Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006091.1 Hibiscus syriacus cultivar Beakdansim tig00014441_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: 59442
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Found at i:1306 original size:13 final size:14
Alignment explanation
Indices: 1267--1318 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
1257 TTCAAATATG
*
1267 TATTTAATATATATA
1 TATTTAATTTA-ATA
1282 TATTTAAATTTAATA
1 TATTT-AATTTAATA
*
1297 -ATTTAATTTAATT
1 TATTTAATTTAATA
*
1310 TAGTTAATT
1 TATTTAATT
1319 AACTGATTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 11 0.34
15 8 0.25
16 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
TATTTAATTTAATA
Found at i:7995 original size:14 final size:15
Alignment explanation
Indices: 7971--8014 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
7961 TATTAGAAGA
7971 TAATTTA-TTAATTT
1 TAATTTATTTAATTT
7985 TAA-TTATTTAA-TT
1 TAATTTATTTAATTT
*
7998 TAATTTATTTTATTT
1 TAATTTATTTAATTT
8013 TA
1 TA
8015 TTTCCAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 8 0.31
14 14 0.54
15 4 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTATTTAATTT
Found at i:8465 original size:15 final size:16
Alignment explanation
Indices: 8437--8469 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
8427 TTTAAATTAT
*
8437 ATTTATTTTTTATATA
1 ATTTATTTTATATATA
8453 ATTTA-TTTATATATA
1 ATTTATTTTATATATA
8468 AT
1 AT
8470 CATTAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTATTTTATATATA
Found at i:8497 original size:22 final size:22
Alignment explanation
Indices: 8455--8499 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
8445 TTTATATAAT
*
8455 TTATTTATATATAATCATTAAA
1 TTATTTATATATAATAATTAAA
*
8477 TTATTTATATAT-ATAATTTAA
1 TTATTTATATATAATAATTAAA
8498 TT
1 TT
8500 TTTTTTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TTATTTATATATAATAATTAAA
Found at i:17455 original size:49 final size:50
Alignment explanation
Indices: 17358--17455 Score: 117
Period size: 49 Copynumber: 2.0 Consensus size: 50
17348 GATGAGTTCT
* *
17358 AATAAAATATAATTTTTATTAAAATTTATCATATCGAGGTAAAAAATTTG
1 AATAAAATATAATTTTTATTAAAATTTATCACATCGACGTAAAAAATTTG
* * * * * *
17408 AATAAAA-ATATTTTTTATTAGAATTTGTCACCTCGACGTGAAGAATTT
1 AATAAAATATAATTTTTATTAAAATTTATCACATCGACGTAAAAAATTT
17456 CATGCACTGT
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
49 33 0.82
50 7 0.17
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (50 bp):
AATAAAATATAATTTTTATTAAAATTTATCACATCGACGTAAAAAATTTG
Found at i:21461 original size:42 final size:42
Alignment explanation
Indices: 21362--21462 Score: 184
Period size: 42 Copynumber: 2.4 Consensus size: 42
21352 GACACCAACT
*
21362 CCAACACCACCTCCAACCTCTGCACCTGCTCCACCGCCAGCA
1 CCAACACCACCTCCAGCCTCTGCACCTGCTCCACCGCCAGCA
*
21404 CCAACACCACTTCCAGCCTCTGCACCTGCTCCACCGCCAGCA
1 CCAACACCACCTCCAGCCTCTGCACCTGCTCCACCGCCAGCA
21446 CCAACACCACCTCCAGC
1 CCAACACCACCTCCAGC
21463 TCCTCCTCCT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.24, C:0.54, G:0.10, T:0.12
Consensus pattern (42 bp):
CCAACACCACCTCCAGCCTCTGCACCTGCTCCACCGCCAGCA
Found at i:21465 original size:30 final size:30
Alignment explanation
Indices: 21431--21490 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
21421 CTCTGCACCT
21431 GCTCCACCGCC-AGCACCAACACCACCTCCA
1 GCTCCACCGCCTA-CACCAACACCACCTCCA
* * *
21461 GCTCCTCCTCCTACACCAGCACCACCTCCA
1 GCTCCACCGCCTACACCAACACCACCTCCA
21491 CCACGTCCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.23, C:0.57, G:0.08, T:0.12
Consensus pattern (30 bp):
GCTCCACCGCCTACACCAACACCACCTCCA
Found at i:21500 original size:30 final size:30
Alignment explanation
Indices: 21444--21510 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
21434 CCACCGCCAG
* *
21444 CACCAACACCACCTCCAGCTCCTCCTCCTA
1 CACCAACACCACCTCCACCACCTCCTCCTA
* * *
21474 CACCAGCACCACCTCCACCACGTCCTCCTC
1 CACCAACACCACCTCCACCACCTCCTCCTA
21504 CACCAAC
1 CACCAAC
21511 TCTGGCGCCA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.24, C:0.58, G:0.04, T:0.13
Consensus pattern (30 bp):
CACCAACACCACCTCCACCACCTCCTCCTA
Found at i:21581 original size:12 final size:12
Alignment explanation
Indices: 21530--21585 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
21520 AGCATCACCT
*
21530 CCAACACCTACA
1 CCAACACCGACA
* *
21542 CCACCACCGAAA
1 CCAACACCGACA
*
21554 CCAACACC-AGCT
1 CCAACACCGA-CA
*
21566 CCAACACCGCCA
1 CCAACACCGACA
21578 CCAACACC
1 CCAACACC
21586 TCCTCCACCG
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
11 1 0.03
12 33 0.97
ACGTcount: A:0.38, C:0.54, G:0.05, T:0.04
Consensus pattern (12 bp):
CCAACACCGACA
Found at i:21591 original size:24 final size:24
Alignment explanation
Indices: 21530--21592 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
21520 AGCATCACCT
* *
21530 CCAACACCTACACCACCACCGAAA
1 CCAACACCTACTCCAACACCGAAA
**
21554 CCAACACC-AGCTCCAACACCGCCA
1 CCAACACCTA-CTCCAACACCGAAA
*
21578 CCAACACCTCCTCCA
1 CCAACACCTACTCCA
21593 CCGCTACCAC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
23 1 0.03
24 31 0.97
ACGTcount: A:0.35, C:0.54, G:0.05, T:0.06
Consensus pattern (24 bp):
CCAACACCTACTCCAACACCGAAA
Found at i:21594 original size:21 final size:21
Alignment explanation
Indices: 21564--21628 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
21554 CCAACACCAG
21564 CTCCAACACCGCCACCAACAC
1 CTCCAACACCGCCACCAACAC
** * * *
21585 CTCCTCCACCGCTACCACCAG
1 CTCCAACACCGCCACCAACAC
* *
21606 CTCCAACACCACCTCCAACAC
1 CTCCAACACCGCCACCAACAC
21627 CT
1 CT
21629 ACACCACCAC
Statistics
Matches: 32, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.28, C:0.57, G:0.05, T:0.11
Consensus pattern (21 bp):
CTCCAACACCGCCACCAACAC
Found at i:21621 original size:12 final size:12
Alignment explanation
Indices: 21600--21658 Score: 57
Period size: 12 Copynumber: 4.9 Consensus size: 12
21590 CCACCGCTAC
*
21600 CACCAGCTCCAA
1 CACCACCTCCAA
21612 CACCACCTCCAA
1 CACCACCTCCAA
* *
21624 CACCTA-CACCAC
1 CACC-ACCTCCAA
*
21636 CACCAACTCCAA
1 CACCACCTCCAA
*
21648 CTCCACCTCCA
1 CACCACCTCCA
21659 CCACGTCCTC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
11 1 0.03
12 36 0.95
13 1 0.03
ACGTcount: A:0.32, C:0.56, G:0.02, T:0.10
Consensus pattern (12 bp):
CACCACCTCCAA
Found at i:21627 original size:24 final size:24
Alignment explanation
Indices: 21600--21702 Score: 64
Period size: 24 Copynumber: 4.2 Consensus size: 24
21590 CCACCGCTAC
21600 CACCAGCTCCAACACCACCTCCAA
1 CACCAGCTCCAACACCACCTCCAA
* * *
21624 CACCTA-CACCACCACCAACTCCAA
1 CACC-AGCTCCAACACCACCTCCAA
* * * * **
21648 CTCCACCTCCACCACGTCCTCCTCCTC
1 CACCAGCTCCA--AC-ACCACCTCCAA
* *
21675 CACCTGCTCCAACACCACCTCCAG
1 CACCAGCTCCAACACCACCTCCAA
21699 CACC
1 CACC
21703 TACACCACCG
Statistics
Matches: 56, Mismatches: 18, Indels: 10
0.67 0.21 0.12
Matches are distributed among these distances:
23 1 0.02
24 37 0.66
25 3 0.05
26 1 0.02
27 14 0.25
ACGTcount: A:0.26, C:0.57, G:0.04, T:0.13
Consensus pattern (24 bp):
CACCAGCTCCAACACCACCTCCAA
Found at i:21634 original size:18 final size:18
Alignment explanation
Indices: 21608--21658 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
21598 ACCACCAGCT
21608 CCAACACCACCTCCAACA
1 CCAACACCACCTCCAACA
* * *
21626 CCTACACCACCACCAACT
1 CCAACACCACCTCCAACA
*
21644 CCAACTCCACCTCCA
1 CCAACACCACCTCCA
21659 CCACGTCCTC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.33, C:0.57, G:0.00, T:0.10
Consensus pattern (18 bp):
CCAACACCACCTCCAACA
Found at i:21769 original size:12 final size:12
Alignment explanation
Indices: 21752--21824 Score: 53
Period size: 12 Copynumber: 6.3 Consensus size: 12
21742 ACTGCACCAA
21752 CACCACCTCCAC
1 CACCACCTCCAC
*
21764 CACCACCTCCTC
1 CACCACCTCCAC
* *
21776 CTCCTCCT-C-C
1 CACCACCTCCAC
*
21786 C-CCTCCTCCAC
1 CACCACCTCCAC
** *
21797 CACCTGCTCCAG
1 CACCACCTCCAC
*
21809 CACCACCTCCAG
1 CACCACCTCCAC
21821 CACC
1 CACC
21825 TACACCACCA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
9 6 0.12
10 3 0.06
11 3 0.06
12 39 0.76
ACGTcount: A:0.16, C:0.64, G:0.04, T:0.15
Consensus pattern (12 bp):
CACCACCTCCAC
Found at i:21836 original size:24 final size:24
Alignment explanation
Indices: 21790--21836 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
21780 TCCTCCCCCT
* * *
21790 CCTCCACCACCTGCTCCAGCACCA
1 CCTCCACCACCTACACCACCACCA
*
21814 CCTCCAGCACCTACACCACCACC
1 CCTCCACCACCTACACCACCACC
21837 GACACCAACT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.23, C:0.60, G:0.06, T:0.11
Consensus pattern (24 bp):
CCTCCACCACCTACACCACCACCA
Found at i:21998 original size:24 final size:24
Alignment explanation
Indices: 21970--22019 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
21960 AACTCCAACT
* * *
21970 CCAACTCCAGCTCCTCCACCTGCA
1 CCAACACCACCTCCACCACCTGCA
*
21994 CCAACACCACCTCCAGCACCTGCA
1 CCAACACCACCTCCACCACCTGCA
22018 CC
1 CC
22020 TCCTCCTACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.24, C:0.56, G:0.08, T:0.12
Consensus pattern (24 bp):
CCAACACCACCTCCACCACCTGCA
Found at i:22008 original size:30 final size:30
Alignment explanation
Indices: 21964--22020 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
21954 GACACCAACT
* *
21964 CCAACTCCAACTCCAGCTCCTCCACCTGCA
1 CCAACACCAACTCCAGCACCTCCACCTGCA
* *
21994 CCAACACCACCTCCAGCACCTGCACCT
1 CCAACACCAACTCCAGCACCTCCACCT
22021 CCTCCTACAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.25, C:0.54, G:0.07, T:0.14
Consensus pattern (30 bp):
CCAACACCAACTCCAGCACCTCCACCTGCA
Found at i:22019 original size:18 final size:18
Alignment explanation
Indices: 21992--22040 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
21982 CCTCCACCTG
*
21992 CACCAACACCACCTCC-A
1 CACCTACACCACCTCCTA
* *
22009 GCACCTGCACCTCCTCCTA
1 -CACCTACACCACCTCCTA
22028 CACCTACACCACC
1 CACCTACACCACC
22041 ACCTCCGCCA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 24 0.96
19 1 0.04
ACGTcount: A:0.27, C:0.57, G:0.04, T:0.12
Consensus pattern (18 bp):
CACCTACACCACCTCCTA
Found at i:22022 original size:36 final size:36
Alignment explanation
Indices: 21926--22040 Score: 106
Period size: 36 Copynumber: 3.2 Consensus size: 36
21916 CCTCCTCCAC
* * *
21926 CACCACCTCTAGCACCTACACCACCA-CTGACACCAA
1 CACCACCTCCAGCACCTGCACCTCCACCTG-CACCAA
* * * * * *
21962 CTCCAACTCCAACTCCAGCTCCTCCACCTGCACCAA
1 CACCACCTCCAGCACCTGCACCTCCACCTGCACCAA
* * *
21998 CACCACCTCCAGCACCTGCACCTCCTCCTACACCTA
1 CACCACCTCCAGCACCTGCACCTCCACCTGCACCAA
22034 CACCACC
1 CACCACC
22041 ACCTCCGCCA
Statistics
Matches: 60, Mismatches: 18, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
36 57 0.95
37 3 0.05
ACGTcount: A:0.27, C:0.54, G:0.05, T:0.14
Consensus pattern (36 bp):
CACCACCTCCAGCACCTGCACCTCCACCTGCACCAA
Found at i:22031 original size:30 final size:30
Alignment explanation
Indices: 21964--22102 Score: 76
Period size: 30 Copynumber: 4.9 Consensus size: 30
21954 GACACCAACT
* * * *
21964 CCAACTCCAACTCCAGCTCCTCCACCTGCA
1 CCAACACCACCTCCAGCACCTCCACCTCCA
* *
21994 CCAACACCACCTCCAGCACCTGCACCTCCT
1 CCAACACCACCTCCAGCACCTCCACCTCCA
* * *
22024 CC--TA-CACCT--A-CACCACCACCTCCG
1 CCAACACCACCTCCAGCACCTCCACCTCCA
* * * ** *
22048 CCAACTCCACC-CCAACACCACCACCAACT
1 CCAACACCACCTCCAGCACCTCCACCTCCA
* *
22077 CCAATACCACCTCCAGCACCTACACC
1 CCAACACCACCTCCAGCACCTCCACC
22103 ACCGCTAGCA
Statistics
Matches: 82, Mismatches: 20, Indels: 14
0.71 0.17 0.12
Matches are distributed among these distances:
24 13 0.16
25 1 0.01
27 9 0.11
28 2 0.02
29 20 0.24
30 37 0.45
ACGTcount: A:0.27, C:0.56, G:0.04, T:0.12
Consensus pattern (30 bp):
CCAACACCACCTCCAGCACCTCCACCTCCA
Found at i:22103 original size:18 final size:18
Alignment explanation
Indices: 22082--22120 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
22072 CAACTCCAAT
*
22082 ACCACCTCCAGCACCTAC
1 ACCACCGCCAGCACCTAC
* *
22100 ACCACCGCTAGCACCTCC
1 ACCACCGCCAGCACCTAC
22118 ACC
1 ACC
22121 TCCACCCGCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.56, G:0.08, T:0.10
Consensus pattern (18 bp):
ACCACCGCCAGCACCTAC
Found at i:22196 original size:30 final size:30
Alignment explanation
Indices: 22162--22230 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
22152 CCACCGCTGG
*
22162 CACCTCCACCACTACCACCGAATCCGCCAC
1 CACCTCCACCACCACCACCGAATCCGCCAC
*
22192 CACCTCCACCACCACCTCCGAATCCGCCAC
1 CACCTCCACCACCACCACCGAATCCGCCAC
22222 CACCTCCAC
1 CACCTCCAC
22231 TACCTACACC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.25, C:0.59, G:0.06, T:0.10
Consensus pattern (30 bp):
CACCTCCACCACCACCACCGAATCCGCCAC
Found at i:22207 original size:36 final size:36
Alignment explanation
Indices: 22131--22230 Score: 97
Period size: 36 Copynumber: 2.9 Consensus size: 36
22121 TCCACCCGCT
* * * * *
22131 CCACCACTACCACCGAACCCACCACC-GCTGGCACCT
1 CCACCACTACCACCGAATCCGCCACCACCT-CCACCA
22167 CCACCACTACCACCGAATCCGCCACCACCTCCACCA
1 CCACCACTACCACCGAATCCGCCACCACCTCCACCA
22203 CCA-C-CT----CCGAATCCGCCACCACCTCCAC
1 CCACCACTACCACCGAATCCGCCACCACCTCCAC
22231 TACCTACACC
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
30 22 0.38
34 2 0.03
35 1 0.02
36 31 0.53
37 2 0.03
ACGTcount: A:0.25, C:0.58, G:0.08, T:0.09
Consensus pattern (36 bp):
CCACCACTACCACCGAATCCGCCACCACCTCCACCA
Found at i:32433 original size:26 final size:26
Alignment explanation
Indices: 32397--32484 Score: 176
Period size: 26 Copynumber: 3.4 Consensus size: 26
32387 CTTTGAGCTA
32397 TACAATTCTTTAAATTAAGAAAGATT
1 TACAATTCTTTAAATTAAGAAAGATT
32423 TACAATTCTTTAAATTAAGAAAGATT
1 TACAATTCTTTAAATTAAGAAAGATT
32449 TACAATTCTTTAAATTAAGAAAGATT
1 TACAATTCTTTAAATTAAGAAAGATT
32475 TACAATTCTT
1 TACAATTCTT
32485 CATTCTTAGG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 62 1.00
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (26 bp):
TACAATTCTTTAAATTAAGAAAGATT
Found at i:39854 original size:30 final size:30
Alignment explanation
Indices: 39758--39855 Score: 106
Period size: 30 Copynumber: 3.3 Consensus size: 30
39748 CGCTGGTCCA
* *
39758 TCGACACAGGCAGCTCCGAACGCACGTTCG
1 TCGACACCGGCAGCTCCGAACGCAGGTTCG
* * * *
39788 TTGACACTGGCAGCTCCGAAAGTAGGTTCG
1 TCGACACCGGCAGCTCCGAACGCAGGTTCG
* * * *
39818 TTGACACCGGCTGCTCCGGACGCAGGCTCG
1 TCGACACCGGCAGCTCCGAACGCAGGTTCG
39848 TCGACACC
1 TCGACACC
39856 CGCTACGCCG
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.20, C:0.34, G:0.29, T:0.17
Consensus pattern (30 bp):
TCGACACCGGCAGCTCCGAACGCAGGTTCG
Found at i:40801 original size:29 final size:30
Alignment explanation
Indices: 40765--40827 Score: 110
Period size: 29 Copynumber: 2.1 Consensus size: 30
40755 TATACATAGA
40765 AAATCTGCTCAAATTATTTCCTAT-TTATT
1 AAATCTGCTCAAATTATTTCCTATATTATT
*
40794 AAATCTGCTCAAATTATTTCCTTTATTATT
1 AAATCTGCTCAAATTATTTCCTATATTATT
40824 AAAT
1 AAAT
40828 AATTAGTCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 23 0.72
30 9 0.28
ACGTcount: A:0.33, C:0.16, G:0.03, T:0.48
Consensus pattern (30 bp):
AAATCTGCTCAAATTATTTCCTATATTATT
Found at i:43838 original size:30 final size:30
Alignment explanation
Indices: 43804--43868 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
43794 CTGGTCCATC
*
43804 GACACAGGCAGCTCCGAACGCACGTTCGTT
1 GACACAGGCAGCTCCGAAAGCACGTTCGTT
* * *
43834 GACACTGGCAGCTCCGAAAGTAGGTTCGTT
1 GACACAGGCAGCTCCGAAAGCACGTTCGTT
43864 GACAC
1 GACAC
43869 CGGCTGCCCC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.28, T:0.18
Consensus pattern (30 bp):
GACACAGGCAGCTCCGAAAGCACGTTCGTT
Found at i:44820 original size:20 final size:20
Alignment explanation
Indices: 44797--44848 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
44787 AACGCGATCC
44797 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
44817 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
44837 CCAAAATCGCAA
1 CCAGAATCGCAA
44849 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:44865 original size:21 final size:20
Alignment explanation
Indices: 44838--44936 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
44828 AATCAGTTTC
44838 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
44859 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
44880 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
44900 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
44921 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
44937 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:44965 original size:20 final size:20
Alignment explanation
Indices: 44903--45096 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
44893 CGATTTTCCA
* ** *
44903 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
44923 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
44943 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
44963 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
44983 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
45003 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
45023 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
45043 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
45063 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
45084 AAATCGCAACGCG
1 AAATCGCAACGCG
45097 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:44987 original size:60 final size:60
Alignment explanation
Indices: 44903--45096 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
44893 CGATTTTCCA
* ** * *
44903 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
44963 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
45023 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
45084 AAATCGCAACGCG
1 AAATCGCAACGCG
45097 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:45516 original size:33 final size:33
Alignment explanation
Indices: 45477--45547 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
45467 TTCACTTAGA
*
45477 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
45510 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
45543 TTTCA
1 TTTCA
45548 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:45687 original size:14 final size:14
Alignment explanation
Indices: 45668--45722 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
45658 AGAATGACTG
45668 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
45682 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
45701 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
45715 TCGCAACG
1 TCGCAACG
45723 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:45735 original size:33 final size:33
Alignment explanation
Indices: 45668--45738 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
45658 AGAATGACTG
***
45668 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
45701 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
45734 TCGCA
1 TCGCA
45739 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:45756 original size:19 final size:19
Alignment explanation
Indices: 45734--45831 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
45724 GAAACCAAAA
*
45734 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
45753 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
45767 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
45786 TCGCGTTGCGA--TTC-TA
1 TCGCGTTGCGATTTTCATT
* *
45802 T--CGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
45819 TCGCGTTGCGATT
1 TCGCGTTGCGATT
45832 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 18 0.29
16 7 0.11
17 8 0.13
19 30 0.48
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:45775 original size:14 final size:14
Alignment explanation
Indices: 45756--45845 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
45746 TTTCATTTCG
45756 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
45770 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
*
45789 CGTTGCGATTCTAT
1 CGTTGCGATTCTCT
45803 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
45820 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
45836 CGTTGCGATT
1 CGTTGCGATT
45846 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 27 0.44
15 1 0.02
16 8 0.13
17 7 0.11
18 1 0.02
19 18 0.29
ACGTcount: A:0.10, C:0.24, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:45781 original size:33 final size:33
Alignment explanation
Indices: 45739--45853 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
45729 CAAAATCGCA
45739 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
45772 TTGCGATTTTCATTTCGCGTTGCGATTCTATCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
45805 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
45838 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
45854 AACCAAAAGA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:47779 original size:185 final size:186
Alignment explanation
Indices: 47550--47929 Score: 753
Period size: 185 Copynumber: 2.0 Consensus size: 186
47540 TAGATTGCTT
47550 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
47615 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
47680 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
47735 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
47800 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
47865 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
47921 AGTAAATTT
1 AGTAAATTT
47930 ATCCATTCAA
Statistics
Matches: 194, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
185 155 0.80
186 39 0.20
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:47864 original size:93 final size:93
Alignment explanation
Indices: 47550--47929 Score: 753
Period size: 93 Copynumber: 4.1 Consensus size: 93
47540 TAGATTGCTT
47550 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
47615 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
47643 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
47707 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
47735 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
47800 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
47828 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
47893 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
47921 AGTAAATTT
1 AGTAAATTT
47930 ATCCATTCAA
Statistics
Matches: 286, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 194 0.68
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:48013 original size:19 final size:19
Alignment explanation
Indices: 47973--48101 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
47963 TAGTTTACTT
* *
47973 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
47993 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
48012 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
48031 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
48045 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
48064 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
48078 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
48097 TCGCA
1 TCGCA
48102 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:48052 original size:33 final size:32
Alignment explanation
Indices: 48009--48101 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
47999 CGCGAAACCA
**
48009 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
48041 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
48074 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
48102 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:48099 original size:52 final size:52
Alignment explanation
Indices: 47973--48101 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
47963 TAGTTTACTT
**
47973 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
48025 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
48078 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
48102 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:48119 original size:19 final size:19
Alignment explanation
Indices: 48097--48231 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
48087 GAAACCAAAA
*
48097 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
48116 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
48132 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
48149 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
48165 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
48182 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
48201 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
48221 TCGTGTTGCGA
1 TCGCGTTGCGA
48232 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:48138 original size:14 final size:14
Alignment explanation
Indices: 48119--48175 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
48109 TTTCATTTCG
48119 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
48133 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
48150 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
48166 CGTTGCGATT
1 CGTTGCGATT
48176 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:48144 original size:33 final size:33
Alignment explanation
Indices: 48102--48194 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
48092 CAAAATCGCA
*
48102 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
48135 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
48168 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
48195 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:50092 original size:38 final size:38
Alignment explanation
Indices: 50049--50121 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
50039 AATTGATTGT
*
50049 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
50087 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
50122 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:50108 original size:19 final size:19
Alignment explanation
Indices: 50044--50108 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
50034 AGTTTAATTG
*
50044 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
50063 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
50081 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
50101 ATTGATTT
1 ATTGATTT
50109 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:50122 original size:14 final size:14
Alignment explanation
Indices: 50103--50138 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
50093 ATTGTTTAAT
50103 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
50117 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
50131 TGATTTGT
1 TGATTTGT
50139 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:50260 original size:19 final size:19
Alignment explanation
Indices: 50244--50345 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
50234 CAAAATGACT
50244 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
50263 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
50282 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
50296 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
50315 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
50335 ATCGCAATGCG
1 ATCGCAATGCG
50346 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:50394 original size:33 final size:33
Alignment explanation
Indices: 50352--50680 Score: 203
Period size: 33 Copynumber: 9.5 Consensus size: 33
50342 TGCGTTTATA
50352 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
50385 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
50421 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
* *
50456 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTA
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
50494 ATTTCGCATTGCGATTATGTCGGTT-CGATTTTC
1 ATTTCGCATTGCGATTATCTC-GTTGCGATTTTC
*
50527 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATT-T-TC
* * * * *
50567 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTATCTCGTTGCGATTTTC
*
50598 ATTTCGCATTGCG-TATCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGAT-TATCTCGTTGCGATTTTC
* *
50631 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTATC-TCGTTGCGATTTTC
*
50665 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
50681 GTATTTTCCG
Statistics
Matches: 249, Mismatches: 20, Indels: 54
0.77 0.06 0.17
Matches are distributed among these distances:
31 10 0.04
32 3 0.01
33 97 0.39
34 29 0.12
35 21 0.08
36 20 0.08
37 4 0.02
38 53 0.21
39 3 0.01
40 9 0.04
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (33 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
Found at i:50398 original size:19 final size:19
Alignment explanation
Indices: 50374--50680 Score: 349
Period size: 19 Copynumber: 17.4 Consensus size: 19
50364 GATTATCTCG
50374 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
50393 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
50412 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
50426 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
50445 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
50464 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
50483 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
50502 TTGCGA--TT-ATGTCG-G
1 TTGCGATTTTCATTTCGCA
50517 TT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
50535 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
50554 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
50568 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
50587 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
50606 TTGCG--TATC-TCTCG--
1 TTGCGATTTTCATTTCGCA
50620 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
50640 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
50654 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
50673 TTGCGATT
1 TTGCGATT
50681 GTATTTTCCG
Statistics
Matches: 247, Mismatches: 15, Indels: 52
0.79 0.05 0.17
Matches are distributed among these distances:
14 31 0.13
15 2 0.01
16 31 0.13
17 28 0.11
18 5 0.02
19 138 0.56
20 12 0.05
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:50449 original size:71 final size:71
Alignment explanation
Indices: 50374--50610 Score: 349
Period size: 71 Copynumber: 3.3 Consensus size: 71
50364 GATTATCTCG
50374 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
50439 TTCGCA
66 TTCGCA
* *
50445 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG--TTGCGATT
* *
50508 TT-ATGTCG-G
61 TTCATTTCGCA
*
50517 TT-CGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
50581 TTCGCA
66 TTCGCA
50587 TTGCGATTTTCATTTCGCATTGCG
1 TTGCGATTTTCATTTCGCATTGCG
50611 TATCTCTCGT
Statistics
Matches: 147, Mismatches: 9, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
66 6 0.04
68 6 0.04
69 7 0.05
70 2 0.01
71 104 0.71
72 2 0.01
73 7 0.05
74 7 0.05
76 6 0.04
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (71 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
TTCGCA
Found at i:50533 original size:142 final size:136
Alignment explanation
Indices: 50342--50680 Score: 495
Period size: 142 Copynumber: 2.4 Consensus size: 136
50332 AAAATCGCAA
50342 TGCG-TTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
1 TGCGATTT-TAATTTCGCATTGCGATTAT-TCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
*
50406 TTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
64 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG--
* *
50471 TTTCATTTCGTAT
127 TATC-TCTCG--T
50484 TGCGATTTTAATTTCGCATTGCGATTATGTCGGTT-CGATTTTCATTTCGCATTGCGATTTTCAT
1 TGCGATTTTAATTTCGCATTGCGATTAT-TC-GTTGCGATTTTCATTTCGCATTGCGATTTTCAT
50548 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGTA
64 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGTA
50613 TCTCTCGT
129 TCTCTCGT
* * *
50621 TGCGATTTTCATTTCCGCATTGCGATT-TTCATGTTGGGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTAATTT-CGCATTGCGATTATTC--GTTGCGATTTTCATTTCGCATTGCGATT
50681 GTATTTTCCG
Statistics
Matches: 184, Mismatches: 8, Indels: 14
0.89 0.04 0.07
Matches are distributed among these distances:
136 2 0.01
137 18 0.10
138 34 0.18
139 4 0.02
140 3 0.02
142 117 0.64
143 6 0.03
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (136 bp):
TGCGATTTTAATTTCGCATTGCGATTATTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGTATC
TCTCGT
Found at i:50617 original size:52 final size:53
Alignment explanation
Indices: 50374--50652 Score: 333
Period size: 52 Copynumber: 5.2 Consensus size: 53
50364 GATTATCTCG
* *
50374 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA-TATC-TCTCG--TTGCGATTTTCATTTCGCA
* * *
50426 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCATTGCGA-TATC-TCTCG--TTGCGATTTTCATTTCGCA
* * *
50483 TTGCGATTTTAATTTCGCATTGCGATTATGTC-GGTT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGA-TATCTCTCGTTGCGATTTTCATTTCGCA
50535 TTGCGATTTTCATTTCGCATTGCGAT-TCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATATCTCTCGTTGCGATTTTCATTTCGCA
50587 TTGCGATTTTCATTTCGCATTGCG-TATCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATATCTCTCGTTGCGATTTTCATTT-CGCA
50640 TTGCGATTTTCAT
1 TTGCGATTTTCAT
50653 GTTGGGATTT
Statistics
Matches: 209, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
50 3 0.01
51 5 0.02
52 145 0.69
53 19 0.09
54 3 0.01
55 6 0.03
56 1 0.00
57 27 0.13
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (53 bp):
TTGCGATTTTCATTTCGCATTGCGATATCTCTCGTTGCGATTTTCATTTCGCA
Found at i:53002 original size:12 final size:12
Alignment explanation
Indices: 52985--53009 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52975 TCTTCGGGGA
52985 CTTTTTCTTCTT
1 CTTTTTCTTCTT
52997 CTTTTTCTTCTT
1 CTTTTTCTTCTT
53009 C
1 C
53010 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:53218 original size:24 final size:24
Alignment explanation
Indices: 53184--53230 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
53174 CTGAAACATC
53184 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
53208 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
53231 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:53932 original size:20 final size:20
Alignment explanation
Indices: 53904--54268 Score: 422
Period size: 20 Copynumber: 18.4 Consensus size: 20
53894 AAATTTCAGT
* * * *
53904 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
53924 GTTGCGA-TTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
53943 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
53963 GTTGCGA-TTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
53982 GTTGCGA-TTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
54001 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
54021 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
54041 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
54061 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
54081 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
54101 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
54121 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
54141 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
54161 ATTGCGA-TTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
54180 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
54200 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
54220 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
54240 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
54260 GTTGCGATT
1 GTTGCGATT
54269 ATGGAAAATC
Statistics
Matches: 302, Mismatches: 32, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
18 2 0.01
19 63 0.21
20 234 0.77
21 3 0.01
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:54649 original size:30 final size:30
Alignment explanation
Indices: 54615--54678 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
54605 TATACGTAGA
54615 AAATCTGCTCAAATTATTTCCTTTATTATT
1 AAATCTGCTCAAATTATTTCCTTTATTATT
54645 AAATCTGCTCAAATTATTTCCTTTATTATT
1 AAATCTGCTCAAATTATTTCCTTTATTATT
54675 AAAT
1 AAAT
54679 AATTAGTCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.33, C:0.16, G:0.03, T:0.48
Consensus pattern (30 bp):
AAATCTGCTCAAATTATTTCCTTTATTATT
Done.