Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007942.1 Hibiscus syriacus cultivar Beakdansim tig00110361_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: 198765
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7163 original size:22 final size:21
Alignment explanation
Indices: 7134--7182 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
7124 AGAAAAAATA
*
7134 TGAATTCGTCAATTTCGCAAC
1 TGAATTCGCCAATTTCGCAAC
*
7155 TCGAATTCGCCAATTTCGTAAC
1 T-GAATTCGCCAATTTCGCAAC
7177 TGAATT
1 TGAATT
7183 ACCGATATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (21 bp):
TGAATTCGCCAATTTCGCAAC
Found at i:7441 original size:22 final size:22
Alignment explanation
Indices: 7412--7495 Score: 125
Period size: 22 Copynumber: 3.9 Consensus size: 22
7402 CTATACTGGT
7412 AATT-GAGTTGCGAATTTGGCG
1 AATTCGAGTTGCGAATTTGGCG
7433 AATTCGAGTTGCGAATTTGGCG
1 AATTCGAGTTGCGAATTTGGCG
* * *
7455 AATTCGAGTTACGAAATTGACG
1 AATTCGAGTTGCGAATTTGGCG
*
7477 AATTCGCGTTGCGAATTTG
1 AATTCGAGTTGCGAATTTG
7496 AAAACTGTAT
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
21 4 0.07
22 52 0.93
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (22 bp):
AATTCGAGTTGCGAATTTGGCG
Found at i:7812 original size:17 final size:16
Alignment explanation
Indices: 7789--7827 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
7779 CGAAACCTAA
*
7789 AATTTTAAATTTTCTT
1 AATTTTAAATTTTATT
*
7805 ATATTTTAGATTTTATT
1 A-ATTTTAAATTTTATT
7822 AATTTT
1 AATTTT
7828 TTTAATTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (16 bp):
AATTTTAAATTTTATT
Found at i:7853 original size:25 final size:24
Alignment explanation
Indices: 7820--7882 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 24
7810 TTAGATTTTA
* *
7820 TTAATTTTTTTAATTTCATAATTC
1 TTAAATTTTTTAATTTCACAATTC
* *
7844 TTAAAATTTTATAATTTCACACTTC
1 TT-AAATTTTTTAATTTCACAATTC
7869 TTAAATTTTTTAAT
1 TTAAATTTTTTAAT
7883 ATAATTTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
24 13 0.39
25 20 0.61
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (24 bp):
TTAAATTTTTTAATTTCACAATTC
Found at i:12944 original size:24 final size:25
Alignment explanation
Indices: 12874--12972 Score: 96
Period size: 24 Copynumber: 4.0 Consensus size: 25
12864 CACAATAAGT
*
12874 AGTCATAATTGCTTAAATTGAACGC
1 AGTCATAATTGCTAAAATTGAACGC
* * * * *
12899 AGACGTAACTACTAAAATTGAACAC
1 AGTCATAATTGCTAAAATTGAACGC
*
12924 AGTCATAATTGC-AAAATTGAACGT
1 AGTCATAATTGCTAAAATTGAACGC
*
12948 AGTCATAACTT-C-AAAACTGAACGC
1 AGTCATAA-TTGCTAAAATTGAACGC
12972 A
1 A
12973 CCCTTGGTGA
Statistics
Matches: 59, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
24 30 0.51
25 29 0.49
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.25
Consensus pattern (25 bp):
AGTCATAATTGCTAAAATTGAACGC
Found at i:14579 original size:14 final size:14
Alignment explanation
Indices: 14554--14588 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
14544 TCATTCTTAA
14554 TCCAAC-TTAAAAT
1 TCCAACATTAAAAT
14567 TCCAACATTAAAAT
1 TCCAACATTAAAAT
14581 T-CAACATT
1 TCCAACATT
14589 GAACACCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (14 bp):
TCCAACATTAAAAT
Found at i:16937 original size:18 final size:18
Alignment explanation
Indices: 16928--17094 Score: 205
Period size: 18 Copynumber: 9.4 Consensus size: 18
16918 TTCTTTCCTA
16928 GGCTCCTCTTCCTTCTTC
1 GGCTCCTCTTCCTTCTTC
* *
16946 GGTTCTTCTTCCTTCTTC
1 GGCTCCTCTTCCTTCTTC
* *
16964 GGTTCTTCTTCCTTCTTC
1 GGCTCCTCTTCCTTCTTC
16982 GGCTCCTCTTCCTTCTTC
1 GGCTCCTCTTCCTTCTTC
*
17000 GGTTCCTCTTCCTTCTTC
1 GGCTCCTCTTCCTTCTTC
*
17018 GGTTCCTCTTCCTTCTTC
1 GGCTCCTCTTCCTTCTTC
* *
17036 GGCTCCTCTTCTTTCTTG
1 GGCTCCTCTTCCTTCTTC
* * *
17054 GGTTCCTCTTCTTTCTTT
1 GGCTCCTCTTCCTTCTTC
*
17072 GG-T--TCTTCCTTCTTT
1 GGCTCCTCTTCCTTCTTC
17087 GGCTCCTC
1 GGCTCCTC
17095 CTTCTTTGGT
Statistics
Matches: 135, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
15 13 0.10
16 1 0.01
17 1 0.01
18 120 0.89
ACGTcount: A:0.00, C:0.37, G:0.13, T:0.51
Consensus pattern (18 bp):
GGCTCCTCTTCCTTCTTC
Found at i:16944 original size:36 final size:36
Alignment explanation
Indices: 16880--17094 Score: 217
Period size: 36 Copynumber: 6.1 Consensus size: 36
16870 CAGCTGTTGC
* * * *
16880 TCCTCTTCCTTCTT---CTCCTCCTCTTTCTTAGCT
1 TCCTCTTCCTTCTTCGGCTCCTCTTCCTTCTTCGGT
* * * *
16913 TCTTCTTCTTTCCTAGGCTCCTCTTCCTTCTTCGGT
1 TCCTCTTCCTTCTTCGGCTCCTCTTCCTTCTTCGGT
* * * *
16949 TCTTCTTCCTTCTTCGGTTCTTCTTCCTTCTTCGGC
1 TCCTCTTCCTTCTTCGGCTCCTCTTCCTTCTTCGGT
*
16985 TCCTCTTCCTTCTTCGGTTCCTCTTCCTTCTTCGGT
1 TCCTCTTCCTTCTTCGGCTCCTCTTCCTTCTTCGGT
* *
17021 TCCTCTTCCTTCTTCGGCTCCTCTTCTTTCTTGGGT
1 TCCTCTTCCTTCTTCGGCTCCTCTTCCTTCTTCGGT
* * * *
17057 TCCTCTTCTTTCTTTGG-T--TCTTCCTTCTTTGGC
1 TCCTCTTCCTTCTTCGGCTCCTCTTCCTTCTTCGGT
17090 TCCTC
1 TCCTC
17095 CTTCTTTGGT
Statistics
Matches: 155, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.18
35 1 0.01
36 126 0.81
ACGTcount: A:0.01, C:0.37, G:0.10, T:0.52
Consensus pattern (36 bp):
TCCTCTTCCTTCTTCGGCTCCTCTTCCTTCTTCGGT
Found at i:16986 original size:54 final size:54
Alignment explanation
Indices: 16878--17094 Score: 266
Period size: 54 Copynumber: 4.1 Consensus size: 54
16868 TGCAGCTGTT
* * * * * * *
16878 GCTCCTCTTCCTTCTTC---TCCTCCTCTTTCTTAGCTTCTTCTTCTTTCCTAG
1 GCTCCTCTTCCTTCTTCGGTTCCTCTTCCTTCTTCGGTTCTTCTTCCTTCTTCG
*
16929 GCTCCTCTTCCTTCTTCGGTTCTTCTTCCTTCTTCGGTTCTTCTTCCTTCTTCG
1 GCTCCTCTTCCTTCTTCGGTTCCTCTTCCTTCTTCGGTTCTTCTTCCTTCTTCG
*
16983 GCTCCTCTTCCTTCTTCGGTTCCTCTTCCTTCTTCGGTTCCTCTTCCTTCTTCG
1 GCTCCTCTTCCTTCTTCGGTTCCTCTTCCTTCTTCGGTTCTTCTTCCTTCTTCG
* * * * *
17037 GCTCCTCTTCTTTCTTGGGTTCCTCTTCTTTCTTTGG---TTCTTCCTTCTTTG
1 GCTCCTCTTCCTTCTTCGGTTCCTCTTCCTTCTTCGGTTCTTCTTCCTTCTTCG
17088 GCTCCTC
1 GCTCCTC
17095 CTTCTTTGGT
Statistics
Matches: 147, Mismatches: 16, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
51 36 0.24
54 111 0.76
ACGTcount: A:0.01, C:0.37, G:0.11, T:0.51
Consensus pattern (54 bp):
GCTCCTCTTCCTTCTTCGGTTCCTCTTCCTTCTTCGGTTCTTCTTCCTTCTTCG
Found at i:17078 original size:15 final size:15
Alignment explanation
Indices: 17060--17114 Score: 83
Period size: 15 Copynumber: 3.7 Consensus size: 15
17050 CTTGGGTTCC
*
17060 TCTTCTTTCTTTGGT
1 TCTTCCTTCTTTGGT
*
17075 TCTTCCTTCTTTGGC
1 TCTTCCTTCTTTGGT
*
17090 TCCTCCTTCTTTGGT
1 TCTTCCTTCTTTGGT
17105 TCTTCCTTCT
1 TCTTCCTTCT
17115 CCGGCTCCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.00, C:0.31, G:0.11, T:0.58
Consensus pattern (15 bp):
TCTTCCTTCTTTGGT
Found at i:17081 original size:21 final size:18
Alignment explanation
Indices: 16895--17070 Score: 123
Period size: 18 Copynumber: 9.8 Consensus size: 18
16885 TTCCTTCTTC
* *
16895 TCCTCCTCTTTCTTAGCT
1 TCCTCTTCTTTCTTGGCT
* *
16913 TCTTCTTCTTTCCTAGGC-
1 TCCTCTTCTTT-CTTGGCT
*
16931 TCCTCTTCCTTCTTCGG-T
1 TCCTCTTCTTTCTT-GGCT
* *
16949 TCTTCTTCCTTCTTCGG-T
1 TCCTCTTCTTTCTT-GGCT
* *
16967 TCTTCTTCCTTCTTCGGC-
1 TCCTCTTCTTTCTT-GGCT
*
16985 TCCTCTTCCTTCTTCGG-T
1 TCCTCTTCTTTCTT-GGCT
*
17003 TCCTCTTCCTTCTTCGG-T
1 TCCTCTTCTTTCTT-GGCT
*
17021 TCCTCTTCCTTCTTCGGC-
1 TCCTCTTCTTTCTT-GGCT
*
17039 TCCTCTTCTTTCTTGGGT
1 TCCTCTTCTTTCTTGGCT
17057 TCCTCTTCTTTCTT
1 TCCTCTTCTTTCTT
17071 TGGTTCTTCC
Statistics
Matches: 140, Mismatches: 11, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
17 4 0.03
18 132 0.94
19 4 0.03
ACGTcount: A:0.01, C:0.37, G:0.10, T:0.52
Consensus pattern (18 bp):
TCCTCTTCTTTCTTGGCT
Found at i:17100 original size:30 final size:30
Alignment explanation
Indices: 17066--17123 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
17056 TTCCTCTTCT
**
17066 TTCTTTGGTTCTTCCTTCTTTGGCTCCTCC
1 TTCTTTGGTTCTTCCTTCTCCGGCTCCTCC
17096 TTCTTTGGTTCTTCCTTCTCCGGCTCCT
1 TTCTTTGGTTCTTCCTTCTCCGGCTCCT
17124 TCGCTGGCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.14, T:0.52
Consensus pattern (30 bp):
TTCTTTGGTTCTTCCTTCTCCGGCTCCTCC
Found at i:19146 original size:31 final size:30
Alignment explanation
Indices: 19111--19186 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 30
19101 ATGATTTCGG
19111 ATTTAACAATTAAATTAATATTTCATTTAAA
1 ATTTAA-AATTAAATTAATATTTCATTTAAA
* * * *
19142 ATTTAAAGAATAAATTATTATTTTATTTTAA
1 ATTTAAA-ATTAAATTAATATTTCATTTAAA
*
19173 ATTAAAAATTAAAT
1 ATTTAAAATTAAAT
19187 CTTTTTATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 7 0.18
31 31 0.82
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (30 bp):
ATTTAAAATTAAATTAATATTTCATTTAAA
Found at i:21291 original size:28 final size:28
Alignment explanation
Indices: 21249--21308 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 28
21239 ATGCAATGTC
21249 ATTGCTTTATCTGTT-TCCTTATAAAGG
1 ATTGCTTTATCTGTTGTCCTTATAAAGG
*
21276 ATTGCTGTTGTCTGTTGTCCTTATAAAGG
1 ATTGCT-TTATCTGTTGTCCTTATAAAGG
21305 ATTG
1 ATTG
21309 TTGGTGTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 6 0.20
28 8 0.27
29 16 0.53
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (28 bp):
ATTGCTTTATCTGTTGTCCTTATAAAGG
Found at i:30959 original size:24 final size:24
Alignment explanation
Indices: 30931--30977 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
30921 TTAATCATTA
30931 ATTTAAATTCAAGAAAAAAAAATT
1 ATTTAAATTCAAGAAAAAAAAATT
* *
30955 ATTTAAATTCGAGAAGAAAAAAT
1 ATTTAAATTCAAGAAAAAAAAAT
30978 AGTAAACGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.60, C:0.04, G:0.09, T:0.28
Consensus pattern (24 bp):
ATTTAAATTCAAGAAAAAAAAATT
Found at i:37983 original size:15 final size:16
Alignment explanation
Indices: 37963--37996 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
37953 AACAACTTAG
37963 GTTTATAGCCCAAT-T
1 GTTTATAGCCCAATAT
*
37978 GTTTATAGCTCAATAT
1 GTTTATAGCCCAATAT
37994 GTT
1 GTT
37997 GATAAACTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (16 bp):
GTTTATAGCCCAATAT
Found at i:38422 original size:16 final size:16
Alignment explanation
Indices: 38401--38445 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
38391 GAGTCTCCAA
38401 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
38417 CGTTTATATTCGTGTT
1 CGTTTATGTTCGTGTT
38433 CGTTTATGTTCGT
1 CGTTTATGTTCGT
38446 TTATTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.09, C:0.13, G:0.22, T:0.56
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:41180 original size:17 final size:18
Alignment explanation
Indices: 41158--41194 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
41148 ACTCAAGTCG
*
41158 TAAAATTAT-TATTATTT
1 TAAAATTATATATAATTT
41175 TAAAATTATATATAATTT
1 TAAAATTATATATAATTT
41193 TA
1 TA
41195 TTTGTGATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TAAAATTATATATAATTT
Found at i:43172 original size:11 final size:12
Alignment explanation
Indices: 43145--43171 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
43135 TTAAATTATA
43145 TTTTATTGATTT
1 TTTTATTGATTT
43157 TTTTATTGATTT
1 TTTTATTGATTT
43169 TTT
1 TTT
43172 AAATTTTGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (12 bp):
TTTTATTGATTT
Found at i:43185 original size:23 final size:21
Alignment explanation
Indices: 43159--43209 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
43149 ATTGATTTTT
* *
43159 TTATTGATTTTTTAAATTTTGA
1 TTATTGATTATTTAAAATTT-A
43181 CTTATTG-TTATTTAAAATTTA
1 -TTATTGATTATTTAAAATTTA
43202 TTATTGAT
1 TTATTGAT
43210 AAAAATATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 6 0.24
21 2 0.08
22 11 0.44
23 6 0.24
ACGTcount: A:0.29, C:0.02, G:0.08, T:0.61
Consensus pattern (21 bp):
TTATTGATTATTTAAAATTTA
Found at i:53063 original size:183 final size:183
Alignment explanation
Indices: 52677--53050 Score: 635
Period size: 183 Copynumber: 2.0 Consensus size: 183
52667 ATTAAATTTT
* *
52677 AAATTTTAAATATATTATATATAACATATGGGCTCAACCCAAATCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
*
52742 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAATTTTT
66 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
* *
52807 TATTTTATAATTATATATTATTTAAATTATTTGTAAACTGTTTTTTAATTAAA
131 TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTAATTAAA
*
52860 AAATATTAAATATATTATATATAACATATGGGCT-AAGCCCAAACCATTTAAAATCCAATTAATA
1 AAATATTAAATATATTATATATAACATATGGGCTCAA-CCCAAACCATTTAAAACCCAATTAATA
*
52924 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTTATCTAAAATT
65 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAA-TTATATAAAATT
*
52989 TTTATTTTATATTTATATATTATTTAAATTAATTATAAACT-TTTTTTGAATTAAA
129 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTT-AATTAAA
53044 AAATATT
1 AAATATT
53051 TATTTTTTAT
Statistics
Matches: 180, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
182 2 0.01
183 116 0.64
184 62 0.34
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (183 bp):
AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTAATTAAA
Found at i:54531 original size:17 final size:17
Alignment explanation
Indices: 54511--54545 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
54501 AAATATTTTT
54511 TATATTAAATTATTAAA
1 TATATTAAATTATTAAA
**
54528 TATATTTTATTATTAAA
1 TATATTAAATTATTAAA
54545 T
1 T
54546 TAATTTTGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATATTAAATTATTAAA
Found at i:54535 original size:24 final size:25
Alignment explanation
Indices: 54501--54547 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
54491 TAACTTTAAC
*
54501 AAATATTTTTTA-TATTAAATTATT
1 AAATATATTTTATTATTAAATTATT
54525 AAATATATTTTATTATTAAATTA
1 AAATATATTTTATTATTAAATTA
54548 ATTTTGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
AAATATATTTTATTATTAAATTATT
Found at i:54535 original size:25 final size:24
Alignment explanation
Indices: 54501--54547 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
54491 TAACTTTAAC
54501 AAATATTTTT-TATATTAAATTATT
1 AAATATTTTTAT-TATTAAATTATT
54525 AAATATATTTTATTATTAAATTA
1 AAATAT-TTTTATTATTAAATTA
54548 ATTTTGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.29
25 14 0.67
26 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
AAATATTTTTATTATTAAATTATT
Found at i:54699 original size:31 final size:31
Alignment explanation
Indices: 54647--54730 Score: 80
Period size: 33 Copynumber: 2.6 Consensus size: 31
54637 GTAAATTAAC
* * *
54647 ATAAAATATATACTTTGAAAAGTTTTA-ATAATA
1 ATAAAATATAT--TTTTAAAAG-ATTAGATAAAA
54680 ATAAAATATATTTTTAAAAGATTAGATAAAA
1 ATAAAATATATTTTTAAAAGATTAGATAAAA
*
54711 ATAATATATATATATTTAAA
1 ATAA-A-ATATATTTTTAAA
54731 TAAAAAATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
30 3 0.07
31 17 0.39
32 1 0.02
33 23 0.52
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.39
Consensus pattern (31 bp):
ATAAAATATATTTTTAAAAGATTAGATAAAA
Found at i:54722 original size:33 final size:32
Alignment explanation
Indices: 54650--54730 Score: 85
Period size: 31 Copynumber: 2.5 Consensus size: 32
54640 AATTAACATA
* * * *
54650 AAATATATACTTTGAAAAGTTTTAATAATAAT
1 AAATATATATTTTTAAAAGTATTAATAAAAAT
54682 AAA-ATATATTTTTAAAAG-ATTAGATAAAAAT
1 AAATATATATTTTTAAAAGTATTA-ATAAAAAT
*
54713 AATATATATATATTTAAA
1 AA-ATATATATTTTTAAA
54731 TAAAAAATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
30 3 0.07
31 22 0.54
32 4 0.10
33 12 0.29
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.40
Consensus pattern (32 bp):
AAATATATATTTTTAAAAGTATTAATAAAAAT
Found at i:54756 original size:27 final size:27
Alignment explanation
Indices: 54726--54810 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
54716 ATATATATAT
54726 TTAAATAAAAAATATTTTTAAATTAAG
1 TTAAATAAAAAATATTTTTAAATTAAG
*
54753 TT-AATGTAAAAATATTTTTTAAAATTAA-
1 TTAAAT-AAAAAATA-TTTTT-AAATTAAG
* * * * *
54781 -TATATATAAAATATTATGAATTTAAG
1 TTAAATAAAAAATATTTTTAAATTAAG
54807 TTAA
1 TTAA
54811 TTATTTACAC
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
25 6 0.14
26 6 0.14
27 18 0.41
28 7 0.16
29 7 0.16
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.44
Consensus pattern (27 bp):
TTAAATAAAAAATATTTTTAAATTAAG
Found at i:54790 original size:28 final size:28
Alignment explanation
Indices: 54729--54795 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 28
54719 TATATATTTA
54729 AATA-AAAAATA-TTTTTAAATTAAGTT
1 AATATAAAAATATTTTTTAAATTAAGTT
*
54755 AATGTAAAAATATTTTTTAAAATTAA--T
1 AATATAAAAATATTTTTT-AAATTAAGTT
54782 -ATATATAAAATATT
1 AATATA-AAAATATT
54796 ATGAATTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
26 7 0.20
27 16 0.46
28 5 0.14
29 7 0.20
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (28 bp):
AATATAAAAATATTTTTTAAATTAAGTT
Found at i:70357 original size:29 final size:29
Alignment explanation
Indices: 70325--70381 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
70315 TTAAACTTAT
70325 AATAATCATATT-TAACATTACGATATTAC
1 AATAATCA-ATTATAACATTACGATATTAC
* * *
70354 AATAATTAATTATAATATTATGATATTA
1 AATAATCAATTATAACATTACGATATTA
70382 ATTGATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (29 bp):
AATAATCAATTATAACATTACGATATTAC
Found at i:77108 original size:22 final size:21
Alignment explanation
Indices: 77083--77123 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
77073 TCTTAATCAC
*
77083 AATAACTAAACTCTAAATTGAA
1 AATAA-TAAACCCTAAATTGAA
*
77105 AATAATGAACCCTAAATTG
1 AATAATAAACCCTAAATTG
77124 GTTGAGGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.51, C:0.15, G:0.07, T:0.27
Consensus pattern (21 bp):
AATAATAAACCCTAAATTGAA
Found at i:77340 original size:24 final size:23
Alignment explanation
Indices: 77312--77360 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
77302 AAAAAAAGAA
77312 AATCACATAAATTGAAAGTATAAG
1 AATCACATAAATTGAAA-TATAAG
* *
77336 AATCATATAAATTGAAATATTAG
1 AATCACATAAATTGAAATATAAG
77359 AA
1 AA
77361 AATGCAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.55, C:0.06, G:0.10, T:0.29
Consensus pattern (23 bp):
AATCACATAAATTGAAATATAAG
Found at i:79744 original size:102 final size:99
Alignment explanation
Indices: 79527--79752 Score: 301
Period size: 102 Copynumber: 2.3 Consensus size: 99
79517 AACAAGTTGG
* * * *
79527 CAGATGAATGTCTTCCCCTTGAACTTGAAGGCATTGTGTCATAGGTTTTGAATAGATTGTTGTGT
1 CAGATGAATGTCTTCCCCTTGAACTTGAAGGCATAGTGTCATAGGTATTGAACAGACTGTTGTGT
* *
79592 CAATACATCTCCATATTGAGATCCAAGAAGTTGA
66 CAATACATCTCCATATTGAGATCAAAGAAGATGA
79626 CAGATGAATGTCTTCCCCTAT-AACTTGAAGGCATAGTGTCATATGGGTATTGAACAGACTGTTG
1 CAGATGAATGTCTTCCCCT-TGAACTTGAAGGCATAGTGTCATA--GGTATTGAACAGACTGTTG
* * * *
79690 TGTCGATGACATTTCCATGTTGAGATCAAAGAAGATGG
63 TGTCAAT-ACATCTCCATATTGAGATCAAAGAAGATGA
* *
79728 TAGATGAATGTTTTCCCCTTGAACT
1 CAGATGAATGTCTTCCCCTTGAACT
79753 ATAGGGATGT
Statistics
Matches: 110, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
99 40 0.36
100 1 0.01
101 23 0.21
102 46 0.42
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.33
Consensus pattern (99 bp):
CAGATGAATGTCTTCCCCTTGAACTTGAAGGCATAGTGTCATAGGTATTGAACAGACTGTTGTGT
CAATACATCTCCATATTGAGATCAAAGAAGATGA
Found at i:86746 original size:2 final size:2
Alignment explanation
Indices: 86739--86790 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
86729 GTGCGATCAG
86739 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
86781 AT AT AT AT AT
1 AT AT AT AT AT
86791 GGTTCAAATC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:87795 original size:23 final size:21
Alignment explanation
Indices: 87767--87840 Score: 75
Period size: 20 Copynumber: 3.6 Consensus size: 21
87757 AATTATTTAT
87767 TATATTTTAAATGATTAAATTAA
1 TATATTTT-AAT-ATTAAATTAA
*
87790 TATATTTT-ATAATAAATT--
1 TATATTTTAATATTAAATTAA
*
87808 TATATTCTAATAATTAAA-TAA
1 TATATTTTAAT-ATTAAATTAA
87829 TATATTTTAATA
1 TATATTTTAATA
87841 ATATAAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
18 7 0.16
19 3 0.07
20 13 0.30
21 12 0.28
23 8 0.19
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (21 bp):
TATATTTTAATATTAAATTAA
Found at i:87834 original size:21 final size:20
Alignment explanation
Indices: 87744--87851 Score: 73
Period size: 21 Copynumber: 5.3 Consensus size: 20
87734 ATATATATGT
87744 AATAATAT-TTT-ATAATTA
1 AATAATATATTTAATAATTA
** * *
87762 TTTATTATATTTTAAATGATTA
1 AATAATATA-TTT-AATAATTA
*
87784 AATTAATATATTTTATAA-TA
1 AA-TAATATATTTAATAATTA
*
87804 AAT-TTATATTCTAATAATTA
1 AATAATATATT-TAATAATTA
87824 AATAATATATTTTAATAATATA
1 AATAATATA-TTTAATAAT-TA
87846 AA-AATA
1 AATAATA
87852 AAATTTATTA
Statistics
Matches: 68, Mismatches: 12, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
18 11 0.16
19 6 0.09
20 12 0.18
21 18 0.26
22 15 0.22
23 6 0.09
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (20 bp):
AATAATATATTTAATAATTA
Found at i:87842 original size:40 final size:41
Alignment explanation
Indices: 87743--87843 Score: 116
Period size: 40 Copynumber: 2.4 Consensus size: 41
87733 GATATATATG
** * *
87743 TAATAATATTTTATAATTATTTATTATATTTTAAATGATTAAAT
1 TAAT-ATATTTTATAA-TAAAT-TTATATTCTAAATAATTAAAT
87787 TAATATATTTTATAATAAATTTATATTCT-AATAATTAAA-
1 TAATATATTTTATAATAAATTTATATTCTAAATAATTAAAT
87826 TAATATATTTTAATAATA
1 TAATATATTTT-ATAATA
87844 TAAAAATAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
39 11 0.21
40 15 0.29
41 8 0.15
42 3 0.06
43 11 0.21
44 4 0.08
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (41 bp):
TAATATATTTTATAATAAATTTATATTCTAAATAATTAAAT
Found at i:87858 original size:21 final size:21
Alignment explanation
Indices: 87815--87858 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
87805 ATTTATATTC
* *
87815 TAATAATTAAATAATATATTT
1 TAATAATTAAATAATAAAATT
87836 TAATAATATAAA-AATAAAATT
1 TAATAAT-TAAATAATAAAATT
87857 TA
1 TA
87859 TTAAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAATAATTAAATAATAAAATT
Found at i:89970 original size:10 final size:10
Alignment explanation
Indices: 89957--90000 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
89947 TCATTAAGTC
*
89957 TAATTAATAT
1 TAATTAAAAT
89967 TAATTAAAATT
1 TAATTAAAA-T
*
89978 TAATTAATAT
1 TAATTAAAAT
*
89988 CAATTAAAAT
1 TAATTAAAAT
89998 TAA
1 TAA
90001 AGAAACATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
10 19 0.68
11 9 0.32
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (10 bp):
TAATTAAAAT
Found at i:89982 original size:21 final size:21
Alignment explanation
Indices: 89957--89998 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
89947 TCATTAAGTC
*
89957 TAATTAATATTAATTAAAATT
1 TAATTAATATCAATTAAAATT
89978 TAATTAATATCAATTAAAATT
1 TAATTAATATCAATTAAAATT
89999 AAAGAAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TAATTAATATCAATTAAAATT
Found at i:93443 original size:23 final size:23
Alignment explanation
Indices: 93409--93455 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
93399 TTCATCTGCC
93409 TTTATTTGCCTTTATGACACGTT
1 TTTATTTGCCTTTATGACACGTT
* *
93432 TTTATATT-CCTTTGTGAGACGTT
1 TTTAT-TTGCCTTTATGACACGTT
93455 T
1 T
93456 CTTTTGTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.17, C:0.15, G:0.15, T:0.53
Consensus pattern (23 bp):
TTTATTTGCCTTTATGACACGTT
Found at i:101254 original size:26 final size:24
Alignment explanation
Indices: 101225--101296 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
101215 AAAGTCCAAC
101225 AAATTTAACAAAATAAAGTAAGTATT
1 AAATTTAACAAAATAAAGTAA--ATT
*
101251 AAA-TGAGA-AATAATAAA--AAATT
1 AAATTTA-ACAA-AATAAAGTAAATT
101273 ACAATTTAACAAAATAAAGTAAAT
1 A-AATTTAACAAAATAAAGTAAAT
101297 ACAAATATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 9 0.24
24 6 0.16
25 8 0.22
26 10 0.27
ACGTcount: A:0.62, C:0.04, G:0.07, T:0.26
Consensus pattern (24 bp):
AAATTTAACAAAATAAAGTAAATT
Found at i:101432 original size:15 final size:15
Alignment explanation
Indices: 101412--101444 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
101402 ACTCCTCGCT
101412 GTCATCATCATCGTC
1 GTCATCATCATCGTC
101427 GTCATCATCATCGTC
1 GTCATCATCATCGTC
101442 GTC
1 GTC
101445 GTCGTCTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.33, G:0.15, T:0.33
Consensus pattern (15 bp):
GTCATCATCATCGTC
Found at i:101436 original size:18 final size:18
Alignment explanation
Indices: 101413--101447 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
101403 CTCCTCGCTG
101413 TCATCATCATCGTCGTCA
1 TCATCATCATCGTCGTCA
*
101431 TCATCATCGTCGTCGTC
1 TCATCATCATCGTCGTC
101448 GTCTTGCGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.34, G:0.14, T:0.34
Consensus pattern (18 bp):
TCATCATCATCGTCGTCA
Found at i:103119 original size:111 final size:111
Alignment explanation
Indices: 102977--103198 Score: 392
Period size: 111 Copynumber: 2.0 Consensus size: 111
102967 ATTACAAAAA
* *
102977 TTAATTCTTAATCTAATAATCATGTATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAAT-AACTAAATATTACTAATAATTTAAATTA
* *
103042 AATT-AAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
65 AATTAAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
103088 TTAATTCTTAATCTAATAATCATGCATTAAATAAATAACTAAATATTACTAATAATTTAAATTAA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATAACTAAATATTACTAATAATTTAAATTAA
103153 ATTAAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
66 ATTAAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
103199 ATGATTTCCA
Statistics
Matches: 106, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
110 31 0.29
111 75 0.71
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATAACTAAATATTACTAATAATTTAAATTAA
ATTAAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:103336 original size:12 final size:10
Alignment explanation
Indices: 103322--103362 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
103312 ACCTTAAAAA
*
103322 GAGAGTATTT
1 GAGAGAATTT
103332 GAGAGAAATTT
1 GAGAG-AATTT
103343 -AGAGAATTT
1 GAGAGAATTT
103352 GAGAGAATTT
1 GAGAGAATTT
103362 G
1 G
103363 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:104756 original size:23 final size:23
Alignment explanation
Indices: 104724--104807 Score: 116
Period size: 23 Copynumber: 3.7 Consensus size: 23
104714 CTCATATAAA
*
104724 TGCACCGAAGTGCCATGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
104747 TACACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
104770 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
104793 TGCACC-ATAGTGCCA
1 TGCACCGA-AGTGCCA
104808 TATAAGATGT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
22 1 0.02
23 54 0.98
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:105924 original size:22 final size:22
Alignment explanation
Indices: 105894--105947 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
105884 CAGGTTCATG
*
105894 TAACTCATATAGCATTTTCC-TA
1 TAACACATATAGCA-TTTCCATA
* * *
105916 TAATACATAAATCATTTCCATA
1 TAACACATATAGCATTTCCATA
105938 TAACACATAT
1 TAACACATAT
105948 CATATAAATT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.41, C:0.20, G:0.02, T:0.37
Consensus pattern (22 bp):
TAACACATATAGCATTTCCATA
Found at i:109719 original size:5 final size:5
Alignment explanation
Indices: 109703--109734 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
109693 TTTAATAGTT
109703 TATTA T-TT- TATTA TATTA TATTA TATTA TATT
1 TATTA TATTA TATTA TATTA TATTA TATTA TATT
109735 TAATATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
3 1 0.04
4 4 0.16
5 20 0.80
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (5 bp):
TATTA
Found at i:109755 original size:39 final size:39
Alignment explanation
Indices: 109678--109756 Score: 92
Period size: 39 Copynumber: 2.0 Consensus size: 39
109668 AAAATTTTTC
* *
109678 ATTATATTATAATCATTTAATAGTTTATTATTTTATTAT
1 ATTATATTATAATCATTTAATAGTTAATTATTTAATTAT
109717 ATTATATTATATTAT-ATTTAATA-TTAATT-TTGTAATTAT
1 ATTATATTATA--ATCATTTAATAGTTAATTATT-TAATTAT
109756 A
1 A
109757 AAATGGCAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
38 2 0.06
39 23 0.66
40 8 0.23
41 2 0.06
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (39 bp):
ATTATATTATAATCATTTAATAGTTAATTATTTAATTAT
Found at i:109872 original size:26 final size:27
Alignment explanation
Indices: 109842--109893 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
109832 ATTCTATTAT
109842 TTTATTTATAATGAAT-GTTT-TATTTA
1 TTTATTTATAAT-AATAGTTTATATTTA
*
109868 TTTATTTTTAATAATAGTTTATATTT
1 TTTATTTATAATAATAGTTTATATTT
109894 TAATTTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 3 0.13
26 15 0.65
27 5 0.22
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (27 bp):
TTTATTTATAATAATAGTTTATATTTA
Found at i:119512 original size:94 final size:87
Alignment explanation
Indices: 119340--119512 Score: 213
Period size: 94 Copynumber: 1.9 Consensus size: 87
119330 TAGACTAAAC
*
119340 TATTCATTTATTTATTTTTATTGAAAAGATGAATAAATTATTCATTTAACGATCTGAAAAGATAT
1 TATTCATTTATTTATTTTTATTGAAAAGATGAATAAATTATTCATTCAACGATCTGAAAAGATAT
**
119405 AGATCGACTAAATTATACTATT
66 AGATAAACTAAATTATACTATT
* *
119427 TATTTATTTATTTATTTCGATTCATTGAAAAGATGTAGAATAAATTATTCATTCAATGATCTGAA
1 TATTCATTTATTTATTT---TT-ATTGAAAAGA--T-GAATAAATTATTCATTCAACGATCTGAA
*
119492 AAGATGTAGACTAAAC-AAATT
59 AAGATATAGA-TAAACTAAATT
119513 TAGTCATGAA
Statistics
Matches: 72, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
87 16 0.22
90 2 0.03
91 10 0.14
93 1 0.01
94 40 0.56
95 3 0.04
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.41
Consensus pattern (87 bp):
TATTCATTTATTTATTTTTATTGAAAAGATGAATAAATTATTCATTCAACGATCTGAAAAGATAT
AGATAAACTAAATTATACTATT
Found at i:120669 original size:21 final size:21
Alignment explanation
Indices: 120623--120669 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
120613 TTACAAAATA
120623 ATTAATTGTCATAAACATTAT
1 ATTAATTGTCATAAACATTAT
*
120644 TTTAA-TGATCATAAA-ATATAT
1 ATTAATTG-TCATAAACAT-TAT
120665 ATTAA
1 ATTAA
120670 ATATTTTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (21 bp):
ATTAATTGTCATAAACATTAT
Found at i:125353 original size:65 final size:64
Alignment explanation
Indices: 125221--125378 Score: 203
Period size: 64 Copynumber: 2.5 Consensus size: 64
125211 GAACACTTGA
* ***
125221 TGCATCGGTGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGGTGCATCGATGCATGGCTTG
1 TGCATC-GTGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCGATGCATGGAGAG
* **
125285 TGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAGA
1 TGCATCG-TGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAG-GTGCATCGATGCATGGAGA
125349 G
64 G
*
125350 TGCATCGTGCATGGAATGCATTCGATGTT
1 TGCATCGTGCATGAAATGCATTCGATGTT
125379 CATTAATCAT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
63 1 0.01
64 53 0.65
65 28 0.34
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (64 bp):
TGCATCGTGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCGATGCATGGAGAG
Found at i:125362 original size:18 final size:19
Alignment explanation
Indices: 125327--125376 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
125317 GAAAATATTC
125327 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
125346 AGAGTGCATCG-TGCATGG
1 AGAGTGCATCGATGCATGG
125364 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
125377 TTCATTAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.14
17 4 0.14
18 10 0.34
19 11 0.38
ACGTcount: A:0.26, C:0.16, G:0.34, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:131607 original size:22 final size:21
Alignment explanation
Indices: 131565--131604 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
131555 GAGTTTGTTT
*
131565 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
131586 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
131605 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:133599 original size:64 final size:64
Alignment explanation
Indices: 133546--133708 Score: 202
Period size: 65 Copynumber: 2.5 Consensus size: 64
133536 CGGTGCACCA
* *
133546 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATTGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
** * ** *
133610 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTACATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
* * *
133675 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
133709 CAATTAATTC
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
64 39 0.47
65 44 0.53
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:133684 original size:19 final size:19
Alignment explanation
Indices: 133656--133706 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
133646 GAAAATATTC
*
133656 AGAGTACATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
133675 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
133694 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
133707 TTCAATTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 18 0.64
ACGTcount: A:0.27, C:0.16, G:0.33, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:136501 original size:3 final size:3
Alignment explanation
Indices: 136490--136521 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
136480 AAAAAACAGA
136490 AAG AGAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG A-AG AAG AAG AAG AAG AAG AAG AAG AAG A
136522 CATACAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:158850 original size:205 final size:204
Alignment explanation
Indices: 158458--158872 Score: 706
Period size: 205 Copynumber: 2.0 Consensus size: 204
158448 TCTCGGGATT
* *
158458 TTAGTTTTAATTATCTTTTTATATTACATTATAATATTTATATATATTTTATATTATTATTAGTT
1 TTAGTTTTAATTACCTTTTTATATTACATTATAATATTTATATATATTTTATACTATTATTAG--
*
158523 TTTTTTTTACACATTCGTATATATTTATTATTAGTATAGTATTATTTCACTTATATGTTATATTA
64 -TTTTTTTACACATTCGTATACATTTATTATTAGTATAGTATTATTTCACTTATATGTTATATTA
*
158588 TATATATATATGTATATATGTACACATTTTGTATTTTACCCTATTTGTTTACTTCTTTATTATTA
128 TATATATATATGTATATATGTACACATTTTGTATTTTACCCTATTTGTTTACTTCTTTATTATCA
158653 TATTTATTTACA
193 TATTTATTTACA
158665 TTAGTTTTAATTACCTTTTTATATTACATTATAATATTTATATATATTTTATACTATTATTAG-T
1 TTAGTTTTAATTACCTTTTTATATTACATTATAATATTTATATATATTTTATACTATTATTAGTT
* * *
158729 TTTTTATACATTCGTATACATTTATTATTAGTATAGTATTATTTCATTTATGTGTTATATTATAT
66 TTTTTACACATTCGTATACATTTATTATTAGTATAGTATTATTTCACTTATATGTTATA-T-TAT
*
158794 ATATATATATGTATATATGTACACATTTTGTATTTTACCCTATTTTTTTACTTCTTTATTATCAT
129 ATATATATATGTATATATGTACACATTTTGTATTTTACCCTATTTGTTTACTTCTTTATTATCAT
158859 ATTTATTTACA
194 ATTTATTTACA
158870 TTA
1 TTA
158873 TTTATTTTTT
Statistics
Matches: 198, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
203 56 0.28
204 1 0.01
205 80 0.40
207 61 0.31
ACGTcount: A:0.30, C:0.08, G:0.05, T:0.57
Consensus pattern (204 bp):
TTAGTTTTAATTACCTTTTTATATTACATTATAATATTTATATATATTTTATACTATTATTAGTT
TTTTTACACATTCGTATACATTTATTATTAGTATAGTATTATTTCACTTATATGTTATATTATAT
ATATATATGTATATATGTACACATTTTGTATTTTACCCTATTTGTTTACTTCTTTATTATCATAT
TTATTTACA
Found at i:159075 original size:15 final size:14
Alignment explanation
Indices: 159033--159070 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
159023 TATATATATA
159033 TATTTTC-TTATTT
1 TATTTTCATTATTT
159046 TATTTTCATTATTT
1 TATTTTCATTATTT
159060 T-TTTT-ATTATT
1 TATTTTCATTATT
159071 ATTTTACATG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 6 0.25
13 11 0.46
14 7 0.29
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (14 bp):
TATTTTCATTATTT
Found at i:170628 original size:105 final size:105
Alignment explanation
Indices: 170446--171030 Score: 1134
Period size: 105 Copynumber: 5.6 Consensus size: 105
170436 AGGTTTTACC
*
170446 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAATTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
170511 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
66 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
170551 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
170616 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
170656 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
170721 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
170761 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
170826 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
170866 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
170931 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
*
170971 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACT
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
171031 CAACCTCATG
Statistics
Matches: 476, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 476 1.00
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
Found at i:172629 original size:2 final size:2
Alignment explanation
Indices: 172617--172656 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
172607 ATTTATGTGT
*
172617 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
172657 GTACACATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:172910 original size:12 final size:13
Alignment explanation
Indices: 172875--172915 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
172865 TATATATATA
*
172875 TATTTTCTTATTT
1 TATTTTATTATTT
172888 TATTTTCATTATTT
1 TATTTT-ATTATTT
172902 T-TTTTATTATTT
1 TATTTTATTATTT
172914 TA
1 TA
172916 CATGTACATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 8 0.32
13 10 0.40
14 7 0.28
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTTTATTATTT
Found at i:178835 original size:25 final size:24
Alignment explanation
Indices: 178760--178860 Score: 77
Period size: 24 Copynumber: 4.2 Consensus size: 24
178750 TTTTTAATAA
*
178760 TTTATAA-ATATTT-T-TTTTTAT
1 TTTATAATATATTTATATTTATAT
**
178781 TTT-TAACCTATTTATATTTATAT
1 TTTATAATATATTTATATTTATAT
*
178804 TTTATAATATATTTATCTTT-TATT
1 TTTATAATATATTTATATTTATA-T
* *
178828 TTTAATAATATACTTTTTATATTATTT
1 TTT-ATAATATA-TTTATAT-TTATAT
178855 TTTATA
1 TTTATA
178861 CTTAATATTT
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
20 3 0.05
21 8 0.13
22 1 0.02
23 11 0.17
24 17 0.27
25 8 0.13
26 8 0.13
27 6 0.10
28 1 0.02
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTATAATATATTTATATTTATAT
Found at i:178847 original size:46 final size:43
Alignment explanation
Indices: 178750--178850 Score: 105
Period size: 46 Copynumber: 2.2 Consensus size: 43
178740 AGTGTCTAAT
* * *
178750 TTTTTAATAATTTATAAATATTTTTTTTTATTTTTAACCTATTTA
1 TTTTT-ATATTTTATAAATATTTTCTTTTATTTTTAA-CTATATA
*
178795 TATTTATATTTTATAATATATTTATCTTTTATTTTTAA-TAATATA
1 TTTTTATATTTTATAA-ATATTT-TCTTTTATTTTTAACT-ATATA
178840 CTTTTTATATT
1 -TTTTTATATT
178851 ATTTTTTATA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
44 11 0.23
45 14 0.30
46 22 0.47
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (43 bp):
TTTTTATATTTTATAAATATTTTCTTTTATTTTTAACTATATA
Found at i:178850 original size:23 final size:23
Alignment explanation
Indices: 178795--178850 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
178785 AACCTATTTA
*
178795 TATTTATA-TTTTATAATATATT
1 TATTTATATTTTTATAATATACT
*
178817 TATCTTTTATTTTTAATAATATACT
1 TAT-TTATATTTTT-ATAATATACT
178842 T-TTTATATT
1 TATTTATATT
178851 ATTTTTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 3 0.11
23 10 0.36
24 5 0.18
25 10 0.36
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (23 bp):
TATTTATATTTTTATAATATACT
Found at i:179066 original size:36 final size:36
Alignment explanation
Indices: 179026--179136 Score: 137
Period size: 36 Copynumber: 3.2 Consensus size: 36
179016 TATTATCAAC
*
179026 ATGTATATTATTGTATTATTAATATACATACGAATA
1 ATGTATATTATTATATTATTAATATACATACGAATA
**
179062 ATGTATATTGCTATATATATT-ATAT-CA-AC----A
1 ATGTATATTATTATAT-TATTAATATACATACGAATA
179092 ATGTATATTATTATATTATTAATATACATACGAATA
1 ATGTATATTATTATATTATTAATATACATACGAATA
179128 ATGTATATT
1 ATGTATATT
179137 GCTATGTTAG
Statistics
Matches: 62, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
29 4 0.06
30 19 0.31
31 2 0.03
32 2 0.03
34 2 0.03
35 2 0.03
36 27 0.44
37 4 0.06
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.45
Consensus pattern (36 bp):
ATGTATATTATTATATTATTAATATACATACGAATA
Found at i:179095 original size:30 final size:30
Alignment explanation
Indices: 178999--179100 Score: 86
Period size: 36 Copynumber: 3.3 Consensus size: 30
178989 GTCATTATCC
178999 ATGTATATTGCTATATATA-T-TATCAAC-
1 ATGTATATTGCTATATATATTATATCAACA
** *
179026 ATGTATATTATTGTAT-TATTAATATACATACGAATA
1 ATGTATATTGCTATATATATT-ATAT-CA-AC----A
179062 ATGTATATTGCTATATATATTATATCAACA
1 ATGTATATTGCTATATATATTATATCAACA
179092 ATGTATATT
1 ATGTATATT
179101 ATTATATTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
26 2 0.03
27 14 0.24
29 3 0.05
30 12 0.21
31 2 0.03
34 2 0.03
35 2 0.03
36 17 0.29
37 4 0.07
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (30 bp):
ATGTATATTGCTATATATATTATATCAACA
Found at i:179120 original size:66 final size:63
Alignment explanation
Indices: 178999--179141 Score: 250
Period size: 66 Copynumber: 2.2 Consensus size: 63
178989 GTCATTATCC
*
178999 ATGTATATTGCTATATATATTATCAACATGTATATTATTGTATTATTAATATACATACGAATA
1 ATGTATATTGCTATATATATTATCAACATGTATATTATTATATTATTAATATACATACGAATA
179062 ATGTATATTGCTATATATATTATATCAACAATGTATATTATTATATTATTAATATACATACGAAT
1 ATGTATATTGCTATATATA-T-TATCAAC-ATGTATATTATTATATTATTAATATACATACGAAT
179127 A
63 A
179128 ATGTATATTGCTAT
1 ATGTATATTGCTAT
179142 GTTAGTAACG
Statistics
Matches: 76, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
63 19 0.25
64 1 0.01
65 7 0.09
66 49 0.64
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.45
Consensus pattern (63 bp):
ATGTATATTGCTATATATATTATCAACATGTATATTATTATATTATTAATATACATACGAATA
Found at i:179330 original size:33 final size:34
Alignment explanation
Indices: 179287--179366 Score: 85
Period size: 33 Copynumber: 2.3 Consensus size: 34
179277 CAATATATCT
*
179287 TTTATAAAAATATAAGATT-TTAGA-TACTATTAAA-
1 TTTA-AAAAATATAA-ATTATTA-ATTAATATTAAAC
*
179321 TTTAAAAAATATCAATTATTAATTAATATTAAAC
1 TTTAAAAAATATAAATTATTAATTAATATTAAAC
179355 TTTAAATAAATA
1 TTTAAA-AAATA
179367 AGAATCACCC
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
32 4 0.10
33 21 0.52
34 10 0.25
35 5 0.12
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.41
Consensus pattern (34 bp):
TTTAAAAAATATAAATTATTAATTAATATTAAAC
Found at i:179720 original size:26 final size:26
Alignment explanation
Indices: 179691--179740 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
179681 GACAGATGAA
* *
179691 ATTTAATTATTATATAAGTTTAAAAT
1 ATTTAATTATAATATAAATTTAAAAT
*
179717 ATTTTATTATAATATAAATTTAAA
1 ATTTAATTATAATATAAATTTAAA
179741 CAAACAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
ATTTAATTATAATATAAATTTAAAAT
Found at i:185098 original size:14 final size:14
Alignment explanation
Indices: 185079--185108 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
185069 TTTAGATTTT
*
185079 TTAAAATTACATTA
1 TTAAAAATACATTA
185093 TTAAAAATACATTA
1 TTAAAAATACATTA
185107 TT
1 TT
185109 GATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:185317 original size:17 final size:17
Alignment explanation
Indices: 185288--185320 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
185278 AATTAAAATT
185288 ACAAGACACAATTGAAA
1 ACAAGACACAATTGAAA
185305 ACAAG-CACAAATTGAA
1 ACAAGACAC-AATTGAA
185321 TGAACACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.58, C:0.18, G:0.12, T:0.12
Consensus pattern (17 bp):
ACAAGACACAATTGAAA
Found at i:186432 original size:11 final size:11
Alignment explanation
Indices: 186416--186491 Score: 53
Period size: 11 Copynumber: 6.6 Consensus size: 11
186406 GAGTTTGAGT
186416 TCGAGCTTGAA
1 TCGAGCTTGAA
186427 TCGAGCTTGAA
1 TCGAGCTTGAA
* **
186438 CCGAGCTCAAA
1 TCGAGCTTGAA
* *
186449 TTCGAGTTTGAGT
1 -TCGAGCTTGA-A
**
186462 TCGAGCTCAAAA
1 TCGAGCT-TGAA
*
186474 TCGAGCTTCAA
1 TCGAGCTTGAA
186485 TCGAGCT
1 TCGAGCT
186492 CGAGTCTCGA
Statistics
Matches: 48, Mismatches: 14, Indels: 6
0.71 0.21 0.09
Matches are distributed among these distances:
11 28 0.58
12 19 0.40
13 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:186492 original size:23 final size:23
Alignment explanation
Indices: 186425--186492 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
186415 TTCGAGCTTG
*
186425 AATCGAGCTTGAACCGAGCTCAA
1 AATCGAGCTTGAATCGAGCTCAA
* * *
186448 ATTCGAGTTTGAGTTCGAGCTCAA
1 AATCGAGCTTGA-ATCGAGCTCAA
*
186472 AATCGAGCTTCAATCGAGCTC
1 AATCGAGCTTGAATCGAGCTC
186493 GAGTCTCGAG
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
23 18 0.50
24 18 0.50
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (23 bp):
AATCGAGCTTGAATCGAGCTCAA
Found at i:187230 original size:20 final size:21
Alignment explanation
Indices: 187205--187297 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
187195 TTTTCCCAAT
*
187205 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
187225 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
187246 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
187266 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
187287 TCGCAATGCGA
1 TCGCAATGCGA
187298 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:187262 original size:41 final size:41
Alignment explanation
Indices: 187205--187297 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
187195 TTTTCCCAAT
187205 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
187246 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
187287 TCGCAATGCGA
1 TCGCAATGCGA
187298 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:187310 original size:41 final size:41
Alignment explanation
Indices: 187224--187358 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
187214 GAATAAGTAA
* *
187224 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
187265 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
187306 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
187347 TTCGCAACGCGA
1 ATCGCAACGCGA
187359 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:187311 original size:20 final size:20
Alignment explanation
Indices: 187286--187417 Score: 117
Period size: 20 Copynumber: 6.7 Consensus size: 20
187276 AATTGGGAAA
*
187286 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
187306 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
187327 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
187347 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
187367 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
187387 TTCGCAACGCGATAAT-AC-
1 ATCGCAACGCGATACTGACT
*
187405 ATCGCAATGCGAT
1 ATCGCAACGCGAT
187418 TTTCAAAGCG
Statistics
Matches: 95, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
18 11 0.12
19 4 0.04
20 65 0.68
21 13 0.14
22 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:187611 original size:21 final size:22
Alignment explanation
Indices: 187585--187627 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
187575 CACTCTCTCA
187585 CCCATCTCCGACG-AATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
187606 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
187628 TATCTCCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.19, C:0.47, G:0.16, T:0.19
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:187927 original size:20 final size:20
Alignment explanation
Indices: 187888--187946 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
187878 GCGATTCTCT
*
187888 CGTTGCGATAGTCGA-ATTCG
1 CGTTGCGATAGTC-ATTTTCG
187908 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
187928 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
187947 AGAAACTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 1 0.03
20 33 0.97
ACGTcount: A:0.15, C:0.19, G:0.24, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:188128 original size:21 final size:22
Alignment explanation
Indices: 188084--188128 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
188074 GTTTATTATT
*
188084 GTTTTTGGTATATCTTCATGTA
1 GTTTTTGGTATATCTTAATGTA
*
188106 GTTTTTGGTATATC-TAATTTA
1 GTTTTTGGTATATCTTAATGTA
188127 GT
1 GT
188129 ATGTTTATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.20, C:0.07, G:0.18, T:0.56
Consensus pattern (22 bp):
GTTTTTGGTATATCTTAATGTA
Found at i:189286 original size:18 final size:18
Alignment explanation
Indices: 189260--189304 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
189250 TCCACTTCGG
*
189260 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
189278 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
189296 GAGCCATCA
1 GAGCCATCA
189305 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:189817 original size:20 final size:19
Alignment explanation
Indices: 189794--189838 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
189784 TGCAACACGA
189794 AAATGACTATCACAACGCGG
1 AAATGACTATCACAACGC-G
* * *
189814 AAATGGCTATCGCAATGCG
1 AAATGACTATCACAACGCG
189833 AAATGA
1 AAATGA
189839 AAATCGCAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (19 bp):
AAATGACTATCACAACGCG
Found at i:189837 original size:19 final size:19
Alignment explanation
Indices: 189794--189852 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
189784 TGCAACACGA
* *
189794 AAATGACTATCACAACGCGG
1 AAATGACTATCGCAATGC-G
*
189814 AAATGGCTATCGCAATGCG
1 AAATGACTATCGCAATGCG
**
189833 AAATGAAAATCGCAATGCG
1 AAATGACTATCGCAATGCG
189852 A
1 A
189853 TTTGTGTTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.17
Consensus pattern (19 bp):
AAATGACTATCGCAATGCG
Found at i:189883 original size:14 final size:14
Alignment explanation
Indices: 189864--189921 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
189854 TTGTGTTTCG
189864 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
189878 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
189894 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
189910 CGTTGCGATTTT
1 CGTTGCGATTTT
189922 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:189898 original size:32 final size:33
Alignment explanation
Indices: 189859--189937 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
189849 GCGATTTGTG
189859 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
189891 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
189924 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
189938 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:189936 original size:19 final size:19
Alignment explanation
Indices: 189878--189995 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
189868 GCGATTTTGT
189878 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
189896 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
189910 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
189929 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
189949 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
189968 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
189988 TGTTGCGA
1 CGTTGCGA
189996 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:192010 original size:19 final size:19
Alignment explanation
Indices: 191988--192055 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
191978 ATCGCAACGA
191988 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
192007 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
192026 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
192040 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
192056 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:192096 original size:19 final size:19
Alignment explanation
Indices: 192074--192110 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
192064 TCGCATTGCG
*
192074 ATTTTCTCGTTGCGATAGC
1 ATTTTCGCGTTGCGATAGC
192093 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
192111 TCAAATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.19, G:0.24, T:0.41
Consensus pattern (19 bp):
ATTTTCGCGTTGCGATAGC
Found at i:193177 original size:24 final size:24
Alignment explanation
Indices: 193150--193203 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
193140 AGTATTCGAA
* *
193150 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
193174 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
193198 TTTGAT
1 TTTGAT
193204 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:195700 original size:33 final size:33
Alignment explanation
Indices: 195658--195780 Score: 176
Period size: 33 Copynumber: 3.7 Consensus size: 33
195648 ATTACTATCC
195658 CAATGCGAAATGAAAATCGCAACGAGAGAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCG
* ** *
195691 CAATGCGAAATGAAAATCACAACGCTA-ATTTCG
1 CAATGCGAAATGAAAATCGCAACGAGAGA-ATCG
* *
195724 CAATGCGAAATAAAAATCGCAACGAGGGAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCG
195757 CAATGCGAAATGAAAATCGCAACG
1 CAATGCGAAATGAAAATCGCAACG
195781 CGAATTTAAT
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
32 1 0.01
33 75 0.97
34 1 0.01
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.15
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGAGAGAATCG
Found at i:195764 original size:66 final size:66
Alignment explanation
Indices: 195658--195787 Score: 224
Period size: 66 Copynumber: 2.0 Consensus size: 66
195648 ATTACTATCC
* *
195658 CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCTAATTTC
1 CAATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCGAATTTC
195723 G
66 G
* *
195724 CAATGCGAAATAAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1 CAATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCGAATTT
195788 AATTCGCGTT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (66 bp):
CAATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCGAATTTC
G
Found at i:195801 original size:18 final size:20
Alignment explanation
Indices: 195780--195821 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
195770 AAATCGCAAC
195780 GCGAATTT-A-ATTCGCGTT
1 GCGAATTTCATATTCGCGTT
* *
195798 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCATATTCGCGTT
195818 GCGA
1 GCGA
195822 TTCTCTCGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 7 0.35
19 1 0.05
20 12 0.60
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (20 bp):
GCGAATTTCATATTCGCGTT
Found at i:195977 original size:13 final size:14
Alignment explanation
Indices: 195961--195996 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
195951 CATCAATTAA
195961 ACAAATCAAC-TTT
1 ACAAATCAACTTTT
*
195974 ACAAATCATCTTTT
1 ACAAATCAACTTTT
195988 ACAAATCAA
1 ACAAATCAA
195997 TTAAACAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Done.