89 63 0.72
90 25 0.28
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (90 bp):
AATTTTAATTATAAATTTTTCTATGAAAATATATAATATTAATTTATTACAAAGATATTATTCAC
TTAAAATTAAGTAGTATCAGAAAGG
Found at i:281678 original size:24 final size:26
Alignment explanation
Indices: 281645--281699 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 26
281635 AAACTATTAT
*
281645 TTAAATAATACTATTT-ATA-TAATA
1 TTAAACAATACTATTTAATAGTAATA
*
281669 TTAAACAATATTATTTAATAGTAATA
1 TTAAACAATACTATTTAATAGTAATA
281695 TTAAA
1 TTAAA
281700 TTTTATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 14 0.52
25 3 0.11
26 10 0.37
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (26 bp):
TTAAACAATACTATTTAATAGTAATA
Found at i:281713 original size:26 final size:27
Alignment explanation
Indices: 281684--281741 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
281674 CAATATTATT
* *
281684 TAATAGTA-ATATTAAATTTTATTT-AA
1 TAATAGTACAAATT-AATTTCATTTAAA
*
281710 TAATATTACAAATTAATTTCATTTAAA
1 TAATAGTACAAATTAATTTCATTTAAA
281737 TAATA
1 TAATA
281742 TTATAATTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (27 bp):
TAATAGTACAAATTAATTTCATTTAAA
Found at i:282350 original size:3 final size:3
Alignment explanation
Indices: 282344--282387 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
282334 TGTTTTTTTC
282344 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
282388 GAAACTGATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:283095 original size:28 final size:29
Alignment explanation
Indices: 283063--283142 Score: 112
Period size: 28 Copynumber: 2.9 Consensus size: 29
283053 CAAATGTCAC
283063 CCTTTGTATTTGTCAAATATGGTGGTT-T
1 CCTTTGTATTTGTCAAATATGGTGGTTAT
283091 CCTTTGTATTTGTCAAATATGGTGGTTAT
1 CCTTTGTATTTGTCAAATATGGTGGTTAT
* * *
283120 -TTTTGTA-TTGTAAAAAATGGTGG
1 CCTTTGTATTTGTCAAATATGGTGG
283143 CTTGTTGTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
27 14 0.29
28 33 0.69
29 1 0.02
ACGTcount: A:0.23, C:0.07, G:0.23, T:0.47
Consensus pattern (29 bp):
CCTTTGTATTTGTCAAATATGGTGGTTAT
Found at i:283154 original size:24 final size:25
Alignment explanation
Indices: 283122--283168 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
283112 GTGGTTATTT
283122 TTGTATTGTAAAAAATGGTGGCTTG
1 TTGTATTGTAAAAAATGGTGGCTTG
* *
283147 TTGT-TTGTCAAAATTGGTGGCT
1 TTGTATTGTAAAAAATGGTGGCT
283169 AATTTTTATT
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:0.23, C:0.06, G:0.28, T:0.43
Consensus pattern (25 bp):
TTGTATTGTAAAAAATGGTGGCTTG
Done.