Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005408.1 Hibiscus syriacus cultivar Beakdansim tig00012400_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: 56376
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:7126 original size:11 final size:11
Alignment explanation
Indices: 7110--7134 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
7100 ATGCTAATAA
7110 TGTTTTTTTTT
1 TGTTTTTTTTT
7121 TGTTTTTTTTT
1 TGTTTTTTTTT
7132 TGT
1 TGT
7135 CATTTTCCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (11 bp):
TGTTTTTTTTT
Found at i:13402 original size:21 final size:22
Alignment explanation
Indices: 13378--13432 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
13368 TCCCTTGCTA
*
13378 TGTATCGATACA-GCTTGAATG
1 TGTATCGATACATCCTTGAATG
13399 TGTAAT-GATACATTCCTTGAATG
1 TGT-ATCGATACA-TCCTTGAATG
13422 TGTATCGATAC
1 TGTATCGATAC
13433 CCCTCGAGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
21 9 0.31
22 4 0.14
23 16 0.55
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (22 bp):
TGTATCGATACATCCTTGAATG
Found at i:13872 original size:20 final size:20
Alignment explanation
Indices: 13849--13891 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
13839 TAAAAAATTA
*
13849 TTTTTGTTTTAAAT-TGTTG
1 TTTTTGATTTAAATATGTTG
*
13868 TTTTTGATTTAATTATGTTG
1 TTTTTGATTTAAATATGTTG
13888 TTTT
1 TTTT
13892 AATGAAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.16, C:0.00, G:0.14, T:0.70
Consensus pattern (20 bp):
TTTTTGATTTAAATATGTTG
Found at i:23544 original size:23 final size:23
Alignment explanation
Indices: 23486--23554 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 23
23476 ATTTTAGTGC
* *
23486 AGGAGGAATCGATACCCCCTTTGA
1 AGGA-GAACCGATTCCCCCTTTGA
* * *
23510 AGGGGAATCGATTCCCCCTTTGG
1 AGGAGAACCGATTCCCCCTTTGA
* *
23533 ATGAGAACCGATTTCCACCTTT
1 AGGAGAACCGA-TTCCCCCTTT
23555 AGGGAATCGA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
23 25 0.68
24 12 0.32
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (23 bp):
AGGAGAACCGATTCCCCCTTTGA
Found at i:24105 original size:20 final size:20
Alignment explanation
Indices: 24011--24379 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
24001 GATTTTCCAT
* ** *
24011 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
24031 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
24051 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
24071 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
24091 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
24111 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
24131 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
24151 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
24171 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
24191 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
24211 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
24231 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
24251 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
24271 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
24291 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
24311 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
24331 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
24351 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
24371 AATCACAAC
1 AATCGCAAC
24380 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:25092 original size:24 final size:24
Alignment explanation
Indices: 25053--25099 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
25043 AAATTTGGTC
25053 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
25077 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
25100 GATGTTTCAG
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:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:25291 original size:12 final size:12
Alignment explanation
Indices: 25274--25298 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25264 ATATAATCCT
25274 GAAGAAGAAAAA
1 GAAGAAGAAAAA
25286 GAAGAAGAAAAA
1 GAAGAAGAAAAA
25298 G
1 G
25299 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:27623 original size:19 final size:19
Alignment explanation
Indices: 27601--27886 Score: 302
Period size: 19 Copynumber: 16.4 Consensus size: 19
27591 ACGGAAATAC
*
27601 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
27620 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
27634 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
27654 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
27668 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
27687 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
27706 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
27720 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
27738 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
27757 AATCG-AA-CCGACAT---
1 AATCGCAATGCGAAATGAA
*
27771 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
27790 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
27809 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
27828 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
27847 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
27861 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
27879 AATCGCAA
1 AATCGCAA
27887 CGAGATAATC
Statistics
Matches: 228, Mismatches: 13, Indels: 53
0.78 0.04 0.18
Matches are distributed among these distances:
14 45 0.20
15 4 0.02
16 16 0.07
17 15 0.07
18 30 0.13
19 105 0.46
20 13 0.06
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:27688 original size:33 final size:33
Alignment explanation
Indices: 27601--27835 Score: 196
Period size: 33 Copynumber: 6.8 Consensus size: 33
27591 ACGGAAATAC
* *
27601 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
27634 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAA
27668 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
* *
27706 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGA
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAGA--A
* *
27738 AATCGCAATGCGAAATGAAAATCG-AACCGACAT
1 AATCGCAATGCGAAATGAAAATCGCAA-CGAGAA
*
27771 AATCGCAATGCGAAATTAAAATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGC-A-ACG--A-GAA
27809 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
27836 TGCGAAATGA
Statistics
Matches: 168, Mismatches: 14, Indels: 37
0.77 0.06 0.17
Matches are distributed among these distances:
30 1 0.01
31 1 0.01
32 9 0.05
33 63 0.38
34 32 0.19
35 10 0.06
36 7 0.04
37 10 0.06
38 35 0.21
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:27716 original size:52 final size:53
Alignment explanation
Indices: 27629--27854 Score: 325
Period size: 52 Copynumber: 4.2 Consensus size: 53
27619 AAATCCCAAC
27629 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACCGAGAGAATCGCAATGCGAA
27682 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACCGAGAGAATCGCAATGCGAA
* *
27734 ATG-AAATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACCGAGAGAATCGCAATGCGAA
* * * *
27785 ATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CCG--A-GAGAATCGCAATGCGAA
27842 ATGAAAATCGCAA
1 ATGAAAATCGCAA
27855 CGAAAGAATC
Statistics
Matches: 158, Mismatches: 8, Indels: 10
0.90 0.05 0.06
Matches are distributed among these distances:
50 2 0.01
51 45 0.28
52 63 0.40
53 18 0.11
54 2 0.01
56 1 0.01
57 27 0.17
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (53 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACCGAGAGAATCGCAATGCGAA
Found at i:27780 original size:103 final size:108
Alignment explanation
Indices: 27629--27854 Score: 338
Period size: 103 Copynumber: 2.1 Consensus size: 108
27619 AAATCCCAAC
*
27629 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATGAAAATCGCA
* *
27694 ATGCGAAATGAAAATCGCAA-CG-A-GAGAATCGCAATGCGAA
66 ATACGAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
* *
27734 ATG-AAATCGCAATGC-GAAATGAAAATCG-AACCGACATAATCGCAATGCGAAATTAAAATCGC
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CGACAGAATCGCAATGCGAAATGAAAATCGC
27796 AATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
65 AATACGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
27842 ATGAAAATCGCAA
1 ATGAAAATCGCAA
27855 CGAAAGAATC
Statistics
Matches: 109, Mismatches: 5, Indels: 10
0.88 0.04 0.08
Matches are distributed among these distances:
102 2 0.02
103 61 0.56
104 12 0.11
105 5 0.05
107 1 0.01
108 19 0.17
109 9 0.08
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (108 bp):
ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATGAAAATCGCA
ATACGAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
Found at i:27809 original size:122 final size:121
Alignment explanation
Indices: 27668--27918 Score: 361
Period size: 122 Copynumber: 2.1 Consensus size: 121
27658 GCAACGAGAG
* *
27668 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CG-A-GAGAATCGCAATG
1 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAA--
27730 CGAAATGAAATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAAATTA-A
64 CGAAA-G-AATCGCAATGCGAAATG-AAATCGCAA-CGACATAATCGCAATGCGAAATTATA
27790 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAA
*
27855 CGAAAGAATCGCAATGCGAAATGAAATCGCAACGAGATAATCGCAATGCGAAATTATA
64 CGAAAGAATCGCAATGCGAAATGAAATCGCAACGACATAATCGCAATGCGAAATTATA
27913 AA-CGCA
1 AATCGCA
27919 TTGCGATTTT
Statistics
Matches: 119, Mismatches: 3, Indels: 14
0.88 0.02 0.10
Matches are distributed among these distances:
122 78 0.66
123 22 0.18
124 3 0.03
125 5 0.04
126 1 0.01
127 10 0.08
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.16
Consensus pattern (121 bp):
AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAACG
AAAGAATCGCAATGCGAAATGAAATCGCAACGACATAATCGCAATGCGAAATTATA
Found at i:27847 original size:141 final size:137
Alignment explanation
Indices: 27601--27888 Score: 438
Period size: 141 Copynumber: 2.1 Consensus size: 137
27591 ACGGAAATAC
*
27601 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAG
1 AATCGCAACGCGAAATGAAAATCCCAACACGAAAATCGCAATGCGGAAATGAAAATCGCAACGAG
* *
27666 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC
66 AAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGC
27731 GAAATGA
131 GAAATGA
* * *
27738 AATCGCAATGCGAAATGAAAAT-CGAAC-CGACATAATCGCAATGC-GAAATTAAAATCGCAATA
1 AATCGCAACGCGAAATGAAAATCCCAACACGA-A-AATCGCAATGCGGAAATGAAAATCGC-A-A
27800 CGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATC
62 CG--A-GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATC
27865 GCAATGCGAAATGA
124 GCAATGCGAAATGA
27879 AATCGCAACG
1 AATCGCAACG
27889 AGATAATCGC
Statistics
Matches: 137, Mismatches: 7, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
135 2 0.01
136 18 0.13
137 33 0.24
138 3 0.02
140 1 0.01
141 80 0.58
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (137 bp):
AATCGCAACGCGAAATGAAAATCCCAACACGAAAATCGCAATGCGGAAATGAAAATCGCAACGAG
AAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGC
GAAATGA
Found at i:27866 original size:14 final size:14
Alignment explanation
Indices: 27847--27900 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
27837 GCGAAATGAA
27847 AATCGCAACGAAAG
1 AATCGCAACGAAAG
27861 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
* *
27878 AAATCGCAACGAGAT
1 -AATCGCAACGAAAG
27893 AATCGCAA
1 AATCGCAA
27901 TGCGAAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
14 16 0.47
16 9 0.26
17 1 0.03
18 8 0.24
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.13
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:28024 original size:19 final size:19
Alignment explanation
Indices: 27915--28016 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
27905 AAATTATAAA
27915 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
27934 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
27954 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
27970 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
27987 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
28006 CGCATTGCGAT
1 CGCATTGCGAT
28017 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:28141 original size:14 final size:14
Alignment explanation
Indices: 28122--28158 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
28112 CATCAATTAC
28122 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
28136 ACAAATCATCTTTT
1 ACAAATCAACTTTT
28150 ACAAATCAA
1 ACAAATCAA
28159 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:28170 original size:12 final size:12
Alignment explanation
Indices: 28153--28225 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
28143 ATCTTTTACA
28153 AATCAATTAAAC
1 AATCAATTAAAC
*
28165 AATCAA--AAATTG
1 AATCAATTAAA--C
**
28177 AATCAACTTTTAC
1 AATCAA-TTAAAC
28190 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
28203 AATCAA-AAAAC
1 AATCAATTAAAC
28214 AATCAATTAAAC
1 AATCAATTAAAC
28226 TATGAATCAA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:28187 original size:38 final size:38
Alignment explanation
Indices: 28139--28211 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
28129 AACTTTTACA
*
28139 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
28177 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
28212 ACAATCAATT
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:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:30099 original size:14 final size:14
Alignment explanation
Indices: 30080--30136 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
30070 GCGAAATGAA
*
30080 AATCGCAACGACAG
1 AATCGCAACGAAAG
30094 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
30111 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
30127 AATCGCAACG
1 AATCGCAACG
30137 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:30107 original size:33 final size:33
Alignment explanation
Indices: 30061--30153 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
30051 GCGAAACCAA
*
30061 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
30094 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
30127 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
30154 TGCGATTTTG
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:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:30118 original size:19 final size:19
Alignment explanation
Indices: 30024--30158 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
30014 TAGTTTACTT
* *
30024 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
30044 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
30063 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
30082 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
30096 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
30115 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
30129 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
30148 TCGCAATGCGA
1 TCGCAACGCGA
30159 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:30176 original size:19 final size:19
Alignment explanation
Indices: 30154--30282 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
30144 AAAATCGCAA
30154 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
30173 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
30187 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
30206 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
30220 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
30239 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
30258 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
30278 TGCGA
1 TGCGA
30283 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:30196 original size:33 final size:33
Alignment explanation
Indices: 30154--30245 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
30144 AAAATCGCAA
30154 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
30187 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
30220 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
30246 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:30465 original size:92 final size:93
Alignment explanation
Indices: 30326--30610 Score: 549
Period size: 92 Copynumber: 3.1 Consensus size: 93
30316 TTGAATGGAT
30326 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
30390 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
30418 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
30482 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
30510 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
30575 AGTTTAGCA-AATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
30602 AAATTTACT
1 AAATTTACT
30611 AAGCAATCTA
Statistics
Matches: 191, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
92 142 0.74
93 49 0.26
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:32333 original size:14 final size:14
Alignment explanation
Indices: 32314--32403 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
32304 TTGAAATGAA
32314 AATCGCAACGAGAG
1 AATCGCAACGAGAG
32328 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
32345 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
32361 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
32380 AATCGCAACGAGAG
1 AATCGCAACGAGAG
32394 AATCGCAACG
1 AATCGCAACG
32404 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:32351 original size:33 final size:33
Alignment explanation
Indices: 32306--32420 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
32296 TCTTTTGGTT
32306 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
32339 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
32372 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
32405 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
32421 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:32352 original size:19 final size:18
Alignment explanation
Indices: 32313--32425 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
32303 GTTGAAATGA
32313 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
32328 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
32345 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
32361 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
32378 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
32394 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
32411 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
32426 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:32456 original size:14 final size:14
Alignment explanation
Indices: 32437--32491 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
32427 TTTGGTTTCG
32437 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
32451 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
32470 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
32484 CGTTGCGA
1 CGTTGCGA
32492 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:32654 original size:33 final size:33
Alignment explanation
Indices: 32612--32682 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
32602 AATACTAACT
32612 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
32645 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
32678 TGAAA
1 TGAAA
32683 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:32915 original size:22 final size:22
Alignment explanation
Indices: 32863--32917 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
32853 TGGTTGTGAG
**
32863 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
32885 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
32907 GGATTTCTTCG
1 GGATTTCTTCG
32918 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:33088 original size:20 final size:20
Alignment explanation
Indices: 33063--33256 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
33053 CTTTAAATAT
33063 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
33083 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
33105 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
33124 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
33144 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
33164 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
33184 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
33204 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
33224 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
33244 CGCGTTGCGATTT
1 CGCGTTGCGATTT
33257 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:33250 original size:60 final size:60
Alignment explanation
Indices: 33063--33256 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
33053 CTTTAAATAT
**
33063 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
33124 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
33184 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
33244 CGCGTTGCGATTT
1 CGCGTTGCGATTT
33257 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:33273 original size:21 final size:20
Alignment explanation
Indices: 33249--33325 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
33239 ATATTCGCGT
33249 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
33270 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
33290 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
33312 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
33326 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:33336 original size:20 final size:20
Alignment explanation
Indices: 33311--33362 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
33301 AAGAATCGCG
*
33311 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
33331 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
33351 TTGCGATTCTGG
1 TTGCGATTCTGG
33363 GGATCGCGTT
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:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:36618 original size:17 final size:17
Alignment explanation
Indices: 36596--36643 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
36586 GGCTCGTTAA
36596 GAACTCGAGTCGAGCTC
1 GAACTCGAGTCGAGCTC
*
36613 GAACTCGAGTCAAGCTC
1 GAACTCGAGTCGAGCTC
36630 -AAGCTCGAGTCGAG
1 GAA-CTCGAGTCGAG
36644 TCCATTCGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 2 0.07
17 26 0.93
ACGTcount: A:0.27, C:0.27, G:0.29, T:0.17
Consensus pattern (17 bp):
GAACTCGAGTCGAGCTC
Found at i:42480 original size:20 final size:20
Alignment explanation
Indices: 42440--42482 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
42430 ACTAAAGTTT
* *
42440 CGAATTTGAAAATCGCGTTG
1 CGAATTTGAAAATCACATTG
42460 CGAATTTGAAAATCACATTG
1 CGAATTTGAAAATCACATTG
42480 CGA
1 CGA
42483 TAGTATTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (20 bp):
CGAATTTGAAAATCACATTG
Found at i:42499 original size:77 final size:77
Alignment explanation
Indices: 42406--42693 Score: 450
Period size: 77 Copynumber: 3.7 Consensus size: 77
42396 ACGCGAATTT
* * ** *
42406 TAGTACTGTTTACCTATATCGATAACTAAAGTTTCGAATTTGAAAATCGCGTTGCGAATTTGAAA
1 TAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGAATTTGAAA
*
42471 ATCACATTGCGA
66 ATCGCATTGCGA
* *
42483 TAGTATTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTACGAATTTGAAA
1 TAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGAATTTGAAA
42548 ATCGCATTGCGA
66 ATCGCATTGCGA
* * * *
42560 TAGTACTGTTTACCTATATCTGTAATTAGCGTTGTGAATTTGAATATCGTGTTGCGAATTTGAAA
1 TAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGAATTTGAAA
42625 ATCGCATTGCGA
66 ATCGCATTGCGA
* *
42637 TAGTACTGTTTACCTATATCGGTAATTATCGTTGCAAATTTGAAAATCGCGTTGCGA
1 TAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGA
42694 TTTACCTATT
Statistics
Matches: 191, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 191 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (77 bp):
TAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGAATTTGAAA
ATCGCATTGCGA
Found at i:42540 original size:20 final size:20
Alignment explanation
Indices: 42511--42552 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
42501 TCGGTAATTA
*
42511 GCGTTGCGAATTTGAAAATC
1 GCGTTACGAATTTGAAAATC
42531 GCGTTACGAATTTGAAAATC
1 GCGTTACGAATTTGAAAATC
42551 GC
1 GC
42553 ATTGCGATAG
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:0.31, C:0.17, G:0.24, T:0.29
Consensus pattern (20 bp):
GCGTTACGAATTTGAAAATC
Found at i:42618 original size:20 final size:20
Alignment explanation
Indices: 42590--42628 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42580 TGTAATTAGC
* *
42590 GTTGTGAATTTGAATATCGT
1 GTTGCGAATTTGAAAATCGT
42610 GTTGCGAATTTGAAAATCG
1 GTTGCGAATTTGAAAATCG
42629 CATTGCGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (20 bp):
GTTGCGAATTTGAAAATCGT
Found at i:42634 original size:20 final size:20
Alignment explanation
Indices: 42595--42636 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
42585 TTAGCGTTGT
* **
42595 GAATTTGAATATCGTGTTGC
1 GAATTTGAAAATCGCATTGC
42615 GAATTTGAAAATCGCATTGC
1 GAATTTGAAAATCGCATTGC
42635 GA
1 GA
42637 TAGTACTGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (20 bp):
GAATTTGAAAATCGCATTGC
Found at i:42709 original size:20 final size:20
Alignment explanation
Indices: 42685--42736 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
42675 TTTGAAAATC
*
42685 GCGTTGCGATTTACCTATTA
1 GCGTTGCGATTTACATATTA
* * *
42705 TCGTTGCAATTTACATATTC
1 GCGTTGCGATTTACATATTA
42725 GCGTTGCGATTT
1 GCGTTGCGATTT
42737 TGGAACCTGT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (20 bp):
GCGTTGCGATTTACATATTA
Found at i:42727 original size:40 final size:40
Alignment explanation
Indices: 42661--42736 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
42651 TATATCGGTA
42661 ATTATCGTTGCAAATTTGAAAATCGCGTTGCGATTTACCT
1 ATTATCGTTGCAAATTTGAAAATCGCGTTGCGATTTACCT
*
42701 ATTATCGTTGC-AATTT-ACATATTCGCGTTGCGATTT
1 ATTATCGTTGCAAATTTGA-A-AATCGCGTTGCGATTT
42737 TGGAACCTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
38 1 0.03
39 6 0.18
40 26 0.79
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (40 bp):
ATTATCGTTGCAAATTTGAAAATCGCGTTGCGATTTACCT
Found at i:45436 original size:18 final size:18
Alignment explanation
Indices: 45413--45447 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
45403 TATTAACGAC
*
45413 ACAATTATAATATGGAAA
1 ACAATTATAACATGGAAA
*
45431 ACAATTGTAACATGGAA
1 ACAATTATAACATGGAA
45448 TTATATAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.09, G:0.14, T:0.26
Consensus pattern (18 bp):
ACAATTATAACATGGAAA
Found at i:46198 original size:43 final size:43
Alignment explanation
Indices: 46150--46231 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
46140 AAGCACAATG
*
46150 TTGTCATTGATCCAAATCCTTCTGTGAAAGATCGAGTGAAAGT
1 TTGTCAATGATCCAAATCCTTCTGTGAAAGATCGAGTGAAAGT
* * * *
46193 TTGTCAATGATCCAACTCTTTCTGTGAATGATTGAGTGA
1 TTGTCAATGATCCAAATCCTTCTGTGAAAGATCGAGTGA
46232 CATGAAAAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (43 bp):
TTGTCAATGATCCAAATCCTTCTGTGAAAGATCGAGTGAAAGT
Found at i:49271 original size:76 final size:77
Alignment explanation
Indices: 49123--49573 Score: 343
Period size: 77 Copynumber: 5.9 Consensus size: 77
49113 AATGCCCTAC
* * *
49123 TTGCGATAGTACTGTTTATCTATATCGGTAATTAGCGTTGTGAATTTGAATATCGCGTTGCGAAT
1 TTGCGATAGTACTGTTTACCTATATCAGTAATTAGCGTTGTGAATTTGAAAATCGCGTTGCGAAT
*
49188 ATGAAAATCACA
66 ATAAAAATCACA
* * * *
49200 TTGCGATAGTACTGTTTGCCTATGTCAGTAATTAGCG-TGCGAATTTGAAAATCGCGTTGTGAAT
1 TTGCGATAGTACTGTTTACCTATATCAGTAATTAGCGTTGTGAATTTGAAAATCGCGTTGCGAAT
*
49264 ATAAAAATCGCA
66 ATAAAAATCACA
* * *
49276 TTGCGATAGTACTGTTTACCTATAT-TGATAATTCGCGTTGTGAATTTGAAAATCGCATTGCGAA
1 TTGCGATAGTACTGTTTACCTATATCAG-TAATTAGCGTTGTGAATTTGAAAATCGCGTTGCGAA
* * * *
49340 TTTGGAAAATCGCG
65 TAT-AAAAATCACA
* * * * * * * *
49354 TTGCGAT-TTACCT-ATTATCGT-TA-CAATTTACCTATTATCGTTGCG-ATTT-ACATATTCAC
1 TTGCGATAGTA-CTGTTTA-CCTATATC-A-GTA---ATTAGCGTTGTGAATTTGA-A-AATCGC
* * * * *
49413 GTTGCAAATTTGGAAAATCGCG
57 GTTGCGAATAT-AAAAATCACA
* * * *
49435 TTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAGTTTGAAAATCGCGTTACGAAT
1 TTGCGATAGTACTGTTTACCTATATCAGTAATTAGCGTTGTGAATTTGAAAATCGCGTTGCGAAT
* * *
49500 TTGAAAATCGCA
66 ATAAAAATCACA
* * *
49512 TTGCG--A-TACTGTTTACCTATAT-ATGTAATTCGCGTTGCGAATTTGAAAATCGCATTGC-AA
1 TTGCGATAGTACTGTTTACCTATATCA-GTAATTAGCGTTGTGAATTTGAAAATCGCGTTGCGAA
49572 TA
65 TA
49574 GTACTGTTTA
Statistics
Matches: 305, Mismatches: 49, Indels: 44
0.77 0.12 0.11
Matches are distributed among these distances:
73 3 0.01
74 46 0.15
75 2 0.01
76 65 0.21
77 79 0.26
78 45 0.15
79 5 0.02
80 6 0.02
81 46 0.15
82 7 0.02
83 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (77 bp):
TTGCGATAGTACTGTTTACCTATATCAGTAATTAGCGTTGTGAATTTGAAAATCGCGTTGCGAAT
ATAAAAATCACA
Found at i:49362 original size:20 final size:20
Alignment explanation
Indices: 49308--49359 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 20
49298 TATTGATAAT
*
49308 TCGCGTTGTGAATTTGAAAA
1 TCGCGTTGCGAATTTGAAAA
*
49328 TCGCATTGCGAATTTGGAAAA
1 TCGCGTTGCGAATTT-GAAAA
49349 TCGCGTTGCGA
1 TCGCGTTGCGA
49360 TTTACCTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGAAAA
Found at i:49417 original size:20 final size:20
Alignment explanation
Indices: 49352--49409 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
49342 TGGAAAATCG
49352 CGTTGCGATTTACCTATTAT
1 CGTTGCGATTTACCTATTAT
* *
49372 CGTTACAATTTACCTATTAT
1 CGTTGCGATTTACCTATTAT
*
49392 CGTTGCGATTTACATATT
1 CGTTGCGATTTACCTATT
49410 CACGTTGCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.24, C:0.19, G:0.12, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTACCTATTAT
Found at i:49502 original size:20 final size:20
Alignment explanation
Indices: 49469--49510 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
49459 TCGGTAATTA
* *
49469 GCGTTGCGAGTTTGAAAATC
1 GCGTTACGAATTTGAAAATC
49489 GCGTTACGAATTTGAAAATC
1 GCGTTACGAATTTGAAAATC
49509 GC
1 GC
49511 ATTGCGATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (20 bp):
GCGTTACGAATTTGAAAATC
Found at i:49569 original size:54 final size:56
Alignment explanation
Indices: 49487--49620 Score: 182
Period size: 57 Copynumber: 2.4 Consensus size: 56
49477 AGTTTGAAAA
* *
49487 TCGCGTTACGAATTTGAAAATCGCATTGC-GA-TACTGTTTACCTATATATGTAAT
1 TCGCGTTGCGAATTTGAAAATCGCATTGCAGAGTACTGTTTACCTATATAGGTAAT
* *
49541 TCGCGTTGCGAATTTGAAAATCGCATTGCAATAGTACTGTTTACCTATATCGGTAAT
1 TCGCGTTGCGAATTTGAAAATCGCATTGC-AGAGTACTGTTTACCTATATAGGTAAT
* * *
49598 TAGCATTGCAAATTTGAAAATCG
1 TCGCGTTGCGAATTTGAAAATCG
49621 AGTTGTGATT
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
54 28 0.40
56 1 0.01
57 41 0.59
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (56 bp):
TCGCGTTGCGAATTTGAAAATCGCATTGCAGAGTACTGTTTACCTATATAGGTAAT
Found at i:49664 original size:20 final size:20
Alignment explanation
Indices: 49622--49671 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
49612 TGAAAATCGA
*
49622 GTTGTGATTTACCTATTATC
1 GTTGTGATTTACCTATTAGC
*
49642 GTTGTGATTTACCTATTCGC
1 GTTGTGATTTACCTATTAGC
*
49662 GTTGCGATTT
1 GTTGTGATTT
49672 TGGAACCTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.16, C:0.16, G:0.20, T:0.48
Consensus pattern (20 bp):
GTTGTGATTTACCTATTAGC
Found at i:49685 original size:20 final size:20
Alignment explanation
Indices: 49662--49726 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
49652 ACCTATTCGC
49662 GTTGCGATTTTGGAACCTGT
1 GTTGCGATTTTGGAACCTGT
* ** **
49682 GTTGCAAAATTGG-AGTTCGT
1 GTTGCGATTTTGGAACCT-GT
*
49702 ATTGCGATTTTGGAACCTGT
1 GTTGCGATTTTGGAACCTGT
49722 GTTGC
1 GTTGC
49727 AAAATTGAAG
Statistics
Matches: 31, Mismatches: 12, Indels: 4
0.66 0.26 0.09
Matches are distributed among these distances:
19 2 0.06
20 27 0.87
21 2 0.06
ACGTcount: A:0.18, C:0.14, G:0.29, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTTGGAACCTGT
Found at i:49747 original size:40 final size:40
Alignment explanation
Indices: 49657--49753 Score: 158
Period size: 40 Copynumber: 2.4 Consensus size: 40
49647 GATTTACCTA
*
49657 TTCGCGTTGCGATTTTGGAACCTGTGTTGCAAAATTGGAG
1 TTCGCGTTGCGATTTTGGAACCTGTGTTGCAAAATTGAAG
**
49697 TTCGTATTGCGATTTTGGAACCTGTGTTGCAAAATTGAAG
1 TTCGCGTTGCGATTTTGGAACCTGTGTTGCAAAATTGAAG
*
49737 TTCGCGTTGCGAATTTG
1 TTCGCGTTGCGATTTTG
49754 TTGGTCATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.21, C:0.14, G:0.28, T:0.37
Consensus pattern (40 bp):
TTCGCGTTGCGATTTTGGAACCTGTGTTGCAAAATTGAAG
Found at i:53937 original size:9 final size:9
Alignment explanation
Indices: 53923--53993 Score: 75
Period size: 9 Copynumber: 8.6 Consensus size: 9
53913 TGACTTTGGT
53923 TTTTTCTTC
1 TTTTTCTTC
53932 TTTTTCTTC
1 TTTTTCTTC
53941 TTTTTC-TC
1 TTTTTCTTC
53949 --TTT-TTC
1 TTTTTCTTC
53955 TTTTTCTT-
1 TTTTTCTTC
53963 TTTTTCTT-
1 TTTTTCTTC
*
53971 TTTTTTTTC
1 TTTTTCTTC
53980 TTTTCTCTT-
1 TTTT-TCTTC
53989 TTTTT
1 TTTTT
53994 TTTGCAACGG
Statistics
Matches: 54, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
6 5 0.09
8 21 0.39
9 25 0.46
10 3 0.06
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:53938 original size:6 final size:6
Alignment explanation
Indices: 53929--53996 Score: 70
Period size: 6 Copynumber: 11.3 Consensus size: 6
53919 TGGTTTTTTC
* *
53929 TTCTTT TTCTTC TT-TTT CTCTTT TTCTTT TTCTTTTT TTCTTT TT-TTT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTC--TTT TTCTTT TTCTTT
53977 TTCTTT TCTCTTT TT-TTT TT
1 TTCTTT T-TCTTT TTCTTT TT
53997 GCAACGGTGG
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
5 13 0.25
6 28 0.53
7 6 0.11
8 6 0.11
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTCTTT
Found at i:53944 original size:8 final size:8
Alignment explanation
Indices: 53924--53990 Score: 52
Period size: 8 Copynumber: 8.5 Consensus size: 8
53914 GACTTTGGTT
53924 TTTTCTTC
1 TTTTCTTC
53932 TTTTTCTTC
1 -TTTTCTTC
53941 -TTT-TTC
1 TTTTCTTC
53947 TCTTT-TTC
1 T-TTTCTTC
*
53955 TTTTTCTTT
1 -TTTTCTTC
*
53964 TTTTCTTT
1 TTTTCTTC
*
53972 TTTTTTTC
1 TTTTCTTC
53980 TTTTC-TC
1 TTTTCTTC
53987 TTTT
1 TTTT
53991 TTTTTTGCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
6 3 0.06
7 9 0.18
8 27 0.54
9 11 0.22
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTCTTC
Found at i:53950 original size:20 final size:19
Alignment explanation
Indices: 53922--53996 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 19
53912 TTGACTTTGG
*
53922 TTTTT-TCTTCTTTTTCTTC
1 TTTTTCTCTT-TTTTTTTTC
53941 TTTTTCTCTTTTTCTTTTTC
1 TTTTTCTCTTTTT-TTTTTC
*
53961 TTTTTTTCTTTTTTTTTTC
1 TTTTTCTCTTTTTTTTTTC
53980 -TTTTCTCTTTTTTTTTT
1 TTTTTCTCTTTTTTTTTT
53997 GCAACGGTGG
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
18 16 0.31
19 14 0.27
20 21 0.41
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTTCTCTTTTTTTTTTC
Found at i:53957 original size:14 final size:14
Alignment explanation
Indices: 53938--53996 Score: 74
Period size: 14 Copynumber: 4.6 Consensus size: 14
53928 CTTCTTTTTC
53938 TTCTTTTTCTCTTT
1 TTCTTTTTCTCTTT
*
53952 TTCTTTTTCTTTTT
1 TTCTTTTTCTCTTT
53966 TTC-TTTT-T-TTT
1 TTCTTTTTCTCTTT
53977 TTC-TTTTCTCTTT
1 TTCTTTTTCTCTTT
53990 TT-TTTTT
1 TTCTTTTT
53997 GCAACGGTGG
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
11 10 0.24
12 2 0.05
13 13 0.32
14 16 0.39
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TTCTTTTTCTCTTT
Found at i:53977 original size:32 final size:31
Alignment explanation
Indices: 53923--53996 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 31
53913 TGACTTTGGT
53923 TTTTTCTTCTTTTTCTTCTTTTTCTCTTTT-TC
1 TTTTTCTT-TTTTTCTTCTTTTT-TCTTTTCTC
*
53955 TTTTTCTTTTTTTCTTTTTTTTTTCTTTTCTC
1 TTTTTCTTTTTTTC-TTCTTTTTTCTTTTCTC
53987 TTTTT-TTTTT
1 TTTTTCTTTTT
53997 GCAACGGTGG
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
31 17 0.44
32 22 0.56
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (31 bp):
TTTTTCTTTTTTTCTTCTTTTTTCTTTTCTC
Found at i:56338 original size:77 final size:77
Alignment explanation
Indices: 56139--56345 Score: 301
Period size: 76 Copynumber: 2.7 Consensus size: 77
56129 TAATGCCCCA
* *
56139 ATTGCGATAGTACTG-TTACCTATATCGGTAATTAGCGTTGCGAATTTGAATATCGCGTTGCGAA
1 ATTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCACGTTGCGAA
* **
56203 TTTGAAAATTGC
66 TATGAAAATCAC
* * * * *
56215 A-TGCGAAAGTACTGTTTACCTATGTCGTTAATTAGCTTTGCAAATTTGAAAATCACGTTGCGAA
1 ATTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCACGTTGCGAA
56279 TATGAAAATCAC
66 TATGAAAATCAC
*
56291 ATTGCGATAGTACTGTTTACCTATATCGGTAATTCGCGTTGCGAATTTGAAAATC
1 ATTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATC
56346 GCATTGTGAA
Statistics
Matches: 113, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
75 12 0.11
76 54 0.48
77 47 0.42
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (77 bp):
ATTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCACGTTGCGAA
TATGAAAATCAC
Found at i:56356 original size:20 final size:21
Alignment explanation
Indices: 56324--56372 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
56314 TATCGGTAAT
* *
56324 TCGCGTTGCGAATTT-GAAAA
1 TCGCATTGTGAATTTGGAAAA
56344 TCGCATTGTGAATTTGGAAAA
1 TCGCATTGTGAATTTGGAAAA
*
56365 TTGCATTG
1 TCGCATTG
56373 CGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGCATTGTGAATTTGGAAAA
Found at i:56365 original size:21 final size:20
Alignment explanation
Indices: 56324--56375 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
56314 TATCGGTAAT
*
56324 TCGCGTTGCGAATTTGAAAA
1 TCGCATTGCGAATTTGAAAA
*
56344 TCGCATTGTGAATTTGGAAAA
1 TCGCATTGCGAATTT-GAAAA
*
56365 TTGCATTGCGA
1 TCGCATTGCGA
56376 T
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (20 bp):
TCGCATTGCGAATTTGAAAA
Done.