Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002616.1 Hibiscus syriacus cultivar Beakdansim tig00005294_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1287628
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 7
Found at i:5577 original size:44 final size:47
Alignment explanation
Indices: 5511--5608 Score: 148
Period size: 44 Copynumber: 2.1 Consensus size: 47
5501 TTATTTTTGT
5511 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTA-GATTTA
1 TTTTT-GAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
* *
5558 TTTTTGAAT-AA-GCATGCGAATTAGATATCATGCGGTTAGGATTTC
1 TTTTTGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
5603 TTTTTG
1 TTTTTG
5609 TGGATAACAA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
44 26 0.54
45 13 0.27
46 4 0.08
47 5 0.10
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (47 bp):
TTTTTGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
Found at i:15287 original size:7 final size:7
Alignment explanation
Indices: 15250--15376 Score: 56
Period size: 7 Copynumber: 16.4 Consensus size: 7
15240 TATTTTGCTT
*
15250 AAAGAAG
1 AAAGAAA
*
15257 AAATAAA
1 AAAGAAA
*
15264 AGAGAAA
1 AAAGAAA
15271 AGAAGAAA
1 A-AAGAAA
15279 AAAGAAA
1 AAAGAAA
**
15286 AAATGATG
1 AAA-GAAA
**
15294 ATGGAAA
1 AAAGAAA
15301 AAACGAAAAA
1 AAA-G--AAA
15311 AAACGAAAA
1 AAA-G-AAA
15320 AAAGAAGA
1 AAAGAA-A
*
15328 AAATGGAA
1 AAA-GAAA
15336 AAAGAAAA
1 AAAG-AAA
15344 AAATGAAA
1 AAA-GAAA
*
15352 AATGAAA
1 AAAGAAA
15359 AAAGAGAA
1 AAAGA-AA
*
15367 AAATAAA
1 AAAGAAA
15374 AAA
1 AAA
15377 AGAGAAATAA
Statistics
Matches: 92, Mismatches: 18, Indels: 20
0.71 0.14 0.15
Matches are distributed among these distances:
7 39 0.42
8 35 0.38
9 10 0.11
10 8 0.09
ACGTcount: A:0.75, C:0.02, G:0.17, T:0.06
Consensus pattern (7 bp):
AAAGAAA
Found at i:15330 original size:10 final size:10
Alignment explanation
Indices: 15298--15322 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
15288 ATGATGATGG
15298 AAAAAACGAA
1 AAAAAACGAA
15308 AAAAAACGAA
1 AAAAAACGAA
15318 AAAAA
1 AAAAA
15323 GAAGAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAACGAA
Found at i:15336 original size:18 final size:18
Alignment explanation
Indices: 15294--15353 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 18
15284 AAAAATGATG
*
15294 ATGGAAAAAACGAAAAAA
1 ATGGAAAAAAAGAAAAAA
** *
15312 AACGAAAAAAAGAAGAAA
1 ATGGAAAAAAAGAAAAAA
15330 ATGG--AAAAAGAAAAAA
1 ATGGAAAAAAAGAAAAAA
15346 AT-GAAAAA
1 ATGGAAAAA
15354 TGAAAAAAGA
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
15 1 0.03
16 13 0.39
17 3 0.09
18 16 0.48
ACGTcount: A:0.75, C:0.03, G:0.17, T:0.05
Consensus pattern (18 bp):
ATGGAAAAAAAGAAAAAA
Found at i:15337 original size:16 final size:15
Alignment explanation
Indices: 15318--15377 Score: 68
Period size: 16 Copynumber: 3.9 Consensus size: 15
15308 AAAAAACGAA
*
15318 AAAAAGAAGAAAATGG
1 AAAAAGAAAAAAAT-G
15334 AAAAAGAAAAAAATG
1 AAAAAGAAAAAAATG
15349 AAAAATGAAAAAAGA-G
1 AAAAA-GAAAAAA-ATG
*
15365 AAAAATAAAAAAA
1 AAAAAGAAAAAAA
15378 GAGAAATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
14 1 0.03
15 12 0.30
16 26 0.65
17 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (15 bp):
AAAAAGAAAAAAATG
Found at i:15346 original size:8 final size:8
Alignment explanation
Indices: 15297--15389 Score: 57
Period size: 9 Copynumber: 11.1 Consensus size: 8
15287 AATGATGATG
*
15297 GAAAAAAC
1 GAAAAAAA
15305 GAAAAAAAA
1 G-AAAAAAA
15314 CGAAAAAAA
1 -GAAAAAAA
*
15323 GAAGAAAAT
1 GAA-AAAAA
*
15332 G-GAAAAA
1 GAAAAAAA
15339 GAAAAAAA
1 GAAAAAAA
*
15347 TG-AAAAAT
1 -GAAAAAAA
15355 GAAAAAAGA
1 GAAAAAA-A
15364 GAAAAATAA
1 GAAAAA-AA
*
15373 -AAAAAGA
1 GAAAAAAA
15380 GAAATAAAA
1 GAAA-AAAA
15389 G
1 G
15390 GAGGGTTCAA
Statistics
Matches: 66, Mismatches: 9, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
7 7 0.11
8 27 0.41
9 30 0.45
10 2 0.03
ACGTcount: A:0.76, C:0.02, G:0.16, T:0.05
Consensus pattern (8 bp):
GAAAAAAA
Found at i:15353 original size:23 final size:23
Alignment explanation
Indices: 15308--15376 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 23
15298 AAAAAACGAA
15308 AAAAAACGAAAAAAA-GAAGAAAATG
1 AAAAAA-GAAAAAAATG-A-AAAATG
*
15333 GAAAAAGAAAAAAATGAAAAATG
1 AAAAAAGAAAAAAATGAAAAATG
* *
15356 AAAAAAGAGAAAAATAAAAAA
1 AAAAAAGAAAAAAATGAAAAA
15377 AGAGAAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 24 0.62
24 9 0.23
25 6 0.15
ACGTcount: A:0.78, C:0.01, G:0.14, T:0.06
Consensus pattern (23 bp):
AAAAAAGAAAAAAATGAAAAATG
Found at i:15378 original size:16 final size:16
Alignment explanation
Indices: 15333--15383 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
15323 GAAGAAAATG
* *
15333 GAAAAAGAAAAAAA-T
1 GAAAAATAAAAAAAGA
*
15348 GAAAAATGAAAAAAGA
1 GAAAAATAAAAAAAGA
15364 GAAAAATAAAAAAAGA
1 GAAAAATAAAAAAAGA
15380 GAAA
1 GAAA
15384 TAAAAGGAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
15 12 0.39
16 19 0.61
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (16 bp):
GAAAAATAAAAAAAGA
Found at i:16765 original size:51 final size:51
Alignment explanation
Indices: 16699--17165 Score: 476
Period size: 51 Copynumber: 8.9 Consensus size: 51
16689 GAAGCAAATT
16699 AGTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 AGTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* *
16750 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * *
16801 AGTTCGTTGAAGATTGGGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* **
16852 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATAAATAGGGAGCGGACA
1 AGTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * *
16903 AGTTTGTTGAAAATTGAGTTCTATACTCCCTGAACGG-ATAGGGAGCGAACA
1 AGTTTGTTGAAGATTGAGTCCTATACTCTCTGAA-GGAATAGGGAGCGGACA
* * * *
16954 CGTTTGTTAAAGAGTGAGTCCTGTACTCTCTGAAGGAATAGGGAGCGGA-A
1 AGTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * * *
17004 CTGTTTATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACT
1 -AGTTTGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * * * * *
17060 CGTTTTATTGAAGATTATTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACA
1 AG-TTTGTTGAAG---ATT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
*
17116 CA-TTT-TATGAAGATTGCTCGAGTCTTATACT-TCCTGAAGGAATAGGGAGC
1 -AGTTTGT-TGAAGA-T--T-GAGTCCTATACTCT-CTGAAGGAATAGGGAGC
17166 AGGCTCGTCA
Statistics
Matches: 359, Mismatches: 39, Indels: 32
0.83 0.09 0.07
Matches are distributed among these distances:
50 3 0.01
51 239 0.67
52 1 0.00
53 1 0.00
54 3 0.01
55 68 0.19
56 43 0.12
59 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (51 bp):
AGTTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
Found at i:17093 original size:56 final size:56
Alignment explanation
Indices: 16977--17173 Score: 226
Period size: 55 Copynumber: 3.6 Consensus size: 56
16967 GTGAGTCCTG
* *
16977 TACTCTCTGAAGGAATAGGGAGCGGAACT-G-TTTATTGAAGATTTTTCGAGT-TCTA
1 TACTCTCTGAAGGAATAGAGAGCGG-ACTCGTTTTATTGAAGATTATTCGAGTCT-TA
*
17032 TACTCTCTGAAGGAATAGAGAGCGGACTCGTTTTATTGAAGATTATTCAAGTCTTA
1 TACTCTCTGAAGGAATAGAGAGCGGACTCGTTTTATTGAAGATTATTCGAGTCTTA
* * * * **
17088 TACTCTCTGAATGAATAGAGAGCAGACACATTTTA-TGAAGATTGCTCGAGTCTTA
1 TACTCTCTGAAGGAATAGAGAGCGGACTCGTTTTATTGAAGATTATTCGAGTCTTA
*
17143 TACT-TCCTGAAGGAATAGGGAGCAGG-CTCGT
1 TACTCT-CTGAAGGAATAGAGAGC-GGACTCGT
17174 CATTTGAAGA
Statistics
Matches: 122, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
54 4 0.03
55 64 0.52
56 53 0.43
57 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.31
Consensus pattern (56 bp):
TACTCTCTGAAGGAATAGAGAGCGGACTCGTTTTATTGAAGATTATTCGAGTCTTA
Found at i:22069 original size:37 final size:36
Alignment explanation
Indices: 21994--22069 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
21984 TTTTTATATT
*
21994 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
22030 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
22067 TTT
1 TTT
22070 GTAAGATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:22443 original size:30 final size:31
Alignment explanation
Indices: 22386--22443 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
22376 TCTAATTCTA
*
22386 ATTTTCGGATATCCGAAAATTTTGGATAATT
1 ATTTTCGGATATCCGAAAATTTCGGATAATT
*
22417 ATTTTTGGATATCCG-AAATTTCGGATA
1 ATTTTCGGATATCCGAAAATTTCGGATA
22444 TGATATCCGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 11 0.44
31 14 0.56
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.41
Consensus pattern (31 bp):
ATTTTCGGATATCCGAAAATTTCGGATAATT
Found at i:22608 original size:35 final size:34
Alignment explanation
Indices: 22543--22609 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 34
22533 AGCTCTTATA
* * ** *
22543 ATTTCCAGTTTAGCAAAGATATGGTGAAACTATG
1 ATTTCCAATTTAACAAAGATACAGTAAAACTATG
22577 ATTTCTCAATTTAACAAAGATACAGTAAAACTA
1 ATTTC-CAATTTAACAAAGATACAGTAAAACTA
22610 GAGGATGATA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 5 0.19
35 22 0.81
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (34 bp):
ATTTCCAATTTAACAAAGATACAGTAAAACTATG
Found at i:23243 original size:16 final size:16
Alignment explanation
Indices: 23219--23252 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
23209 AAATTATAGT
*
23219 ATTTTAGATTAGACAA
1 ATTTGAGATTAGACAA
23235 ATTTGAGATTAGACAA
1 ATTTGAGATTAGACAA
23251 AT
1 AT
23253 CTCAAGGGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (16 bp):
ATTTGAGATTAGACAA
Found at i:26450 original size:61 final size:61
Alignment explanation
Indices: 26361--26485 Score: 196
Period size: 61 Copynumber: 2.0 Consensus size: 61
26351 AGAATAGGTA
*
26361 AAAGAAAATAAATGCAGTGCAGAATGCCTCGTGAACATATTTCTAAATCAAAAGTTAAAAG
1 AAAGAAAATAAATGCAGTGCAGAATGCCTCGTGAACATATTTCCAAATCAAAAGTTAAAAG
* * ** *
26422 AAAGAAAATAAATGCAGTGCAGATTGCCTCGTTAACATATTTCCAAATTGAAATTTAAAAG
1 AAAGAAAATAAATGCAGTGCAGAATGCCTCGTGAACATATTTCCAAATCAAAAGTTAAAAG
26483 AAA
1 AAA
26486 TCAAGACAGA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.47, C:0.13, G:0.15, T:0.25
Consensus pattern (61 bp):
AAAGAAAATAAATGCAGTGCAGAATGCCTCGTGAACATATTTCCAAATCAAAAGTTAAAAG
Found at i:37248 original size:15 final size:15
Alignment explanation
Indices: 37230--37305 Score: 68
Period size: 15 Copynumber: 5.3 Consensus size: 15
37220 GTGAAATTTT
37230 AATTATTTAAATAAA
1 AATTATTTAAATAAA
*
37245 AATTATTTATATAAA
1 AATTATTTAAATAAA
* **
37260 AATT-TATCGAT-AA
1 AATTATTTAAATAAA
* *
37273 TA-TATTCAAATAAA
1 AATTATTTAAATAAA
*
37287 AATTATTTATATAAA
1 AATTATTTAAATAAA
37302 AATT
1 AATT
37306 TATCGATAAT
Statistics
Matches: 46, Mismatches: 12, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
12 1 0.02
13 6 0.13
14 7 0.15
15 32 0.70
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (15 bp):
AATTATTTAAATAAA
Found at i:37297 original size:42 final size:42
Alignment explanation
Indices: 37229--37320 Score: 168
Period size: 42 Copynumber: 2.2 Consensus size: 42
37219 AGTGAAATTT
*
37229 TAAT-TATTTAAATAAAAATTATTTATATAAAAATTTATCGA
1 TAATATATTCAAATAAAAATTATTTATATAAAAATTTATCGA
37270 TAATATATTCAAATAAAAATTATTTATATAAAAATTTATCGA
1 TAATATATTCAAATAAAAATTATTTATATAAAAATTTATCGA
37312 TAATATATT
1 TAATATATT
37321 ATTTTATTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 4 0.08
42 45 0.92
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.43
Consensus pattern (42 bp):
TAATATATTCAAATAAAAATTATTTATATAAAAATTTATCGA
Found at i:40429 original size:42 final size:41
Alignment explanation
Indices: 40363--40442 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 41
40353 AGTGAAATTC
40363 TAATTATTTAAATAAAAATCATTTATATAAAAAATCATTGA
1 TAATTATTTAAATAAAAATCATTTATATAAAAAATCATTGA
* *
40404 TAATATATTTAAATAAAAATTATTTATATAAAAATTCAT
1 TAAT-TATTTAAATAAAAATCATTTATATAAAAAATCAT
40443 ATCATAGTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 4 0.11
42 32 0.89
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (41 bp):
TAATTATTTAAATAAAAATCATTTATATAAAAAATCATTGA
Found at i:40439 original size:15 final size:15
Alignment explanation
Indices: 40364--40439 Score: 61
Period size: 15 Copynumber: 5.3 Consensus size: 15
40354 GTGAAATTCT
*
40364 AATTATTTAAATAAA
1 AATTATTTATATAAA
*
40379 AATCATTTATATAAA
1 AATTATTTATATAAA
* * *
40394 AA--A-TCAT-TGAT
1 AATTATTTATATAAA
*
40405 AATATATTTAAATAAA
1 AAT-TATTTATATAAA
40421 AATTATTTATATAAA
1 AATTATTTATATAAA
40436 AATT
1 AATT
40440 CATATCATAG
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
11 4 0.09
12 3 0.07
13 1 0.02
14 1 0.02
15 32 0.70
16 5 0.11
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (15 bp):
AATTATTTATATAAA
Found at i:46346 original size:15 final size:16
Alignment explanation
Indices: 46325--46361 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
46315 GAGAGCTTTG
46325 ATTTTTAAAAAAAATC
1 ATTTTTAAAAAAAATC
46341 -TTTTT-AAAAAAATC
1 ATTTTTAAAAAAAATC
46355 ATTTTTA
1 ATTTTTA
46362 TTATTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTTTTAAAAAAAATC
Found at i:47112 original size:32 final size:32
Alignment explanation
Indices: 47041--47101 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
47031 ATTTTGGGTC
* *
47041 CGGA-CAATATCAGATCAGTTGATTTTTGAAT
1 CGGATCAACATCAGATCAGTTGATTTTCGAAT
47072 CGGATCAACATCAGATC-GATTGATTTTCGA
1 CGGATCAACATCAGATCAG-TTGATTTTCGA
47102 TTTGGGTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 5 0.19
32 21 0.81
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (32 bp):
CGGATCAACATCAGATCAGTTGATTTTCGAAT
Found at i:49902 original size:18 final size:20
Alignment explanation
Indices: 49861--49899 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
49851 AAAAAATACC
49861 TAAAATATTATTATTTTTACT
1 TAAAATATTATTATTTTTA-T
49882 TAAAATATTATTATTTTT
1 TAAAATATTATTATTTTT
49900 TAACATGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
TAAAATATTATTATTTTTAT
Found at i:50642 original size:21 final size:21
Alignment explanation
Indices: 50590--50636 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
50580 CAGTAAAGCG
50590 CTACCTAAAATGTTATTTTTT
1 CTACCTAAAATGTTATTTTTT
50611 CTACCTAAAATGTTATTTTTT
1 CTACCTAAAATGTTATTTTTT
50632 CTACC
1 CTACC
50637 AGAAATATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.19, G:0.04, T:0.49
Consensus pattern (21 bp):
CTACCTAAAATGTTATTTTTT
Found at i:62490 original size:23 final size:24
Alignment explanation
Indices: 62432--62490 Score: 56
Period size: 23 Copynumber: 2.6 Consensus size: 24
62422 CAGATTAAAC
62432 CAAATC-CA-ATAA-AAAAAATAA
1 CAAATCACACATAATAAAAAATAA
* *
62453 GAAATCAAATC-TAATAAAAAA-AA
1 CAAATCACA-CATAATAAAAAATAA
62476 CAAATCACACATAAT
1 CAAATCACACATAAT
62491 CCATTTTTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
21 5 0.17
22 2 0.07
23 16 0.55
24 6 0.21
ACGTcount: A:0.66, C:0.15, G:0.02, T:0.17
Consensus pattern (24 bp):
CAAATCACACATAATAAAAAATAA
Found at i:63677 original size:30 final size:29
Alignment explanation
Indices: 63615--63680 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
63605 GTGTTAAGCT
* **
63615 TATATTTATTTATTTTAATAATATATTTA
1 TATATTTATTTATTTTAATAAAATATGAA
* *
63644 TATATTGTATTTGTTTTTATAAAATATGAA
1 TATATT-TATTTATTTTAATAAAATATGAA
63674 TATATTT
1 TATATTT
63681 TATTAAAGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 7 0.23
30 24 0.77
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (29 bp):
TATATTTATTTATTTTAATAAAATATGAA
Found at i:72998 original size:21 final size:24
Alignment explanation
Indices: 72954--72999 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 24
72944 AACATGTACT
*
72954 TATATCATTTTCTTTGTAATCACA
1 TATATCATTTTCTTTCTAATCACA
72978 TATATC-TTTTC-TTCT-ATCACA
1 TATATCATTTTCTTTCTAATCACA
72999 T
1 T
73000 TTCTCATGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 3 0.14
23 5 0.24
24 6 0.29
ACGTcount: A:0.26, C:0.20, G:0.02, T:0.52
Consensus pattern (24 bp):
TATATCATTTTCTTTCTAATCACA
Found at i:74922 original size:6 final size:6
Alignment explanation
Indices: 74911--74947 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
74901 TCTTTGTATC
* *
74911 TTTACA TTTACA TTTACA TTTACA TTCACA TTCACA T
1 TTTACA TTTACA TTTACA TTTACA TTTACA TTTACA T
74948 CTTTATATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.00, T:0.46
Consensus pattern (6 bp):
TTTACA
Found at i:74985 original size:28 final size:28
Alignment explanation
Indices: 74945--74999 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
74935 TTCACATTCA
*
74945 CATCTTTATATTTATGTTCACATCTTTT
1 CATCTTTACATTTATGTTCACATCTTTT
* *
74973 CATCTTTACATTTTTGTTCGCATCTTT
1 CATCTTTACATTTATGTTCACATCTTT
75000 GCATTTGCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.18, C:0.20, G:0.05, T:0.56
Consensus pattern (28 bp):
CATCTTTACATTTATGTTCACATCTTTT
Found at i:75016 original size:20 final size:20
Alignment explanation
Indices: 74993--75031 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
74983 TTTTTGTTCG
*
74993 CATCTTTGCATTTGCATTCT
1 CATCTTTGCATTGGCATTCT
75013 CATCTTTGCATTGGCATTC
1 CATCTTTGCATTGGCATTC
75032 ACATTTGTAT
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:0.15, C:0.26, G:0.13, T:0.46
Consensus pattern (20 bp):
CATCTTTGCATTGGCATTCT
Found at i:76079 original size:28 final size:28
Alignment explanation
Indices: 76020--76080 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
76010 CAAGGAAGCC
*
76020 AACCTGAAACACATCACCTCCCTAAATT
1 AACCTGAAACACATCACCTCCCTAAATA
*
76048 AACCTGAAACACTAT-ACCTTCC-AAAGTA
1 AACCTGAAACAC-ATCACCTCCCTAAA-TA
76076 AACCT
1 AACCT
76081 AAGCCTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 3 0.10
28 24 0.83
29 2 0.07
ACGTcount: A:0.41, C:0.33, G:0.05, T:0.21
Consensus pattern (28 bp):
AACCTGAAACACATCACCTCCCTAAATA
Found at i:83947 original size:19 final size:20
Alignment explanation
Indices: 83910--83948 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
83900 AAACCATTCA
83910 GGGGGGAATCGGTACTCCCTT
1 GGGGGGAATCGGTA-TCCCTT
83931 GGGGGGAATCGGT-TCCCT
1 GGGGGGAATCGGTATCCCT
83949 CTGAGCAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
21 13 0.72
ACGTcount: A:0.13, C:0.23, G:0.41, T:0.23
Consensus pattern (20 bp):
GGGGGGAATCGGTATCCCTT
Found at i:90478 original size:22 final size:21
Alignment explanation
Indices: 90436--90475 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
90426 GAGTTTATTT
*
90436 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
90457 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
90476 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:93831 original size:23 final size:23
Alignment explanation
Indices: 93801--93872 Score: 144
Period size: 23 Copynumber: 3.1 Consensus size: 23
93791 GTGTACATAG
93801 GCTAGCTATGAGGAAGCTAGCCT
1 GCTAGCTATGAGGAAGCTAGCCT
93824 GCTAGCTATGAGGAAGCTAGCCT
1 GCTAGCTATGAGGAAGCTAGCCT
93847 GCTAGCTATGAGGAAGCTAGCCT
1 GCTAGCTATGAGGAAGCTAGCCT
93870 GCT
1 GCT
93873 GCTTCTCGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.22
Consensus pattern (23 bp):
GCTAGCTATGAGGAAGCTAGCCT
Found at i:96402 original size:25 final size:25
Alignment explanation
Indices: 96374--96428 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
96364 AAGAAAAACC
96374 TAAAA-AAGATAAGGAAAATAAA-AAG
1 TAAAACAAGATAA--AAAATAAACAAG
* *
96399 TAAAACTATATAAAAAATAAACAAG
1 TAAAACAAGATAAAAAATAAACAAG
96424 TAAAA
1 TAAAA
96429 TAAAAATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 8 0.31
25 13 0.50
26 5 0.19
ACGTcount: A:0.71, C:0.04, G:0.09, T:0.16
Consensus pattern (25 bp):
TAAAACAAGATAAAAAATAAACAAG
Found at i:105746 original size:64 final size:66
Alignment explanation
Indices: 105641--105803 Score: 197
Period size: 65 Copynumber: 2.5 Consensus size: 66
105631 CGGTGCACCA
* * * *
105641 AGTGTGCTTCGATGCATGAAATGCATTCGAT-ATTTGAAAAATAGCCTG-GTGCATCGATGCATG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGAGTGCATCGATACATG
105704 G
66 G
** * **
105705 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATACATG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGAGTGCATCGATACATG
105769 G
66 G
* * *
105770 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
105804 CAATTAATTC
Statistics
Matches: 82, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
64 35 0.43
65 47 0.57
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.31
Consensus pattern (66 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGAGTGCATCGATACATG
G
Found at i:106486 original size:19 final size:19
Alignment explanation
Indices: 106462--106500 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
106452 TCGAATGCAT
106462 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
106481 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
106500 T
1 T
106501 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:106625 original size:64 final size:65
Alignment explanation
Indices: 106448--106610 Score: 222
Period size: 65 Copynumber: 2.5 Consensus size: 65
106438 GAATTAATTG
* * * *
106448 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
* ** **
106513 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-TTTTCA
106576 A
65 A
106577 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
106611 TGGTGCACCG
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 36 0.42
65 49 0.58
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:108287 original size:20 final size:21
Alignment explanation
Indices: 108230--108288 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
108220 TGCATCTTTA
*
108230 CATCTTTACATTTGCATTCGT
1 CATCTTTGCATTTGCATTCGT
* *
108251 -ATATTTGCATTTACATTC-T
1 CATCTTTGCATTTGCATTCGT
*
108270 CATCTTTGCATTGGCATTC
1 CATCTTTGCATTTGCATTC
108289 ATATTTGTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.20, C:0.22, G:0.10, T:0.47
Consensus pattern (21 bp):
CATCTTTGCATTTGCATTCGT
Found at i:109751 original size:14 final size:13
Alignment explanation
Indices: 109732--109777 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
109722 CAAAGAAAAA
109732 AGAAAAAAAGAGAG
1 AGAAAAAAAGA-AG
109746 AGAAAAAAA-AAG
1 AGAAAAAAAGAAG
*
109758 AGAAAAGAAAGAAA
1 AGAAAA-AAAGAAG
109772 AGAAAA
1 AGAAAA
109778 GGGGAAAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 8 0.28
13 4 0.14
14 17 0.59
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAGAAG
Found at i:109763 original size:23 final size:23
Alignment explanation
Indices: 109727--109804 Score: 76
Period size: 21 Copynumber: 3.6 Consensus size: 23
109717 TATAACAAAG
*
109727 AAAAAAGAAAAAAAGAGAGAGAAA
1 AAAAAAGAAGAAAAGA-AGAGAAA
109751 AAAAAAG-AGAAAAGAA-AGAAA
1 AAAAAAGAAGAAAAGAAGAGAAA
* * *
109772 AGAAAAG-GGGAAA-AAGA-AAA
1 AAAAAAGAAGAAAAGAAGAGAAA
109792 AAAAAAGAAGAAA
1 AAAAAAGAAGAAA
109805 GAAAACATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
20 11 0.24
21 19 0.42
22 1 0.02
23 7 0.16
24 7 0.16
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (23 bp):
AAAAAAGAAGAAAAGAAGAGAAA
Found at i:109772 original size:16 final size:15
Alignment explanation
Indices: 109703--109778 Score: 66
Period size: 16 Copynumber: 5.0 Consensus size: 15
109693 AAGAGAGGGT
* *
109703 AAAAAAAGAGAATAT
1 AAAAAAAGAGAAAAG
* *
109718 ATAACAAAGAAAAAAG
1 A-AAAAAAGAGAAAAG
109734 AAAAAAAGAGAGAGAA-
1 AAAAAAAGAGA-A-AAG
109750 AAAAAAAGAGAAAAG
1 AAAAAAAGAGAAAAG
*
109765 AAAGAAA-AGAAAAG
1 AAAAAAAGAGAAAAG
109779 GGGAAAAAGA
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
14 9 0.18
15 16 0.32
16 23 0.46
17 2 0.04
ACGTcount: A:0.76, C:0.01, G:0.18, T:0.04
Consensus pattern (15 bp):
AAAAAAAGAGAAAAG
Found at i:109778 original size:14 final size:13
Alignment explanation
Indices: 109729--109809 Score: 56
Period size: 14 Copynumber: 5.9 Consensus size: 13
109719 TAACAAAGAA
109729 AAAAGAAAAAAAG
1 AAAAGAAAAAAAG
*
109742 AGAGAGAAAAAAA-
1 A-AAAGAAAAAAAG
*
109755 AAGAGAAAAGAAAG
1 AAAAGAAAA-AAAG
***
109769 AAAAGAAAAGGGG
1 AAAAGAAAAAAAG
*
109782 AAAAAGAAAAAAAA
1 -AAAAGAAAAAAAG
109796 AAGAAGAAAGAAAA
1 AA-AAGAAA-AAAA
109810 CATATCAAGT
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
12 8 0.15
13 8 0.15
14 33 0.62
15 4 0.08
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAAG
Found at i:112848 original size:20 final size:20
Alignment explanation
Indices: 112819--112861 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
112809 ATTCCACCAC
112819 ATGCAACTATAT-ACTCCTAA
1 ATGCAACTATATGA-TCCTAA
*
112839 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
112859 ATG
1 ATG
112862 GGCTCTTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:113795 original size:54 final size:54
Alignment explanation
Indices: 113730--114220 Score: 682
Period size: 54 Copynumber: 9.1 Consensus size: 54
113720 CCAAATAATA
* * * **
113730 TGATGTCTTCAAATGAATTTTAAAAGAAACTAAATCTGAATTTT-AGGGGTTTCT
1 TGATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTG-ATTTTCAGGGGTTTCT
*
113784 TGATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTGATTTTCAAGGGTTTCT
1 TGATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCT
* *
113838 TGATGTTTTCAAATGAATTTTTAAAGGAGTTAAGCCTGATTTTCAGGGGTTTCT
1 TGATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCT
* *
113892 TGATGTTTACAAATGAATTTTGAAAGAAGCTAAGCCTGATTTAT-AGGGGTTTCT
1 TGATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTGATTT-TCAGGGGTTTCT
* * * * *
113946 TGATGTATTCAAATAAATTTTTAAAGAAGCTAAGCCTGGTTTTCAAGGGCTTCT
1 TGATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCT
* *
114000 TGATGTCTTCAAATGAATTTTTAAAGGAGCTAAGCCTGATTTTCAGGGGTTTCT
1 TGATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCT
* * * *
114054 TGATATTTTCAAATGAATTTTTAAAGGAGTTAAGCCTGATTTTAAGGGGTTTCT
1 TGATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCT
* * *
114108 TGATGTTTTCAAATGAATTTTTAAAGGAGCTAATCTTGATTTTCAGGGGTTTCT
1 TGATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCT
* * * *
114162 TGATGTTTACAAATGGATTTTGAAAGAAGCTAAGCCTAACTTTT-AGGGGTTTCT
1 TGATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTGA-TTTTCAGGGGTTTCT
114216 TGATG
1 TGATG
114221 ATAACTGTAA
Statistics
Matches: 391, Mismatches: 42, Indels: 8
0.89 0.10 0.02
Matches are distributed among these distances:
53 6 0.02
54 380 0.97
55 5 0.01
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (54 bp):
TGATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCT
Found at i:114962 original size:18 final size:18
Alignment explanation
Indices: 114941--114977 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
114931 TAGGAAGAGT
114941 ATGAAGACTACTCTTGCA
1 ATGAAGACTACTCTTGCA
114959 ATGAAGACTACTCTTGCA
1 ATGAAGACTACTCTTGCA
114977 A
1 A
114978 CCATTTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (18 bp):
ATGAAGACTACTCTTGCA
Found at i:115940 original size:122 final size:124
Alignment explanation
Indices: 115642--115930 Score: 379
Period size: 122 Copynumber: 2.3 Consensus size: 124
115632 TCCAATGAGG
* * *
115642 GAGAAGAAGTTTATAATGAGAAGAACTTGTTCAACATTTGT-TCGATTCCATCACATAATGAGTT
1 GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC-TATGTCTCGATTCCATCACATAAGGAGTT
* * * * *
115706 GGATCAGCACCAGCACTACTTTTGATTCCATCACATAAAGGTTAGGGTTAACATTTTCGA
65 GGATCAACACCAGCACTACGTTTGATTCCATCACATAAAGATTAGGGTCAACATTTCCGA
* **
115766 GAGAAGAAGTTCATAATAAGAAGAACTTGTTCAA-TGCG-CTCGATTCCATCACATAAGGAGTTG
1 GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTATGTCTCGATTCCATCACATAAGGAGTTG
* * * **
115829 GGTCAACACTAGCACTACGTTTGATTCCATCACAT-AAGAATTTGGGTCAATGTTTCCGA
66 GATCAACACCAGCACTACGTTTGATTCCATCACATAAAG-ATTAGGGTCAACATTTCCGA
*
115888 GAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTATGTCTC
1 GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTATGTCTC
115931 ATCTATCACA
Statistics
Matches: 142, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
121 3 0.02
122 102 0.72
123 2 0.01
124 35 0.25
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (124 bp):
GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTATGTCTCGATTCCATCACATAAGGAGTTG
GATCAACACCAGCACTACGTTTGATTCCATCACATAAAGATTAGGGTCAACATTTCCGA
Found at i:117495 original size:2 final size:2
Alignment explanation
Indices: 117488--117525 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
117478 TGTGTTTACG
* *
117488 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
117526 AAGAACACAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:117619 original size:30 final size:29
Alignment explanation
Indices: 117557--117622 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
117547 GTGTCAAGCT
* **
117557 TATATTTATTTATTTTAATAATATATTTA
1 TATATTTATTTATTTTAATAAAATATGAA
* *
117586 TATATTGTATTTGTTTTTATAAAATATGAA
1 TATATT-TATTTATTTTAATAAAATATGAA
117616 TATATTT
1 TATATTT
117623 TATTAAATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 7 0.23
30 24 0.77
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (29 bp):
TATATTTATTTATTTTAATAAAATATGAA
Found at i:120193 original size:7 final size:7
Alignment explanation
Indices: 120181--120224 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
120171 TGAGGTGGAG
120181 TGATTAC
1 TGATTAC
120188 TGATTAC
1 TGATTAC
*
120195 TGTTTAC
1 TGATTAC
120202 TGATTAC
1 TGATTAC
*
120209 TGATTAT
1 TGATTAC
120216 TGA-TAC
1 TGATTAC
120222 TGA
1 TGA
120225 CACTGTATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
6 5 0.15
7 28 0.85
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.45
Consensus pattern (7 bp):
TGATTAC
Found at i:120388 original size:37 final size:37
Alignment explanation
Indices: 120307--120389 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
120297 CGTGTTTCAA
* * * * *
120307 CCAACCCGACCTGACCCGAAAATTATATATCCTTCAC
1 CCAACCTGACCCGACCCGAAAAATATATACCCTCCAC
* *
120344 CTAACCTGACCCGACTCGAAAAATATATACCCTCCAC
1 CCAACCTGACCCGACCCGAAAAATATATACCCTCCAC
*
120381 CCGACCTGA
1 CCAACCTGA
120390 TTTTTTGAGA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.33, C:0.39, G:0.10, T:0.19
Consensus pattern (37 bp):
CCAACCTGACCCGACCCGAAAAATATATACCCTCCAC
Found at i:122614 original size:15 final size:17
Alignment explanation
Indices: 122580--122617 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
122570 TAAGGTGTCC
*
122580 AGTCGAGCTCAAGTTCG
1 AGTCGAGCTCAAGCTCG
122597 AGTCGAG-TCAA-CTCG
1 AGTCGAGCTCAAGCTCG
122612 AGTCGA
1 AGTCGA
122618 TTTTTTATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
16 4 0.20
17 7 0.35
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (17 bp):
AGTCGAGCTCAAGCTCG
Found at i:122870 original size:2 final size:2
Alignment explanation
Indices: 122863--122905 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
122853 ATTATAAAAT
122863 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
122905 T
1 T
122906 TTTATATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:127461 original size:27 final size:25
Alignment explanation
Indices: 127421--127471 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
127411 TGTTTTTTAA
127421 TTAAAAATAATAATT-TACAAATAAT
1 TTAAAAATAATAATTATA-AAATAAT
127446 TTAAATAATATATAATTATAAAATAA
1 TTAAA-AATA-ATAATTATAAAATAA
127472 AAATTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 5 0.22
26 4 0.17
27 12 0.52
28 2 0.09
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (25 bp):
TTAAAAATAATAATTATAAAATAAT
Found at i:131348 original size:18 final size:17
Alignment explanation
Indices: 131325--131358 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
131315 TAAACTCTAT
*
131325 AAAAATATTATATAAAAG
1 AAAAATAATAT-TAAAAG
131343 AAAAATAATATTAAAA
1 AAAAATAATATTAAAA
131359 CAAATCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
AAAAATAATATTAAAAG
Found at i:136107 original size:30 final size:32
Alignment explanation
Indices: 136049--136119 Score: 94
Period size: 31 Copynumber: 2.2 Consensus size: 32
136039 TTAATATGAT
*
136049 TTTTTAAAAATTTAAAGGGATTTAAATTA-AA
1 TTTTTAAAAATTTAAAGGGATCTAAATTATAA
136080 TTTTTAAAAATTGT-AAGGG-TCTAAATTATAA
1 TTTTTAAAAATT-TAAAGGGATCTAAATTATAA
136111 TTTCTTAAA
1 TTT-TTAAA
136120 TTGGGGCATG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
30 8 0.22
31 22 0.61
32 6 0.17
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.44
Consensus pattern (32 bp):
TTTTTAAAAATTTAAAGGGATCTAAATTATAA
Found at i:138679 original size:2 final size:2
Alignment explanation
Indices: 138672--138713 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
138662 AAATCATAAC
138672 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
138714 TCTACTTGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:148728 original size:22 final size:22
Alignment explanation
Indices: 148700--148761 Score: 90
Period size: 22 Copynumber: 2.7 Consensus size: 22
148690 GGTTTTTTAA
148700 AAAAAACCGGATTTTTT-CGGAT
1 AAAAAACCGG-TTTTTTCCGGAT
148722 AAAAAACCGGTTTTTTATCCGGAT
1 AAAAAACCGG-TTTTT-TCCGGAT
148746 AAAAAACCGGTTTTTT
1 AAAAAACCGGTTTTTT
148762 ATCCTGTTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
22 16 0.43
23 6 0.16
24 15 0.41
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (22 bp):
AAAAAACCGGTTTTTTCCGGAT
Found at i:148751 original size:26 final size:25
Alignment explanation
Indices: 148699--148833 Score: 136
Period size: 24 Copynumber: 5.5 Consensus size: 25
148689 CGGTTTTTTA
*
148699 AAAAAAACCGGATTTTT-T-CGGAT
1 AAAAAAACCGGTTTTTTATCCGGAT
148722 -AAAAAACCGGTTTTTTATCCGGAT
1 AAAAAAACCGGTTTTTTATCCGGAT
**
148746 -AAAAAACCGGTTTTTTATCCTGTTT
1 AAAAAAACCGGTTTTTTATCC-GGAT
* * *
148771 GAAAAAACCGGTTTTTTAACCGGTTT
1 AAAAAAACCGGTTTTTTATCCGG-AT
*
148797 GAAAAAAACCGGTTTTTAATCCGG-T
1 -AAAAAAACCGGTTTTTTATCCGGAT
*
148822 AAAAAAATCGGT
1 AAAAAAACCGGT
148834 CGTTCAATTT
Statistics
Matches: 97, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
22 15 0.15
23 1 0.01
24 36 0.37
25 4 0.04
26 21 0.22
27 20 0.21
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.33
Consensus pattern (25 bp):
AAAAAAACCGGTTTTTTATCCGGAT
Found at i:148820 original size:27 final size:26
Alignment explanation
Indices: 148722--148821 Score: 125
Period size: 26 Copynumber: 3.9 Consensus size: 26
148712 TTTTTCGGAT
* *
148722 AAAAAACCGGTTTTTTATCCGG-AT-
1 AAAAAACCGGTTTTTAATCCGGTTTG
* *
148746 AAAAAACCGGTTTTTTATCCTGTTTG
1 AAAAAACCGGTTTTTAATCCGGTTTG
148772 AAAAAACCGGTTTTTTAA-CCGGTTTG
1 AAAAAACCGG-TTTTTAATCCGGTTTG
148798 AAAAAAACCGGTTTTTAATCCGGT
1 -AAAAAACCGGTTTTTAATCCGGT
148822 AAAAAAATCG
Statistics
Matches: 67, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
24 21 0.31
25 1 0.01
26 24 0.36
27 21 0.31
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (26 bp):
AAAAAACCGGTTTTTAATCCGGTTTG
Found at i:152963 original size:41 final size:42
Alignment explanation
Indices: 152905--152983 Score: 142
Period size: 41 Copynumber: 1.9 Consensus size: 42
152895 GTTAGTATTT
152905 ATACGAGACAAATTTTATGGTAGAAGATAAATATATAATCAG
1 ATACGAGACAAATTTTATGGTAGAAGATAAATATATAATCAG
*
152947 ATACG-GACAGATTTTATGGTAGAAGATAAATATATAA
1 ATACGAGACAAATTTTATGGTAGAAGATAAATATATAA
152984 AAAAAAATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
41 31 0.86
42 5 0.14
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (42 bp):
ATACGAGACAAATTTTATGGTAGAAGATAAATATATAATCAG
Found at i:153995 original size:11 final size:11
Alignment explanation
Indices: 153981--154006 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
153971 AGAAGTGAAT
153981 AATTATTTTAA
1 AATTATTTTAA
153992 AATTATTTTAA
1 AATTATTTTAA
154003 AATT
1 AATT
154007 TATGATTCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
AATTATTTTAA
Found at i:154238 original size:13 final size:13
Alignment explanation
Indices: 154222--154246 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
154212 ATACATTATA
154222 AATATTAAATAAT
1 AATATTAAATAAT
154235 AATATTAAATAA
1 AATATTAAATAA
154247 GTTATATATA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATATTAAATAAT
Found at i:156827 original size:3 final size:3
Alignment explanation
Indices: 156805--156854 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
156795 CGAAATTAAT
* *
156805 TAA T-A TAA TATA TAAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TTA
1 TAA TAA TAA TA-A T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
156851 TAA T
1 TAA T
156855 CCTGCAAACC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 33 0.82
4 4 0.10
5 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:161643 original size:28 final size:25
Alignment explanation
Indices: 161612--161663 Score: 59
Period size: 28 Copynumber: 2.0 Consensus size: 25
161602 ATTTCAAAAT
161612 TATAATTATGAGAAAAAAATAATTTATA
1 TATAATTAT-A-AAAAAAAT-ATTTATA
* *
161640 TATATTTATAAATAAAATATTTAT
1 TATAATTATAAAAAAAATATTTAT
161664 TTATTCAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 6 0.27
26 7 0.32
27 1 0.05
28 8 0.36
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (25 bp):
TATAATTATAAAAAAAATATTTATA
Found at i:161675 original size:23 final size:26
Alignment explanation
Indices: 161622--161676 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 26
161612 TATAATTATG
*
161622 AGAAA-AAAATAATTTATATATATTT
1 AGAAATAAAATAATTTATATATATTC
*
161647 ATAAATAAAAT-ATTTAT-T-TATTC
1 AGAAATAAAATAATTTATATATATTC
161670 AGAAATA
1 AGAAATA
161677 TCAGAAAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 10 0.38
24 1 0.04
25 10 0.38
26 5 0.19
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (26 bp):
AGAAATAAAATAATTTATATATATTC
Found at i:161750 original size:23 final size:22
Alignment explanation
Indices: 161726--161770 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
161716 CTTCGATATT
161726 AATAAATATTAATATAATAATTTA
1 AATAAA-ATTAA-ATAATAATTTA
*
161750 AATAAAATTAAATTATAATTT
1 AATAAAATTAAATAATAATTT
161771 TTTTATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AATAAAATTAAATAATAATTTA
Found at i:163356 original size:3 final size:3
Alignment explanation
Indices: 163350--163424 Score: 125
Period size: 3 Copynumber: 24.7 Consensus size: 3
163340 TAATATTTAT
163350 TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
163396 TAA TAA TAA TAA TAA TAA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
163425 TTTAAATGAA
Statistics
Matches: 69, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.03
3 62 0.90
4 5 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:163824 original size:36 final size:36
Alignment explanation
Indices: 163784--163909 Score: 243
Period size: 36 Copynumber: 3.5 Consensus size: 36
163774 TTGAACAAGC
*
163784 TCTTCTCATTGTGAACTTCTTCTTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
163820 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
163856 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
163892 TCTTCTCATTATGAACTT
1 TCTTCTCATTATGAACTT
163910 TCTCTGGAAA
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 89 1.00
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.48
Consensus pattern (36 bp):
TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
Found at i:163844 original size:20 final size:20
Alignment explanation
Indices: 163819--163881 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
163809 TTCAGATGAG
163819 TTCTTCTCATTATGAACTTC
1 TTCTTCTCATTATGAACTTC
* *
163839 TTCTTCTTCA-GATG-A---G
1 TTCTTC-TCATTATGAACTTC
163855 TTCTTCTCATTATGAACTTC
1 TTCTTCTCATTATGAACTTC
163875 TTCTTCT
1 TTCTTCT
163882 TCAGATGAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 12
0.67 0.08 0.24
Matches are distributed among these distances:
15 3 0.09
16 9 0.27
17 1 0.03
19 1 0.03
20 16 0.48
21 3 0.09
ACGTcount: A:0.17, C:0.24, G:0.08, T:0.51
Consensus pattern (20 bp):
TTCTTCTCATTATGAACTTC
Found at i:163986 original size:17 final size:17
Alignment explanation
Indices: 163964--164052 Score: 53
Period size: 17 Copynumber: 5.1 Consensus size: 17
163954 GTTGAACAAA
*
163964 TTCTTCTCATTATGAAT
1 TTCTTCTCATTATGAAC
*
163981 TTCTTCT--TTCA-GACGAG
1 TTCTTCTCATT-ATGA--AC
163998 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
*
164015 TTCTTCTTC-TTCA-GATGAG
1 TTCTTC-TCATT-ATGA--AC
164034 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
164051 TT
1 TT
164053 TCTCTGGAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 24
0.67 0.05 0.29
Matches are distributed among these distances:
15 4 0.07
16 1 0.02
17 29 0.52
18 7 0.12
19 15 0.27
ACGTcount: A:0.20, C:0.21, G:0.10, T:0.48
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:164007 original size:34 final size:36
Alignment explanation
Indices: 163964--164055 Score: 143
Period size: 36 Copynumber: 2.6 Consensus size: 36
163954 GTTGAACAAA
163964 TTCTTCTCATTATGAATTTCTTC-T-TTCAGACGAG
1 TTCTTCTCATTATGAATTTCTTCTTCTTCAGACGAG
* *
163998 TTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAG
1 TTCTTCTCATTATGAATTTCTTCTTCTTCAGACGAG
164034 TTCTTCTCATTATGAACTTTCT
1 TTCTTCTCATTATGAA-TTTCT
164056 CTGGAAAAGT
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
34 22 0.42
35 1 0.02
36 25 0.48
37 4 0.08
ACGTcount: A:0.20, C:0.22, G:0.10, T:0.49
Consensus pattern (36 bp):
TTCTTCTCATTATGAATTTCTTCTTCTTCAGACGAG
Found at i:164017 original size:143 final size:145
Alignment explanation
Indices: 163819--164307 Score: 693
Period size: 143 Copynumber: 3.4 Consensus size: 145
163809 TTCAGATGAG
*
163819 TTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTTCTTC
1 TTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTTCTTC
163884 AGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCTATCAAGTGATGGATTTGAAC
66 AGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCTATCAAGTGATGGATTTGAAC
*
163949 AAAAGGTTGAACAAA
131 AAAAAGTTGAACAAA
*
163964 TTCTTCTCATTATGAATTTCTTC-T-TTCAGACGAGTTCTTCTCATTATGAACTTCTTCTTCTTC
1 TTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTTCTTC
* * *
164027 AGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGGTTTTGAAC
66 AGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCTATCAAGTGATGGATTTGAAC
164092 AAAAAGTTGAACAAA
131 AAAAAGTTGAACAAA
* *
164107 TTCTTCTCATTATGAATTTATTC-T-TTCAGATAAGTTCTTCTCATTATGAACTTCTTCTTCTTC
1 TTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTTCTTC
* **** * * * * * *
164170 AGATGAGTTCTTCTTATTATGAACTCGAACTGGTAATGCTGATATATTGAA-TGAT-GAATTCAA
66 AGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCTA-TCAAGTGATGGATTTGAA
* *
164233 GTAAAAAGTTGAACAAG
130 -CAAAAAGTTGAACAAA
164250 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAA--T-TTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACT
164308 CGAACTGGTA
Statistics
Matches: 309, Mismatches: 27, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
142 5 0.02
143 244 0.79
144 4 0.01
145 23 0.07
146 4 0.01
147 1 0.00
148 1 0.00
149 27 0.09
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (145 bp):
TTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTTCTTC
AGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCTATCAAGTGATGGATTTGAAC
AAAAAGTTGAACAAA
Found at i:164150 original size:34 final size:36
Alignment explanation
Indices: 164107--164194 Score: 126
Period size: 36 Copynumber: 2.5 Consensus size: 36
164097 GTTGAACAAA
*
164107 TTCTTCTCATTATGAATTTATTC-T-TTCAGATAAG
1 TTCTTCTCATTATGAACTTATTCTTCTTCAGATAAG
* *
164141 TTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAG
1 TTCTTCTCATTATGAACTTATTCTTCTTCAGATAAG
*
164177 TTCTTCTTATTATGAACT
1 TTCTTCTCATTATGAACT
164195 CGAACTGGTA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
34 21 0.44
35 1 0.02
36 26 0.54
ACGTcount: A:0.23, C:0.18, G:0.09, T:0.50
Consensus pattern (36 bp):
TTCTTCTCATTATGAACTTATTCTTCTTCAGATAAG
Found at i:164332 original size:113 final size:113
Alignment explanation
Indices: 164138--164646 Score: 918
Period size: 113 Copynumber: 4.5 Consensus size: 113
164128 TCTTTCAGAT
*
164138 AAGTTCTTCTCATTATGAA---CTTCTT-CTTCTTCAGATGAGTTCTTCTTATTATGAACTCGAA
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAA
** ** * *
164199 CTGGTAATGCTGATATATTGAATGATGAATTCAAGTAAAAAGTTGAAC
66 CTGGTAACACTGATCCATTGAATCATGAATTCAAGCAAAAAGTTGAAC
164247 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAA
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAA
164312 CTGGTAACACTGATCCATTGAATCATGAATTCAAGCAAAAAGTTGAAC
66 CTGGTAACACTGATCCATTGAATCATGAATTCAAGCAAAAAGTTGAAC
164360 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAA
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAA
*
164425 CTGGTAACACTGATCCATTAAATCATGAATTCAAGCAAAAAGTTGAAC
66 CTGGTAACACTGATCCATTGAATCATGAATTCAAGCAAAAAGTTGAAC
164473 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAA
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAA
164538 CTGGTAACACTGATCCATTGAATCATGAATTCAAGCAAAAAGTTGAAC
66 CTGGTAACACTGATCCATTGAATCATGAATTCAAGCAAAAAGTTGAAC
164586 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
164647 TTTTTTCTGG
Statistics
Matches: 387, Mismatches: 9, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
109 19 0.05
112 6 0.02
113 362 0.94
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.37
Consensus pattern (113 bp):
AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAA
CTGGTAACACTGATCCATTGAATCATGAATTCAAGCAAAAAGTTGAAC
Found at i:165552 original size:116 final size:114
Alignment explanation
Indices: 165374--165604 Score: 347
Period size: 116 Copynumber: 2.0 Consensus size: 114
165364 GATCATGCAG
* * * *
165374 TTCATCTTTTAATTCCAATGATTGGTTTTGTGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTAAATTCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* * *
165439 ACACTTTCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACA
66 ACACTTCCAGAAGATGCTATTGGGCCCTCTTATTTCTACTATGAGCACA
* *
165488 TTCATCTTTCAAATT-CAATGATTAGTTTTTCGGGGTTCATATCAAACCAGATCAGATAACTCAA
1 TTCATCTTT-AAATTCCAATGATT-GGTTTT-GGGGTTCATACCAAACCAGATCAGATAACTCAA
165552 AGAACACTTCCAGAAGATGCTATTGGGCCCTCTTATTTCTACTATGAGCACA
63 AGAACACTTCCAGAAGATGCTATTGGGCCCTCTTATTTCTACTATGAGCACA
165604 T
1 T
165605 GGCACTTGCT
Statistics
Matches: 105, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
114 17 0.16
115 9 0.09
116 79 0.75
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (114 bp):
TTCATCTTTAAATTCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGCCCTCTTATTTCTACTATGAGCACA
Found at i:166886 original size:7 final size:7
Alignment explanation
Indices: 166874--166936 Score: 74
Period size: 7 Copynumber: 8.9 Consensus size: 7
166864 TCTTGACACC
166874 CTTTTTT
1 CTTTTTT
166881 CTTTTTT
1 CTTTTTT
*
166888 CTCTTTT
1 CTTTTTT
166895 -TTTTTT
1 CTTTTTT
*
166901 CTTTCTT
1 CTTTTTT
166908 CTTTCTTCT
1 CTTT-TT-T
*
166917 TTTTTTT
1 CTTTTTT
166924 CTTTTTT
1 CTTTTTT
166931 CTTTTT
1 CTTTTT
166937 CTTCAAGCAT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
6 5 0.11
7 35 0.74
8 3 0.06
9 4 0.09
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (7 bp):
CTTTTTT
Found at i:166898 original size:11 final size:11
Alignment explanation
Indices: 166882--166930 Score: 55
Period size: 11 Copynumber: 4.3 Consensus size: 11
166872 CCCTTTTTTC
166882 TTTTTTCTCTT
1 TTTTTTCTCTT
*
166893 TTTTTTTTCTT
1 TTTTTTCTCTT
166904 TCTTCTTTCTTCTT
1 T-TT-TTTC-TCTT
166918 TTTTTTCT-TT
1 TTTTTTCTCTT
166928 TTT
1 TTT
166931 CTTTTTCTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
10 5 0.15
11 12 0.36
12 6 0.18
13 5 0.15
14 5 0.15
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTCTCTT
Found at i:178250 original size:23 final size:22
Alignment explanation
Indices: 178226--178270 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
178216 CTTCGATATT
178226 AATAAATATTAATATAATAATTTA
1 AATAAA-ATTAA-ATAATAATTTA
*
178250 AATAAAATTAAATTATAATTT
1 AATAAAATTAAATAATAATTT
178271 TTTATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AATAAAATTAAATAATAATTTA
Found at i:179864 original size:3 final size:3
Alignment explanation
Indices: 179858--179903 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
179848 TAATATTTAT
179858 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
179902 TA
1 TA
179904 TTTAAATGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.10
3 34 0.85
4 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:188066 original size:21 final size:21
Alignment explanation
Indices: 188041--188080 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
188031 AGTATGTTCA
*
188041 GGGGGTATCGATTCCCCCTGG
1 GGGGGAATCGATTCCCCCTGG
188062 GGGGGAATCGATTCCCCCT
1 GGGGGAATCGATTCCCCCT
188081 AAAGGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.30, G:0.35, T:0.23
Consensus pattern (21 bp):
GGGGGAATCGATTCCCCCTGG
Found at i:196558 original size:4 final size:4
Alignment explanation
Indices: 196543--196580 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
196533 AACTGTAAAT
* *
196543 ATAC ACAC ATAC ATAC ATAA ATAC ATAC A-AC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
196581 TATATATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (4 bp):
ATAC
Found at i:198884 original size:29 final size:29
Alignment explanation
Indices: 198835--198945 Score: 73
Period size: 29 Copynumber: 3.8 Consensus size: 29
198825 TTATAACCCT
* *
198835 TATTTTAA-ATTAGTCCTTAAACTTTTAAA
1 TATTTTAATTTTA-TCCCTAAACTTTTAAA
* * *
198864 TATTTTAATTTTATCCCTAAACTATGACTAT
1 TATTTTAATTTTATCCCTAAACTTTTA--AA
* * * *
198895 TGTTTTAAATTAAT-CCTTAACTTTTAAA
1 TATTTTAATTTTATCCCTAAACTTTTAAA
* * *
198923 CATTCTAATTTCATCCCTAAACT
1 TATTTTAATTTTATCCCTAAACT
198946 ATGACTCTCT
Statistics
Matches: 60, Mismatches: 18, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
28 10 0.17
29 26 0.43
30 12 0.20
31 12 0.20
ACGTcount: A:0.34, C:0.16, G:0.03, T:0.47
Consensus pattern (29 bp):
TATTTTAATTTTATCCCTAAACTTTTAAA
Found at i:198903 original size:60 final size:60
Alignment explanation
Indices: 198837--198997 Score: 200
Period size: 59 Copynumber: 2.7 Consensus size: 60
198827 ATAACCCTTA
*
198837 TTTTAAATTAGTCCTTAAACTTTTAAATATTTTAATTTTATCCCTAAACTATGACTAT-T
1 TTTTAAATTAGTCCTTAAACTTTTAAATATTTTAATTTCATCCCTAAACTATGACTATCT
* * * *
198896 GTTTTAAATTAATCCTT-AACTTTTAAACATTCTAATTTCATCCCTAAACTATGACTCTCT
1 -TTTTAAATTAGTCCTTAAACTTTTAAATATTTTAATTTCATCCCTAAACTATGACTATCT
* * * * * *
198956 TTCTAAATTGGTCCCTAACCTTTTGAATAATTTAATTTCATC
1 TTTTAAATTAGTCCTTAAACTTTTAAATATTTTAATTTCATC
198998 TCCAAATTCA
Statistics
Matches: 85, Mismatches: 14, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
59 49 0.58
60 36 0.42
ACGTcount: A:0.32, C:0.18, G:0.04, T:0.46
Consensus pattern (60 bp):
TTTTAAATTAGTCCTTAAACTTTTAAATATTTTAATTTCATCCCTAAACTATGACTATCT
Found at i:199469 original size:82 final size:83
Alignment explanation
Indices: 199357--199512 Score: 260
Period size: 82 Copynumber: 1.9 Consensus size: 83
199347 TTTTACAAAA
*
199357 AAAATGCCGCAATAGAGTGGTAAATTAGCGGCGTTTATACCACAAACGCCGCAATAGATTA-ACA
1 AAAACGCCGCAATAGAGTGGTAAATTAGCGGCGTTTATACCACAAACGCCGCAATAGATTACACA
199421 TATAGTGGCGTTTTAGCC
66 TATAGTGGCGTTTTAGCC
* * * *
199439 AAAACGCCGCAATAGATTGGTAAATTAGCGGTGTTTATACCACAAATGCCGTAATAGATTACACA
1 AAAACGCCGCAATAGAGTGGTAAATTAGCGGCGTTTATACCACAAACGCCGCAATAGATTACACA
199504 TATAGTGGC
66 TATAGTGGC
199513 ATTTATTCTT
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
82 56 0.82
83 12 0.18
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (83 bp):
AAAACGCCGCAATAGAGTGGTAAATTAGCGGCGTTTATACCACAAACGCCGCAATAGATTACACA
TATAGTGGCGTTTTAGCC
Found at i:199518 original size:42 final size:41
Alignment explanation
Indices: 199386--199518 Score: 148
Period size: 42 Copynumber: 3.2 Consensus size: 41
199376 GTAAATTAGC
199386 GGCGTTTATACCACAAACGCCGCAATAGATTAACATATAGT
1 GGCGTTTATACCACAAACGCCGCAATAGATTAACATATAGT
*
199427 GGCGTTT-TAGCCA-AAACGCCGCAATAGATTGGTAA-AT-TAGC
1 GGCGTTTATA-CCACAAACGCCGCAATAGA-T--TAACATATAGT
* * *
199468 GGTGTTTATACCACAAATGCCGTAATAGATTACACATATAGT
1 GGCGTTTATACCACAAACGCCGCAATAGATTA-ACATATAGT
*
199510 GGCATTTAT
1 GGCGTTTAT
199519 TCTTAAAACG
Statistics
Matches: 76, Mismatches: 7, Indels: 17
0.76 0.07 0.17
Matches are distributed among these distances:
39 2 0.03
40 18 0.24
41 26 0.34
42 27 0.36
43 3 0.04
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.28
Consensus pattern (41 bp):
GGCGTTTATACCACAAACGCCGCAATAGATTAACATATAGT
Found at i:199579 original size:41 final size:41
Alignment explanation
Indices: 199505--199681 Score: 180
Period size: 40 Copynumber: 4.3 Consensus size: 41
199495 GATTACACAT
*** * * * *
199505 ATAGTGGCATTTATTCTTAAAACGTCGCAATAGTGATAATAA
1 ATAGTGGCATTT-TTAGAAAAACGCCACAATAGTGTTAATCA
* *
199547 ATAGTGGCATTTTTAGATAAACGCCACAATAGTGTTAATTA
1 ATAGTGGCATTTTTAGAAAAACGCCACAATAGTGTTAATCA
* * * *
199588 ATAGTGGC-GTTTTAGAAAAAAGTCACAATAGTTTTAATCA
1 ATAGTGGCATTTTTAGAAAAACGCCACAATAGTGTTAATCA
*
199628 ATAGTGGCATTTTTTA-ACAAACGCCACAATAGTG-TAATCA
1 ATAGTGGCA-TTTTTAGAAAAACGCCACAATAGTGTTAATCA
*
199668 ATAGTGGCGTTTTT
1 ATAGTGGCATTTTT
199682 TTGTATAAAC
Statistics
Matches: 113, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
39 5 0.04
40 48 0.42
41 43 0.38
42 17 0.15
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (41 bp):
ATAGTGGCATTTTTAGAAAAACGCCACAATAGTGTTAATCA
Found at i:199632 original size:81 final size:80
Alignment explanation
Indices: 199523--199680 Score: 228
Period size: 81 Copynumber: 2.0 Consensus size: 80
199513 ATTTATTCTT
* * * *
199523 AAAACGTCGCAATAGTGATAATAAATAGTGGCA-TTTTTAGATAAACGCCACAATAGTGTTAATT
1 AAAAAGTCACAATAGTGATAATAAATAGTGGCATTTTTTA-ACAAACGCCACAATAGTG-TAATC
199587 AATAGTGGCGTTTTAGA
64 AATAGTGGCGTTTTAGA
** *
199604 AAAAAGTCACAATAGTTTTAATCAATAGTGGCATTTTTTAACAAACGCCACAATAGTGTAATCAA
1 AAAAAGTCACAATAGTGATAATAAATAGTGGCATTTTTTAACAAACGCCACAATAGTGTAATCAA
199669 TAGTGGCGTTTT
66 TAGTGGCGTTTT
199681 TTTGTATAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
80 18 0.26
81 45 0.65
82 6 0.09
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.32
Consensus pattern (80 bp):
AAAAAGTCACAATAGTGATAATAAATAGTGGCATTTTTTAACAAACGCCACAATAGTGTAATCAA
TAGTGGCGTTTTAGA
Found at i:201104 original size:41 final size:41
Alignment explanation
Indices: 201024--201345 Score: 258
Period size: 41 Copynumber: 7.8 Consensus size: 41
201014 TTGTCATTTA
* * *
201024 TAGTGGCGTTTTTCCA-ATAAACGTCGCTATAG-GTACGTACTT
1 TAGTGGCGTTTTT--ATACAAACGCCGCTATAGAAT-CGTACTT
* *
201066 TAGTGGCGTTTTTATACAAACACCGCTATAGAATCGTACGT
1 TAGTGGCGTTTTTATACAAACGCCGCTATAGAATCGTACTT
** * *
201107 TAGTGGCGTTTTTATACAAACGCTACTATATAATAGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTATAGAATCGTACTT
* * * * *
201148 TAGTGGCGTTTCTATACAAACGCTGCTATATACTCATACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTATAGAATCGTACTT
* * * *
201189 TAGTGGCGCTTTGA-ATCTAAATGTCGCTATA-AACTCGTACTT
1 TAGTGGCGTTTTTATA-C-AAACGCCGCTATAGAA-TCGTACTT
* * * * * *
201231 TAGTGGCATTTTGAATGA-AAATGCCGCTAAAGACTTGTACTT
1 TAGTGGCGTTTT-TAT-ACAAACGCCGCTATAGAATCGTACTT
** * * * *
201273 TAGCAGCGTTTTTATATAAACGTCGCTATAGACTAGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTATAGAATCGTACTT
*
201314 TAGTGGCGTTTTTATACAAACGCCGCAATAGA
1 TAGTGGCGTTTTTATACAAACGCCGCTATAGA
201346 TATAATATTT
Statistics
Matches: 226, Mismatches: 44, Indels: 21
0.78 0.15 0.07
Matches are distributed among these distances:
40 3 0.01
41 152 0.67
42 68 0.30
43 2 0.01
45 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (41 bp):
TAGTGGCGTTTTTATACAAACGCCGCTATAGAATCGTACTT
Found at i:201361 original size:41 final size:41
Alignment explanation
Indices: 201278--201400 Score: 131
Period size: 43 Copynumber: 3.0 Consensus size: 41
201268 TACTTTAGCA
* * * * *
201278 GCGTTTTTATATAAACGTCGCTATAGA-CTAGTACTTTAGTG
1 GCGTTTTTATATAAACGCCGCAATAGATATAATA-TTTTGTG
*
201319 GCGTTTTTATACAAACGCCGCAATAGATATAATATTTTGTG
1 GCGTTTTTATATAAACGCCGCAATAGATATAATATTTTGTG
* * *
201360 GCATTTTTTTAGATAAACGCCACAATAGATATAATATTTTG
1 GC--GTTTTTATATAAACGCCGCAATAGATATAATATTTTG
201401 CAAAAAACGT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
41 32 0.46
42 4 0.06
43 33 0.48
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (41 bp):
GCGTTTTTATATAAACGCCGCAATAGATATAATATTTTGTG
Found at i:210176 original size:21 final size:22
Alignment explanation
Indices: 210132--210176 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
210122 ATGTTTTAAA
*
210132 TTTACCTGACTTTATTTATATT
1 TTTACCTGACATTATTTATATT
210154 TTTACCATGACATT-TTT-TATT
1 TTTACC-TGACATTATTTATATT
210175 TT
1 TT
210177 AATTAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 9 0.43
23 6 0.29
ACGTcount: A:0.22, C:0.13, G:0.04, T:0.60
Consensus pattern (22 bp):
TTTACCTGACATTATTTATATT
Found at i:210517 original size:21 final size:21
Alignment explanation
Indices: 210484--210617 Score: 112
Period size: 21 Copynumber: 6.4 Consensus size: 21
210474 AACGGAAAAT
*
210484 GAAGCAAG-GGAAGCAGAGAGA
1 GAAGC-AGCGGAAGCACAGAGA
* * *
210505 GCAGCAGCAGAAGCA-ACCAGA
1 GAAGCAGCGGAAGCACA-GAGA
* * *
210526 GTAGCAGCGGAAGCAGAGAAA
1 GAAGCAGCGGAAGCACAGAGA
* *
210547 GAAACAGCGGCAGCACAGAGA
1 GAAGCAGCGGAAGCACAGAGA
*
210568 GAAGCAGCGGTAGCACAGAGA
1 GAAGCAGCGGAAGCACAGAGA
* *
210589 GAAGCAAC-GACAGTACAGAGA
1 GAAGCAGCGGA-AGCACAGAGA
210610 GAAGCAGC
1 GAAGCAGC
210618 ATATCAGCAG
Statistics
Matches: 91, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
20 4 0.04
21 86 0.95
22 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.35, T:0.02
Consensus pattern (21 bp):
GAAGCAGCGGAAGCACAGAGA
Found at i:210628 original size:21 final size:19
Alignment explanation
Indices: 210562--210630 Score: 50
Period size: 21 Copynumber: 3.3 Consensus size: 19
210552 AGCGGCAGCA
210562 CAGAGAGAAGCAGCGGTAGCA-
1 CAGAGAGAAGCAGC--TA-CAG
* *
210583 CAGAGAGAAGCAACGACAG
1 CAGAGAGAAGCAGCTACAG
210602 TACAGAGAGAAGCAGCATATCAG
1 --CAGAGAGAAGCAGC-TA-CAG
210625 CAGAGA
1 CAGAGA
210631 TGTGAAGAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
18 2 0.05
19 1 0.03
21 32 0.82
22 1 0.03
23 3 0.08
ACGTcount: A:0.43, C:0.19, G:0.32, T:0.06
Consensus pattern (19 bp):
CAGAGAGAAGCAGCTACAG
Found at i:211117 original size:43 final size:42
Alignment explanation
Indices: 211043--211293 Score: 222
Period size: 43 Copynumber: 5.8 Consensus size: 42
211033 GCCGTAAAAC
** * * *
211043 ATCAACACCTGCTGCGACGTTTGTGA-AAAAAACGTCGCTAAAC
1 ATCAACACCTATTGCGGCGTTTGT-ATGAAAAACG-CGCTAAAT
**
211086 ATCATA-ACCTATTATGGCGTTTGTATGAAAAACGCTGCTAAAT
1 ATCA-ACACCTATTGCGGCGTTTGTATGAAAAACGC-GCTAAAT
* * *
211129 ATCAACTCCTATTGCGGCGTTTTTAT-AACAAACGCCACTAAAT
1 ATCAACACCTATTGCGGCGTTTGTATGAA-AAACG-CGCTAAAT
* *
211172 ATCAACACCTATTGCGGCGTTTGTCTGAAAAACGCTGTTAAAT
1 ATCAACACCTATTGCGGCGTTTGTATGAAAAACGC-GCTAAAT
* * *
211215 ATCAACACCTATTGCGGTGTTTGTCA-CACAAACGCCGCTAAAT
1 ATCAACACCTATTGCGGCGTTTGT-ATGAAAAACG-CGCTAAAT
* * *
211258 ATCAATACCTATTGCGGCGTTTTTTGTGAAAAACGC
1 ATCAACACCTATTGCGGCG-TTTGTATGAAAAACGC
211294 CGCGAACTTT
Statistics
Matches: 168, Mismatches: 28, Indels: 24
0.76 0.13 0.11
Matches are distributed among these distances:
42 6 0.04
43 147 0.88
44 15 0.09
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.29
Consensus pattern (42 bp):
ATCAACACCTATTGCGGCGTTTGTATGAAAAACGCGCTAAAT
Found at i:211150 original size:86 final size:86
Alignment explanation
Indices: 211043--211293 Score: 290
Period size: 86 Copynumber: 2.9 Consensus size: 86
211033 GCCGTAAAAC
** * * * * * **
211043 ATCAACACCTGCTGCGACGTTTGTGAAAAAAACGTCGCTAAACATCATA-ACCTATTATGGCGTT
1 ATCAACACCTATTGCGGCGTTTGTCAAACAAACGCCGCTAAATATCA-ACACCTATTGCGGCGTT
211107 TGTATGAAAAACGCTGCTAAAT
65 TGTATGAAAAACGCTGCTAAAT
* * *
211129 ATCAACTCCTATTGCGGCGTTT-TTATAACAAACGCCACTAAATATCAACACCTATTGCGGCGTT
1 ATCAACACCTATTGCGGCGTTTGTCA-AACAAACGCCGCTAAATATCAACACCTATTGCGGCGTT
* *
211193 TGTCTGAAAAACGCTGTTAAAT
65 TGTATGAAAAACGCTGCTAAAT
* * *
211215 ATCAACACCTATTGCGGTGTTTGTCACACAAACGCCGCTAAATATCAATACCTATTGCGGCGTTT
1 ATCAACACCTATTGCGGCGTTTGTCAAACAAACGCCGCTAAATATCAACACCTATTGCGGCG-TT
* *
211280 TTTGTGAAAAACGC
65 TGTATGAAAAACGC
211294 CGCGAACTTT
Statistics
Matches: 140, Mismatches: 21, Indels: 7
0.83 0.12 0.04
Matches are distributed among these distances:
85 3 0.02
86 121 0.86
87 16 0.11
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.29
Consensus pattern (86 bp):
ATCAACACCTATTGCGGCGTTTGTCAAACAAACGCCGCTAAATATCAACACCTATTGCGGCGTTT
GTATGAAAAACGCTGCTAAAT
Found at i:211163 original size:129 final size:129
Alignment explanation
Indices: 211014--211281 Score: 285
Period size: 129 Copynumber: 2.1 Consensus size: 129
211004 AGACCTGAAC
* * * * *
211014 CGGCGTTTTTAGCAGAAACGCC-GTAAAACATCAACACCTGCTGCGACGTTTGTGAAAAAAACG-
1 CGGCGTTTTTAGAACAAACGCCACT-AAACATCAACACCTACTGCGACGTTTGTCAAAAAAACGC
* * *
211077 TCGCTAAACATCATA-ACCTATTATGGCGTTTGT-ATGAAAAACGCTGCTAAATATCAACT-CCT
65 T-GCTAAACATCA-ACACCTATTACGGCGTTTGTCA-CAAAAACGCCGCTAAATATCAA-TACCT
211139 ATTG
126 ATTG
* * * * **
211143 CGGCGTTTTTATAACAAACGCCACTAAATATCAACACCTATTGCGGCGTTTGTCTGAAAAACGCT
1 CGGCGTTTTTAGAACAAACGCCACTAAACATCAACACCTACTGCGACGTTTGTCAAAAAAACGCT
* * * * *
211208 GTTAAATATCAACACCTATTGCGGTGTTTGTCACACAAACGCCGCTAAATATCAATACCTATTG
66 GCTAAACATCAACACCTATTACGGCGTTTGTCACAAAAACGCCGCTAAATATCAATACCTATTG
211272 CGGCGTTTTT
1 CGGCGTTTTT
211282 TGTGAAAAAC
Statistics
Matches: 115, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
128 2 0.02
129 110 0.96
130 3 0.03
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.28
Consensus pattern (129 bp):
CGGCGTTTTTAGAACAAACGCCACTAAACATCAACACCTACTGCGACGTTTGTCAAAAAAACGCT
GCTAAACATCAACACCTATTACGGCGTTTGTCACAAAAACGCCGCTAAATATCAATACCTATTG
Found at i:225625 original size:20 final size:20
Alignment explanation
Indices: 225602--225653 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
225592 CCATATCCTT
225602 GGTATCGATACCAGCCTTAC
1 GGTATCGATACCAGCCTTAC
*
225622 GGTATCAATACCAGCCTTAC
1 GGTATCGATACCAGCCTTAC
225642 GGTATCGATACC
1 GGTATCGATACC
225654 CTATCCAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (20 bp):
GGTATCGATACCAGCCTTAC
Found at i:225866 original size:20 final size:20
Alignment explanation
Indices: 225816--225870 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
225806 AAAACCAACT
*
225816 AAAAGTATCGATACTAGCTC
1 AAAAGTATCGATACTACCTC
*
225836 AAGAGTATCGATACT-CCTGC
1 AAAAGTATCGATACTACCT-C
*
225856 AAAAGTTTCGATACT
1 AAAAGTATCGATACT
225871 TTATATAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (20 bp):
AAAAGTATCGATACTACCTC
Found at i:229050 original size:7 final size:7
Alignment explanation
Indices: 229037--229092 Score: 58
Period size: 7 Copynumber: 7.7 Consensus size: 7
229027 ACATCCGAAC
229037 ATAAAAT
1 ATAAAAT
*
229044 TTAAAATT
1 ATAAAA-T
*
229052 TTAAAAT
1 ATAAAAT
229059 ATAAAAT
1 ATAAAAT
229066 ATAAAAT
1 ATAAAAT
229073 ATAATAAT
1 ATAA-AAT
* *
229081 CTATAAT
1 ATAAAAT
229088 ATAAA
1 ATAAA
229093 TAAAACATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
7 29 0.71
8 12 0.29
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (7 bp):
ATAAAAT
Found at i:229428 original size:2 final size:2
Alignment explanation
Indices: 229421--229472 Score: 83
Period size: 2 Copynumber: 27.5 Consensus size: 2
229411 ATAATTGAAT
229421 TA TA TA TA TA TA TA TA TA TA -A TA TA TA T- TA TA -A 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
229460 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
229473 GACTAATCGG
Statistics
Matches: 47, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.06
2 44 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:241244 original size:28 final size:29
Alignment explanation
Indices: 241213--241275 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
241203 CAAATATTCA
*
241213 AAAAATTATAA-ATAAAAATT-AAATTACT
1 AAAAATTA-AATATAAAAATTAAAAATACT
**
241241 AAAAATTAAATATAAGTATTAAAAATACT
1 AAAAATTAAATATAAAAATTAAAAATACT
241270 AAAAAT
1 AAAAAT
241276 GTTATAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 2 0.07
28 15 0.50
29 13 0.43
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (29 bp):
AAAAATTAAATATAAAAATTAAAAATACT
Found at i:241364 original size:18 final size:18
Alignment explanation
Indices: 241333--241379 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
241323 TGATAATAAT
241333 TATTA-AAAATATTAAAAA
1 TATTATAAAA-ATTAAAAA
* * *
241351 TATTTTAAAAATTATATA
1 TATTATAAAAATTAAAAA
241369 TATTATAAAAA
1 TATTATAAAAA
241380 ATAATATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TATTATAAAAATTAAAAA
Found at i:241370 original size:2 final size:2
Alignment explanation
Indices: 241363--241413 Score: 56
Period size: 2 Copynumber: 27.5 Consensus size: 2
241353 TTTTAAAAAT
* *
241363 TA TA TA TA T- TA TA -A AA AA TA -A 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
241402 TA TA TA TA -A TA T
1 TA TA TA TA TA TA T
241414 GTTATAAAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
1 4 0.09
2 40 0.91
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:241409 original size:104 final size:106
Alignment explanation
Indices: 241291--241482 Score: 336
Period size: 104 Copynumber: 1.8 Consensus size: 106
241281 AAAAAATAAA
241291 ATATATATATATATAATATGTTATAAAATAATTGA-TAATAATTATTAAAAATATTAAAAATATT
1 ATATATATATATATAATATGTTATAAAATAATT-ACTAATAATTATTAAAAATATTAAAAATATT
*
241355 TTAAAAATTATATA-TAT-TATAAAAAATAATATATATATAT
65 TTAAAAATGATATATTATATATAAAAAATAATATATATATAT
*
241395 ATATATATATATATAATATGTTATAAAATAATTACTTATAATTATTAAAAATATTAAAAATATTT
1 ATATATATATATATAATATGTTATAAAATAATTACTAATAATTATTAAAAATATTAAAAATATTT
241460 TAAAAATGATATATTATATATAA
66 TAAAAATGATATATTATATATAA
241483 CATATAGGCA
Statistics
Matches: 83, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
103 1 0.01
104 74 0.89
105 3 0.04
106 5 0.06
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.43
Consensus pattern (106 bp):
ATATATATATATATAATATGTTATAAAATAATTACTAATAATTATTAAAAATATTAAAAATATTT
TAAAAATGATATATTATATATAAAAAATAATATATATATAT
Found at i:242232 original size:25 final size:25
Alignment explanation
Indices: 242176--242232 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
242166 GTAAGTTTTG
*
242176 ACTAATCTAAAATTTATAAGTCTCA
1 ACTAATTTAAAATTTATAAGTCTCA
* *
242201 ACTAATTTAAATTTTGTAAGTCTCA
1 ACTAATTTAAAATTTATAAGTCTCA
*
242226 ATTAATT
1 ACTAATT
242233 CAATAAAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (25 bp):
ACTAATTTAAAATTTATAAGTCTCA
Found at i:242688 original size:77 final size:77
Alignment explanation
Indices: 242603--242768 Score: 210
Period size: 77 Copynumber: 2.2 Consensus size: 77
242593 TTCGATATTC
* * * * *
242603 CAAATTCGCAACGCGAATATGT-AAA-TCGCAACGCTGATTACCGATGTAGGTAAACAGTACTAT
1 CAAATTCGCAACGAG-AT-TGTCAAATTAGCAACGCTAATTACAGATATAGGTAAACAGTACTAT
* * *
242666 CGCAACGAGATTTT
64 CACAACGAGAATTA
*
242680 CAAATTCGCAACGAGATTTTCAAATTAGCAACGCTAATTACAGATATAGGTAAACAGTACTATCA
1 CAAATTCGCAACGAGATTGTCAAATTAGCAACGCTAATTACAGATATAGGTAAACAGTACTATCA
*
242745 CAACGCGAATTA
66 CAACGAGAATTA
242757 CAAATTCGCAAC
1 CAAATTCGCAAC
242769 ACTAATTACC
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
75 2 0.03
76 5 0.06
77 70 0.91
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (77 bp):
CAAATTCGCAACGAGATTGTCAAATTAGCAACGCTAATTACAGATATAGGTAAACAGTACTATCA
CAACGAGAATTA
Found at i:242690 original size:20 final size:20
Alignment explanation
Indices: 242665--242712 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
242655 AACAGTACTA
242665 TCGCAACGAGATTTTCAAAT
1 TCGCAACGAGATTTTCAAAT
242685 TCGCAACGAGATTTTCAAAT
1 TCGCAACGAGATTTTCAAAT
*
242705 TAGCAACG
1 TCGCAACG
242713 CTAATTACAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (20 bp):
TCGCAACGAGATTTTCAAAT
Found at i:242776 original size:57 final size:57
Alignment explanation
Indices: 242700--242830 Score: 201
Period size: 57 Copynumber: 2.3 Consensus size: 57
242690 ACGAGATTTT
* *
242700 CAAATTAGCAACGCTAATTACAGATATAGGTAAACAGTACTATCA-CAACGCGAATTA
1 CAAATTCGCAACGCTAATTACAGATATAGGTAAACAATACTAT-AGCAACGCGAATTA
* * *
242757 CAAATTCGCAACACTAATTACCGATATAGGTAAACAATACTATAGCAACGCGATTTA
1 CAAATTCGCAACGCTAATTACAGATATAGGTAAACAATACTATAGCAACGCGAATTA
242814 CAAATTCGCAACGCTAA
1 CAAATTCGCAACGCTAA
242831 GGTACGGGTA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
56 1 0.01
57 66 0.99
ACGTcount: A:0.43, C:0.21, G:0.13, T:0.23
Consensus pattern (57 bp):
CAAATTCGCAACGCTAATTACAGATATAGGTAAACAATACTATAGCAACGCGAATTA
Found at i:244045 original size:58 final size:58
Alignment explanation
Indices: 243952--244076 Score: 180
Period size: 58 Copynumber: 2.2 Consensus size: 58
243942 GTGGTTGCAG
* * * **
243952 CACGA-TTTACAAATTCGCAACGCTAATTACCGATATAGGTGAACAGTGTTATCGCAA
1 CACGATTTTCCAAAATCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAA
* *
244009 CGCGATTTTCCAAAATCGCAACGCTAATTACTGATATAGGTAAACAGTACTATCGCAA
1 CACGATTTTCCAAAATCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAA
244067 CACGATTTTC
1 CACGATTTTC
244077 AAATTCGTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
57 4 0.07
58 55 0.93
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.27
Consensus pattern (58 bp):
CACGATTTTCCAAAATCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAA
Found at i:244127 original size:20 final size:20
Alignment explanation
Indices: 244061--244128 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
244051 AACAGTACTA
244061 TCGCAACACGATTTTCAAAT
1 TCGCAACACGATTTTCAAAT
* ** *
244081 TCGTAACAAAATTTTCAAAAA
1 TCGCAACACGATTTTC-AAAT
*
244102 TCGCAACACGATTTTCGAAT
1 TCGCAACACGATTTTCAAAT
244122 TCGCAAC
1 TCGCAAC
244129 GCTAATTACC
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.28
Consensus pattern (20 bp):
TCGCAACACGATTTTCAAAT
Found at i:244137 original size:98 final size:99
Alignment explanation
Indices: 244002--244185 Score: 298
Period size: 98 Copynumber: 1.9 Consensus size: 99
243992 GAACAGTGTT
* *
244002 ATCGCAACGCGATTTTCCAAAATCGCAACGCTAATTACTGATATAGGTAAACAGTACTATCGCAA
1 ATCGCAACACGATTTTCCAAAATCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAA
244067 CACGATTTTCAAATTCGTAACAAAATTTTCAAAA
66 CACGATTTTCAAATTCGTAACAAAATTTTCAAAA
* * * **
244101 ATCGCAACACGATTTT-CGAATTCGCAACGCTAATTACCGATTTAGGTAAACAGTGTTATCGCAA
1 ATCGCAACACGATTTTCCAAAATCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAA
244165 CACGATTTTCAAATTCGTAAC
66 CACGATTTTCAAATTCGTAAC
244186 GTGATTTTCA
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
98 63 0.81
99 15 0.19
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (99 bp):
ATCGCAACACGATTTTCCAAAATCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAA
CACGATTTTCAAATTCGTAACAAAATTTTCAAAA
Found at i:244193 original size:20 final size:20
Alignment explanation
Indices: 244168--244206 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
244158 ATCGCAACAC
*
244168 GATTTTCAAATTCGTAACGT
1 GATTTTCAAATTCGCAACGT
244188 GATTTTCAAATTCGCAACG
1 GATTTTCAAATTCGCAACG
244207 CTAATTACTG
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:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (20 bp):
GATTTTCAAATTCGCAACGT
Found at i:244268 original size:20 final size:20
Alignment explanation
Indices: 244243--244284 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
244233 CTATCGCAAC
244243 GCGATTTTGGAAACTGTGTT
1 GCGATTTTGGAAACTGTGTT
*
244263 GCGATTTTGGAACCTGTGTT
1 GCGATTTTGGAAACTGTGTT
244283 GC
1 GC
244285 AAAATTAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.17, C:0.14, G:0.31, T:0.38
Consensus pattern (20 bp):
GCGATTTTGGAAACTGTGTT
Found at i:244270 original size:77 final size:77
Alignment explanation
Indices: 244091--244250 Score: 212
Period size: 77 Copynumber: 2.1 Consensus size: 77
244081 TCGTAACAAA
* * * * * *
244091 ATTTTCAAAAATCGCAACACGATTTTCGAATTCGCAACGCTAATTACCGATTTAGGTAAACAGTG
1 ATTTTC-AAACTCGTAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTA
*
244156 TTATCGCAACACG
65 CTATCGCAACACG
* * *
244169 ATTTTCAAATTCGTAACGTGATTTTCAAATTCGCAACGCTAATTACTGATATAGGTAAACAGTAC
1 ATTTTCAAACTCGTAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTAC
*
244234 TATCGCAACGCG
66 TATCGCAACACG
244246 ATTTT
1 ATTTT
244251 GGAAACTGTG
Statistics
Matches: 72, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
77 66 0.92
78 6 0.08
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (77 bp):
ATTTTCAAACTCGTAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTAC
TATCGCAACACG
Found at i:246144 original size:20 final size:20
Alignment explanation
Indices: 246121--246159 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
246111 GTTGCAATGC
246121 GATTTACAAATTCGCAACGT
1 GATTTACAAATTCGCAACGT
*
246141 GATTTTCAAATTCGCAACG
1 GATTTACAAATTCGCAACG
246160 CTAATTACCG
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:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (20 bp):
GATTTACAAATTCGCAACGT
Found at i:246224 original size:58 final size:58
Alignment explanation
Indices: 246132--246262 Score: 219
Period size: 58 Copynumber: 2.3 Consensus size: 58
246122 ATTTACAAAT
* * *
246132 TCGCAACGTGATTTT-CAAATTCGCAACGCTAATTACCGATATAGGTAAACATTATTA
1 TCGCAACGCGATTTTCCAAAATCGCAACGCTAATTACCGATATAGGTAAACAGTATTA
*
246189 TCGCAACGCGATTTTCCAAAATCGCAACGCTAATTACCGATGTAGGTAAACAGTATTA
1 TCGCAACGCGATTTTCCAAAATCGCAACGCTAATTACCGATATAGGTAAACAGTATTA
246247 TCGCAACGCGATTTTC
1 TCGCAACGCGATTTTC
246263 AAATTCGTAA
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
57 14 0.20
58 55 0.80
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (58 bp):
TCGCAACGCGATTTTCCAAAATCGCAACGCTAATTACCGATATAGGTAAACAGTATTA
Found at i:246281 original size:20 final size:20
Alignment explanation
Indices: 246247--246382 Score: 173
Period size: 20 Copynumber: 6.8 Consensus size: 20
246237 AACAGTATTA
*
246247 TCGCAACGCGATTTTCAAAT
1 TCGCAACGAGATTTTCAAAT
* * *
246267 TCGTAATGAGATTTTCAAAAA
1 TCGCAACGAGATTTTC-AAAT
*
246288 TCGCAACGCGATTTTCAAAT
1 TCGCAACGAGATTTTCAAAT
246308 TCGCAACGAGATTTTCAAAT
1 TCGCAACGAGATTTTCAAAT
* *
246328 TCGCAACGTGATTTTTAAAT
1 TCGCAACGAGATTTTCAAAT
* *
246348 TCGTAACGCGATTTTCAAAT
1 TCGCAACGAGATTTTCAAAT
*
246368 TCGCAACGCGATTTT
1 TCGCAACGAGATTTT
246383 GGAATCTGTG
Statistics
Matches: 100, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
20 84 0.84
21 16 0.16
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (20 bp):
TCGCAACGAGATTTTCAAAT
Found at i:246348 original size:40 final size:40
Alignment explanation
Indices: 246247--246382 Score: 209
Period size: 40 Copynumber: 3.4 Consensus size: 40
246237 AACAGTATTA
* *
246247 TCGCAACGCGATTTTCAAATTCGTAATGAGATTTTCAAAAA
1 TCGCAACGCGATTTTCAAATTCGTAACGAGATTTTC-AAAT
*
246288 TCGCAACGCGATTTTCAAATTCGCAACGAGATTTTCAAAT
1 TCGCAACGCGATTTTCAAATTCGTAACGAGATTTTCAAAT
* * *
246328 TCGCAACGTGATTTTTAAATTCGTAACGCGATTTTCAAAT
1 TCGCAACGCGATTTTCAAATTCGTAACGAGATTTTCAAAT
246368 TCGCAACGCGATTTT
1 TCGCAACGCGATTTT
246383 GGAATCTGTG
Statistics
Matches: 87, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 53 0.61
41 34 0.39
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (40 bp):
TCGCAACGCGATTTTCAAATTCGTAACGAGATTTTCAAAT
Found at i:246398 original size:20 final size:20
Alignment explanation
Indices: 246375--246438 Score: 110
Period size: 20 Copynumber: 3.2 Consensus size: 20
246365 AATTCGCAAC
*
246375 GCGATTTTGGAATCTGTGTT
1 GCGATTTTGGAAACTGTGTT
246395 GCGATTTTGGAAACTGTGTT
1 GCGATTTTGGAAACTGTGTT
*
246415 GCGATTTTGGAACCTGTGTT
1 GCGATTTTGGAAACTGTGTT
246435 GCGA
1 GCGA
246439 AATAAGAGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.17, C:0.12, G:0.31, T:0.39
Consensus pattern (20 bp):
GCGATTTTGGAAACTGTGTT
Found at i:249546 original size:20 final size:20
Alignment explanation
Indices: 249521--249565 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
249511 GAGTGGATGC
249521 AACGCGATTTACAAATTCGA
1 AACGCGATTTACAAATTCGA
* *
249541 AACGCGATTTTCAAATTCGC
1 AACGCGATTTACAAATTCGA
249561 AACGC
1 AACGC
249566 TAATTACCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (20 bp):
AACGCGATTTACAAATTCGA
Found at i:249641 original size:20 final size:20
Alignment explanation
Indices: 249594--249642 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
249584 AACACTACTA
*
249594 TCGCAACACGATTTACAAAT
1 TCGCAACGCGATTTACAAAT
249614 TCGCAACGCGATTTACAAAT
1 TCGCAACGCGATTTACAAAT
*
249634 TTGCAACGC
1 TCGCAACGC
249643 TAATTACCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGATTTACAAAT
Done.