Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003921.1 Hibiscus syriacus cultivar Beakdansim tig00008477_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: 85048
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:1394 original size:14 final size:16
Alignment explanation
Indices: 1375--1407 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
1365 GTGATAATTC
1375 ACGGTCC-TGATG-TG
1 ACGGTCCATGATGTTG
1389 ACGGTCCATGATGTTG
1 ACGGTCCATGATGTTG
1405 ACG
1 ACG
1408 TGACAGTCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 5 0.29
16 5 0.29
ACGTcount: A:0.18, C:0.21, G:0.33, T:0.27
Consensus pattern (16 bp):
ACGGTCCATGATGTTG
Found at i:7993 original size:16 final size:16
Alignment explanation
Indices: 7972--8018 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
7962 TAATAAATAA
7972 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
7988 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
8004 ACGAACATAAACGAA
1 ACGAACATAAACGAA
8019 TATAAACGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.57, C:0.21, G:0.13, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:9138 original size:14 final size:14
Alignment explanation
Indices: 9121--9162 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
9111 AATGAACATA
9121 AACGAACATAACCG
1 AACGAACATAACCG
9135 AACGAACAT----G
1 AACGAACATAACCG
9145 AACGAACATAACCG
1 AACGAACATAACCG
9159 AACG
1 AACG
9163 TTCACGAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 10 0.42
14 14 0.58
ACGTcount: A:0.50, C:0.26, G:0.17, T:0.07
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:9198 original size:24 final size:24
Alignment explanation
Indices: 9121--9196 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
9111 AATGAACATA
** *
9121 AACGAACATAACCGAACGAACATG
1 AACGAACATAACCGAACGTTCACG
9145 AACGAACATAACCGAACGTTCACG
1 AACGAACATAACCGAACGTTCACG
*
9169 AACGTACATAACCGAACGTTCACG
1 AACGAACATAACCGAACGTTCACG
9193 AACG
1 AACG
9197 TAAATTAACG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.43, C:0.28, G:0.17, T:0.12
Consensus pattern (24 bp):
AACGAACATAACCGAACGTTCACG
Found at i:9208 original size:24 final size:24
Alignment explanation
Indices: 9128--9210 Score: 98
Period size: 24 Copynumber: 3.5 Consensus size: 24
9118 ATAAACGAAC
** *
9128 ATAACCGAACGAACATGAACG-AA
1 ATAACCGAACGTTCACGAACGTAA
*
9151 CATAACCGAACGTTCACGAACGTAC
1 -ATAACCGAACGTTCACGAACGTAA
9176 ATAACCGAACGTTCACGAACGTAA
1 ATAACCGAACGTTCACGAACGTAA
9200 ATTAA-CGAACG
1 A-TAACCGAACG
9211 AGACCTATGT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
24 48 0.92
25 4 0.08
ACGTcount: A:0.43, C:0.25, G:0.17, T:0.14
Consensus pattern (24 bp):
ATAACCGAACGTTCACGAACGTAA
Found at i:10825 original size:3 final size:3
Alignment explanation
Indices: 10814--10928 Score: 176
Period size: 3 Copynumber: 37.7 Consensus size: 3
10804 ATTTTTTTCA
* * *
10814 TAT TTT TAT TAT TAT TAT TAT TAT TAA AAT TAT TAT TAT ATAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
*
10860 TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
10908 TAT ATAT TAT TAT TAT TAT TA
1 TAT -TAT TAT TAT TAT TAT TA
10929 AAAAAAATAA
Statistics
Matches: 102, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
3 96 0.94
4 6 0.06
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:12295 original size:15 final size:16
Alignment explanation
Indices: 12260--12295 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
12250 TAGTCATTGT
12260 TTATT-TATATTTATA
1 TTATTATATATTTATA
12275 TT-TTATATATTTA-A
1 TTATTATATATTTATA
12289 TTATTAT
1 TTATTAT
12296 TGTTATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTATATATTTATA
Found at i:12535 original size:148 final size:147
Alignment explanation
Indices: 12397--12708 Score: 378
Period size: 149 Copynumber: 2.1 Consensus size: 147
12387 TAAATTTAAT
12397 TTTATATAAATTA-CTTTTAAGAAAAATAATCATATT-TTAATATTTATTTATTTATTTTTAATA
1 TTTATATAAATTATCTTTTAAG-AAAAT--T--TATTATTAATATTTATTTA--T-TTTTTAATA
*
12460 TTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGTCCTTTTATGATA-TTCTTAAATAAATAAATA
58 TTAAGAAATGGGCTATCTTAAAGCACCTAGAAGT-CTTTTATGATATTTC-TAAATAAATAAATA
12524 TCATATTTTTATAAATTATATATATTAA
121 TCATATTTTTATAAATTATATATATT-A
* * * * *
12552 TTTATTTTAATTATTTTTTTAGAAAATTTTTTATTAATATTTATTTATTTTTTAATATTAAGAAA
1 TTTATATAAATTATCTTTTAAGAAAATTTATTATTAATATTTATTTATTTTTTAATATTAAGAAA
* * * *
12617 TGGGCTATCTTAAAGCACCTAGAAGTCTTTTCTGATATTTCTAAGTAAATAAATATCTTATTTAT
66 TGGGCTATCTTAAAGCACCTAGAAGTCTTTTATGATATTTCTAAATAAATAAATATCATATTTTT
*
12682 AAAAATATATATATATATA
131 ATAAAT-TATATATAT-TA
*
12701 TATATATA
1 TTTATATA
12709 TATATATATA
Statistics
Matches: 138, Mismatches: 14, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
148 36 0.26
149 60 0.43
150 2 0.01
151 3 0.02
152 14 0.10
153 1 0.01
155 16 0.12
156 6 0.04
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (147 bp):
TTTATATAAATTATCTTTTAAGAAAATTTATTATTAATATTTATTTATTTTTTAATATTAAGAAA
TGGGCTATCTTAAAGCACCTAGAAGTCTTTTATGATATTTCTAAATAAATAAATATCATATTTTT
ATAAATTATATATATTA
Found at i:12693 original size:2 final size:2
Alignment explanation
Indices: 12686--12721 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
12676 ATTTATAAAA
12686 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
12722 TTTCTTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13246 original size:18 final size:18
Alignment explanation
Indices: 13223--13258 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
13213 TTCTTTCAAA
13223 AATTTTTCATTATATTTT
1 AATTTTTCATTATATTTT
* *
13241 AATTTTTTATTTTATTTT
1 AATTTTTCATTATATTTT
13259 TCATATATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (18 bp):
AATTTTTCATTATATTTT
Found at i:14814 original size:21 final size:20
Alignment explanation
Indices: 14786--14829 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
14776 GAGTAACACC
*
14786 TTTTCATACATGCATTTTCA
1 TTTTCATACATACATTTTCA
**
14806 TTTTGCATATTTACATTTTCA
1 TTTT-CATACATACATTTTCA
14827 TTT
1 TTT
14830 ATACTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.23, C:0.16, G:0.05, T:0.57
Consensus pattern (20 bp):
TTTTCATACATACATTTTCA
Found at i:14953 original size:20 final size:20
Alignment explanation
Indices: 14893--14958 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
14883 CACATATTTA
* *
14893 CATTTGCATTTGCAT-TTTG
1 CATTTACATTTTCATGTTTG
* *
14912 CATTTTTGCATTTTTATGTTTG
1 CA--TTTACATTTTCATGTTTG
* *
14934 TATTTACATTTTCATTTTTG
1 CATTTACATTTTCATGTTTG
14954 CATTT
1 CATTT
14959 GCATCTTTGC
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
19 2 0.05
20 19 0.51
21 11 0.30
22 5 0.14
ACGTcount: A:0.17, C:0.12, G:0.11, T:0.61
Consensus pattern (20 bp):
CATTTACATTTTCATGTTTG
Found at i:15244 original size:42 final size:42
Alignment explanation
Indices: 15183--15266 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
15173 AGATATGATT
* * * * *
15183 GATCAAGTAAAAAAGTTCCAGGGTGATTCAAATGAACAAATG
1 GATCAAGCAAAAAAATTCCAAGATGATTCAAAAGAACAAATG
*
15225 GATCAAGCAAAAAAATTCCAAGATGATTCAAAAGAGCAAATG
1 GATCAAGCAAAAAAATTCCAAGATGATTCAAAAGAACAAATG
15267 ACAAAACTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.49, C:0.13, G:0.19, T:0.19
Consensus pattern (42 bp):
GATCAAGCAAAAAAATTCCAAGATGATTCAAAAGAACAAATG
Found at i:21801 original size:54 final size:54
Alignment explanation
Indices: 21707--21838 Score: 142
Period size: 54 Copynumber: 2.4 Consensus size: 54
21697 GAAATCTATG
* * * *
21707 CAGAAATCAC-AGAAAAGGATGAACGTGTTGTCAAATGCTTTAC-AAACATCTGGC
1 CAGAAACCACAAGAAAA-GATGAATGTGTTATCAAAAGCTTTACGAAA-ATCTGGC
* * * *
21761 CATAAGCCACAAGAAAAGATGAATGTGTTATCAAAAGCTTTACGAAAATTTGGG
1 CAGAAACCACAAGAAAAGATGAATGTGTTATCAAAAGCTTTACGAAAATCTGGC
* *
21815 CAGAAACCACGAGAAAGGATGAAT
1 CAGAAACCACAAGAAAAGATGAAT
21839 ATATTGTCAC
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
54 55 0.86
55 9 0.14
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.20
Consensus pattern (54 bp):
CAGAAACCACAAGAAAAGATGAATGTGTTATCAAAAGCTTTACGAAAATCTGGC
Found at i:22257 original size:22 final size:22
Alignment explanation
Indices: 22229--22271 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
22219 CATTCTTCAA
22229 AGATTCTCTCTTCAAAGATGAT
1 AGATTCTCTCTTCAAAGATGAT
*
22251 AGATTCTCTTTTCAAAGATGA
1 AGATTCTCTCTTCAAAGATGA
22272 AAGCTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (22 bp):
AGATTCTCTCTTCAAAGATGAT
Found at i:22990 original size:45 final size:45
Alignment explanation
Indices: 22926--23242 Score: 499
Period size: 45 Copynumber: 7.0 Consensus size: 45
22916 CTATTTCCCA
*
22926 CATCTGTAAGCCCTTCAGTGTATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
22971 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACATTCGGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC-GGGT
*
23017 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACTTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
23062 CATTTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
23107 CATCTGTAAGCCCTTCAGTGCATGTTGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
23152 CATCTGTAAGCCCTTCAGTACATGATGTTTTCAAAACCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
** * * *
23197 CATCCATAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTTCGGG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGG
23243 AGCTTTTTTA
Statistics
Matches: 252, Mismatches: 17, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
45 197 0.78
46 48 0.19
47 7 0.03
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:23607 original size:3 final size:3
Alignment explanation
Indices: 23599--23642 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
23589 TAATTTTTCA
* *
23599 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAA AAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
23643 AAAAAATACA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:23648 original size:18 final size:18
Alignment explanation
Indices: 23612--23649 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
23602 TATTATTATT
**
23612 ATTATTATTATTATTAAA
1 ATTATTATTATTAAAAAA
23630 ATTATTATTATTAAAAAA
1 ATTATTATTATTAAAAAA
23648 AT
1 AT
23650 ACAAGCCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTATTATTATTAAAAAA
Found at i:25025 original size:8 final size:7
Alignment explanation
Indices: 24947--25031 Score: 52
Period size: 6 Copynumber: 11.7 Consensus size: 7
24937 TTTTTTTACT
24947 TTTTATA
1 TTTTATA
24954 TTTTA-A
1 TTTTATA
**
24960 TACTATA
1 TTTTATA
24967 GTTTTA-A
1 -TTTTATA
24974 TTTTATTTA
1 TTTTA--TA
24983 TTTTAGTCA
1 TTTTA-T-A
*
24992 TTTTTTA
1 TTTTATA
24999 -TTTATA
1 TTTTATA
25005 -TTTATA
1 TTTTATA
25011 TTTTATA
1 TTTTATA
25018 TGTTTATA
1 T-TTTATA
25026 TATTTA
1 T-TTTA
25032 ATTATTATTG
Statistics
Matches: 62, Mismatches: 8, Indels: 15
0.73 0.09 0.18
Matches are distributed among these distances:
6 20 0.32
7 15 0.24
8 16 0.26
9 11 0.18
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (7 bp):
TTTTATA
Found at i:25030 original size:23 final size:22
Alignment explanation
Indices: 25001--25043 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
24991 ATTTTTTATT
25001 TATATTTATATT-TTATATGTTTA
1 TATATTTA-ATTATTAT-TGTTTA
25024 TATATTTAATTATTATTGTT
1 TATATTTAATTATTATTGTT
25044 ATTATTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (22 bp):
TATATTTAATTATTATTGTTTA
Found at i:25240 original size:148 final size:145
Alignment explanation
Indices: 25112--25442 Score: 376
Period size: 148 Copynumber: 2.3 Consensus size: 145
25102 TTATATATAT
25112 TAAATAAAAATCCTA-TTTATAAATGTA-AT-T-TTA-TA-TAAATTACTTTTAAGAAAAATAAT
1 TAAATAAAAATCCTATTTTATAAAT-TATATATATTATTATTAAATTA-TTTTAAGAAAAAT-AT
25171 CATATT-TTAATATTTATTTATTTTTTAATATTAAGAAATGAGATGTCTTAAAGCACCTAGAAGT
63 --T-TTATTAATATTTATTTATTTTTTAATATTAAGAAATGAGATGTCTTAAAGCACCTAGAAGT
25235 CTTTTT-CTGATATTTTTAAA
125 CTTTTTACTGATATTTTTAAA
* * * * * *
25255 TAAATAAATATCTTATTTTTATAAATTATATATATTATTTTATTTTAATTATTTTTAGAGAAATG
1 TAAATAAAAATCCTA-TTTTATAAATTATATATATTA--TTA-TTAAATTATTTTAAGAAAAATA
* *
25320 TTTTATTAATATTTATTTATTTTTTAATATTAAGAAATGAGTTGTCTTAAAGCACCTAGAAGTCA
62 TTTTATTAATATTTATTTATTTTTTAATATTAAGAAATGAGATGTCTTAAAGCACCTAGAAGTCT
* *
25385 TTTTA-TGATATTTCTAAG
127 TTTTACTGATATTTTTAAA
* *
25403 TAAATAAATATCTTA-TTTATAAATATATATATATATATTA
1 TAAATAAAAATCCTATTTTATAAAT-TATATATAT-TATTA
25443 ATATATTTTC
Statistics
Matches: 164, Mismatches: 10, Indels: 25
0.82 0.05 0.13
Matches are distributed among these distances:
143 13 0.08
144 2 0.01
145 11 0.07
146 13 0.08
147 14 0.09
148 91 0.55
150 3 0.02
151 11 0.07
152 6 0.04
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (145 bp):
TAAATAAAAATCCTATTTTATAAATTATATATATTATTATTAAATTATTTTAAGAAAAATATTTT
ATTAATATTTATTTATTTTTTAATATTAAGAAATGAGATGTCTTAAAGCACCTAGAAGTCTTTTT
ACTGATATTTTTAAA
Found at i:25287 original size:22 final size:22
Alignment explanation
Indices: 25245--25295 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
25235 CTTTTTCTGA
*
25245 TATTTTTAAATAAATAAATATCT
1 TATTTTT-AATAAATAAATATAT
*
25268 TATTTTT-ATAAATTATATATAT
1 TATTTTTAATAAA-TAAATATAT
25290 TATTTT
1 TATTTT
25296 ATTTTAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 5 0.20
22 13 0.52
23 7 0.28
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TATTTTTAATAAATAAATATAT
Found at i:29092 original size:13 final size:13
Alignment explanation
Indices: 29074--29100 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29064 TATGATTAAT
29074 GTCTACTGGTAGC
1 GTCTACTGGTAGC
29087 GTCTACTGGTAGC
1 GTCTACTGGTAGC
29100 G
1 G
29101 GTTTTAGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.22, G:0.33, T:0.30
Consensus pattern (13 bp):
GTCTACTGGTAGC
Found at i:36579 original size:19 final size:19
Alignment explanation
Indices: 36555--36661 Score: 88
Period size: 19 Copynumber: 5.3 Consensus size: 19
36545 TTATTTTGGA
36555 TTTTTCACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
36574 TTTTTCACTATCGCAACAACAC
1 TTTTTCACTATCG---CAACAC
*
36596 GTTTTTCAAACTCTCGCAACAC
1 -TTTTTC--ACTATCGCAACAC
* * * *
36618 ATTTTAACTCTCGTAACAC
1 TTTTTCACTATCGCAACAC
* *
36637 ATTTTAACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
36656 ATTTTT
1 -TTTTT
36662 TAAAATCGCG
Statistics
Matches: 74, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
19 42 0.57
20 4 0.05
21 4 0.05
22 12 0.16
23 6 0.08
25 6 0.08
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (19 bp):
TTTTTCACTATCGCAACAC
Found at i:39779 original size:20 final size:21
Alignment explanation
Indices: 39731--39783 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
39721 TACTATTACG
*
39731 GTGCTGATGTGGTAGTTCACT
1 GTGCTGACGTGGTAGTTCACT
* **
39752 CTATTGACGTGG-AGTTCACT
1 GTGCTGACGTGGTAGTTCACT
39772 GTGCTGACGTGG
1 GTGCTGACGTGG
39784 CAGTCCACGA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.15, C:0.17, G:0.34, T:0.34
Consensus pattern (21 bp):
GTGCTGACGTGGTAGTTCACT
Found at i:41110 original size:84 final size:85
Alignment explanation
Indices: 40884--41156 Score: 467
Period size: 85 Copynumber: 3.2 Consensus size: 85
40874 AATTGCACCT
* *
40884 AAAGAATCAAGAATGTTAGATCGTAAAATAAAGTGAATATTAAATATTAAATAAATCAAAGAGAA
1 AAAGATTCAAAAATGTTAGATCGTAAAATAAAGTGAATATTAAATATTAAATAAATCAAAGAGAA
*
40949 GAAAAAAGGTTAAATTCAAA
66 GAAAAAAGGTTAAATTTAAA
40969 AAAGATTCAAAAATGTTAGATCGTAAAATAAAGTGAATATTAAATATTAAATAAATCAAAGAGAA
1 AAAGATTCAAAAATGTTAGATCGTAAAATAAAGTGAATATTAAATATTAAATAAATCAAAGAGAA
41034 GAAAAAAGGTTAAATTTAAA
66 GAAAAAAGGTTAAATTTAAA
* * *
41054 AAAGATTAAAAAATGTTAGATCGTAAAATAAAGTAAAAATT-AATATTAAATAAATCAAAGAGAA
1 AAAGATTCAAAAATGTTAGATCGTAAAATAAAGTGAATATTAAATATTAAATAAATCAAAGAGAA
41118 GAAAAAAAGGTTAAATTTAAA
66 G-AAAAAAGGTTAAATTTAAA
*
41139 AAAGGTTCAAAAATGTTA
1 AAAGATTCAAAAATGTTA
41157 AAAGAGAAAA
Statistics
Matches: 179, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
84 24 0.13
85 155 0.87
ACGTcount: A:0.58, C:0.04, G:0.13, T:0.25
Consensus pattern (85 bp):
AAAGATTCAAAAATGTTAGATCGTAAAATAAAGTGAATATTAAATATTAAATAAATCAAAGAGAA
GAAAAAAGGTTAAATTTAAA
Found at i:41239 original size:36 final size:34
Alignment explanation
Indices: 41156--41240 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 34
41146 CAAAAATGTT
41156 AAAAGAGAAAAA-AATAAAAAAGATATTAAATTTA
1 AAAAGA-AAAAATAATAAAAAAGATATTAAATTTA
*
41190 AAAAGAAACAAAATAAGTAAAAAA-ATGTTAAATTTTGA
1 AAAAG-AA-AAAATAA-TAAAAAAGATATTAAA-TTT-A
41228 AAAAGAAAAAATA
1 AAAAGAAAAAATA
41241 TCAACCGAGC
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
34 6 0.14
35 5 0.11
36 15 0.34
37 12 0.27
38 6 0.14
ACGTcount: A:0.69, C:0.01, G:0.09, T:0.20
Consensus pattern (34 bp):
AAAAGAAAAAATAATAAAAAAGATATTAAATTTA
Found at i:42205 original size:20 final size:20
Alignment explanation
Indices: 42180--42220 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
42170 AAATCTTTCA
42180 TAGGGGGTATCGGTACCCTC
1 TAGGGGGTATCGGTACCCTC
42200 TAGGGGGTATCGGTACCCTC
1 TAGGGGGTATCGGTACCCTC
42220 T
1 T
42221 GGGTAATCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.24, G:0.34, T:0.27
Consensus pattern (20 bp):
TAGGGGGTATCGGTACCCTC
Found at i:43146 original size:21 final size:21
Alignment explanation
Indices: 43113--43152 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
43103 GGTTAGGTGG
* * *
43113 GAATCTATGGATGTAAACCAT
1 GAATCCATAGATGCAAACCAT
43134 GAATCCATAGATGCAAACC
1 GAATCCATAGATGCAAACC
43153 GTAAGTCGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (21 bp):
GAATCCATAGATGCAAACCAT
Found at i:44909 original size:23 final size:22
Alignment explanation
Indices: 44880--44933 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
44870 CCTCATGTGT
*
44880 GGGTATCGATACCCATTCAAAGA
1 GGGTATC-ATACCCATACAAAGA
*
44903 GGGTATCAGTACCCATACAAAGG
1 GGGTATCA-TACCCATACAAAGA
44926 GGGTATCA
1 GGGTATCA
44934 ATACATAGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 1 0.04
23 27 0.96
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.20
Consensus pattern (22 bp):
GGGTATCATACCCATACAAAGA
Found at i:46341 original size:20 final size:20
Alignment explanation
Indices: 46316--46353 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
46306 ATCTTTCATA
46316 GGGGTATCGGTACCCTCTAG
1 GGGGTATCGGTACCCTCTAG
46336 GGGGTATCGGTACCCTCT
1 GGGGTATCGGTACCCTCT
46354 GGGCAATCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.26, G:0.34, T:0.26
Consensus pattern (20 bp):
GGGGTATCGGTACCCTCTAG
Found at i:48955 original size:18 final size:18
Alignment explanation
Indices: 48932--48966 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
48922 CTAGGAGATT
48932 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
48950 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
48967 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:50032 original size:149 final size:149
Alignment explanation
Indices: 49859--50164 Score: 533
Period size: 149 Copynumber: 2.1 Consensus size: 149
49849 GAGTCGAGGG
* **
49859 TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
49924 A-TATGATCCTTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 ACT-TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
*
49988 ATATGGCACTACGTTGCAAT
130 ATATGGCACTACGGTGCAAT
*
50008 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
50073 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
50138 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
50157 TCTACGCG
1 TCTACGCG
50165 ACACTTCGGT
Statistics
Matches: 149, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
149 148 0.99
150 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:53929 original size:18 final size:18
Alignment explanation
Indices: 53906--53940 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
53896 CTAGGAGATT
53906 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
53924 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
53941 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:54998 original size:149 final size:149
Alignment explanation
Indices: 54825--55131 Score: 553
Period size: 149 Copynumber: 2.1 Consensus size: 149
54815 GAGTCGAGGG
* **
54825 TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
54890 A-TATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 ACT-TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
54954 ATATGGCACTACGGTGCAAT
130 ATATGGCACTACGGTGCAAT
*
54974 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
55039 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
55104 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
55123 TCTACGCGG
1 TCTACGCGG
55132 CAATTCGGTG
Statistics
Matches: 152, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
149 151 0.99
150 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:55851 original size:2 final size:2
Alignment explanation
Indices: 55832--56084 Score: 143
Period size: 2 Copynumber: 132.5 Consensus size: 2
55822 AATAATAGTA
* *
55832 AT AT AT A- AT AA AT A- AT AT AT AT AA AT AT AT A- AT GAT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
* * *
55871 AT AT AT AT AT AT AC AT ACC AT AT -T AC ACT AT AT A- AT AT AT A-
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT
* * *
55912 AT AT AT AA AT AT ACT AT AT CAT AT AT A- AC GT AT AT A- AT AT AT
1 AT AT AT AT AT AT A-T AT AT -AT AT AT AT AT AT AT AT AT AT AT AT
* *
55954 AT AT AT AC ACT AT AT A- AT AT A- AT AT A- AT AT AA AT AT AT A-
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
55993 AT CAT AT A- AT AT GT AT AT AT -T AT AT A- AT AT AA AT AT AA AT
1 AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
56033 AT ACT AT A- AG AT AT AT A- AT AT AT AA AT AT AT A- AT A- AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56072 AT -T AT ACT AT AT A
1 AT AT AT A-T AT AT A
56085 AAAAGGGTCG
Statistics
Matches: 193, Mismatches: 28, Indels: 60
0.69 0.10 0.21
Matches are distributed among these distances:
1 21 0.11
2 157 0.81
3 15 0.08
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (2 bp):
AT
Found at i:55908 original size:5 final size:5
Alignment explanation
Indices: 55907--56082 Score: 81
Period size: 5 Copynumber: 36.0 Consensus size: 5
55897 ACTATATAAT
* **
55907 ATATA ATAT- ATA-A ATATA CTAT- ATCAT- ATATA ACGT- ATATA ATAT-
1 ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA ATATA ATATA ATATA
* *
55952 ATATA TATACA CTATATA ATATA ATATA ATATA A-ATA TATAATC ATATA
1 ATATA -ATATA --ATATA ATATA ATATA ATATA ATATA -AT-ATA ATATA
* * * *
56001 ATAT- GTAT- ATATT ATATA ATATAA ATATAA ATATA CTATA AGAT- ATATA
1 ATATA ATATA ATATA ATATA ATAT-A ATAT-A ATATA ATATA ATATA ATATA
* *
56050 ATAT- ATA-A ATAT- ATAATA ATATA TTATA CTATA
1 ATATA ATATA ATATA AT-ATA ATATA ATATA ATATA
56083 TAAAAAGGGT
Statistics
Matches: 134, Mismatches: 19, Indels: 36
0.71 0.10 0.19
Matches are distributed among these distances:
4 35 0.26
5 73 0.54
6 19 0.14
7 7 0.05
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:55946 original size:66 final size:63
Alignment explanation
Indices: 55833--56085 Score: 185
Period size: 66 Copynumber: 3.8 Consensus size: 63
55823 ATAATAGTAA
* *
55833 TATATAATAAATAATATATATAA-ATATATAATGATATAATATATATATATACATACCATAT-TA
1 TATATAATATATAATATATA-AATATATAT-ATCATAT-ATATATATATA-ACATA-CATATATA
55896 CAC
61 CAC
* *
55899 TATATAATATATAATATATAAATATACTATATCATATATA-ACGTATATAATATATATATATACA
1 TATATAATATATAATATATAAATATA-TATATCATATATATA--TATATAACATACATATATACA
55963 C
63 C
* * *
55964 TATATAATATA-ATATAATATAAATATATAATCATATAATATGTATATATTATATAATATAAATA
1 TATATAATATATA-AT-ATAT-AA-ATAT-AT-ATATCATA--TATATA-TATATAACATACATA
*
56028 TAAATATAC
57 T--ATACAC
*
56037 TATA-AGATATATAATATATAAATATATA-ATAATATATTATACTATATAA
1 TATATA-ATATATAATATATAAATATATATATCATATA-TATA-TATATAA
56086 AAAGGGTCGG
Statistics
Matches: 159, Mismatches: 9, Indels: 38
0.77 0.04 0.18
Matches are distributed among these distances:
64 6 0.04
65 29 0.18
66 49 0.31
67 11 0.07
68 6 0.04
69 10 0.06
70 4 0.03
71 21 0.13
72 6 0.04
73 16 0.10
74 1 0.01
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (63 bp):
TATATAATATATAATATATAAATATATATATCATATATATATATATAACATACATATATACAC
Found at i:55984 original size:73 final size:70
Alignment explanation
Indices: 55823--56073 Score: 190
Period size: 77 Copynumber: 3.5 Consensus size: 70
55813 ATAATATTTA
55823 ATAATAGTAATAT-ATA-ATAAATAATATATATAAATATATAA-TGATATAATATATATATATAC
1 ATAATA-TAATATAATATATAAATAATATATAT--ATATATAAGT-ATATAATATATATATATAC
55885 ATACCATATTACACT
62 --A-CATA-TA-A-T
55900 AT-ATA-ATATATAATATATAAAT-ATACTATATCATATATAACGTATATAATATATATATATAC
1 ATAATATA-ATATAATATATAAATAATA-TATAT-ATATATAA-GTATATAATATATATATATAC
55962 ACTATATAAT
62 AC-ATATAAT
* * *
55972 ATAATATAATATAA-ATATATAATCATATA-ATATGTATATATTATATAATATA-A-ATATA-A-
1 ATAATATAATATAATATATA-AATAATATATATATATATA-AGTATATAATATATATATATACAC
*
56031 ATATACT
64 ATATAAT
*
56038 ATAAGAT-ATATAATATATAAAT-ATATA-ATAATATAT
1 ATAATATAATATAATATATAAATAATATATAT-ATATAT
56074 TATACTATAT
Statistics
Matches: 154, Mismatches: 6, Indels: 40
0.77 0.03 0.20
Matches are distributed among these distances:
64 7 0.05
65 14 0.09
66 17 0.11
68 1 0.01
69 5 0.03
70 1 0.01
71 17 0.11
72 11 0.07
73 15 0.10
74 8 0.05
75 8 0.05
76 17 0.11
77 32 0.21
78 1 0.01
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (70 bp):
ATAATATAATATAATATATAAATAATATATATATATATAAGTATATAATATATATATATACACAT
ATAAT
Found at i:65648 original size:21 final size:24
Alignment explanation
Indices: 65622--65666 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
65612 CCCCCCCCCC
65622 TTTTC-TTT-TACTTTCTC-CTTT
1 TTTTCTTTTGTACTTTCTCTCTTT
65643 TTTTCTTTTGTACTTTCTCTCTTT
1 TTTTCTTTTGTACTTTCTCTCTTT
65667 CCAACATGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.24
22 3 0.14
23 9 0.43
24 4 0.19
ACGTcount: A:0.04, C:0.22, G:0.02, T:0.71
Consensus pattern (24 bp):
TTTTCTTTTGTACTTTCTCTCTTT
Found at i:68938 original size:2 final size:2
Alignment explanation
Indices: 68933--68981 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
68923 GCACACATAC
*
68933 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
68975 AT -T AT AT
1 AT AT AT AT
68982 TCTGAGCTAC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:70738 original size:20 final size:20
Alignment explanation
Indices: 70713--70750 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
70703 TCCTTGATAA
70713 TGTTTTCTCAAATGTTTTAT
1 TGTTTTCTCAAATGTTTTAT
* *
70733 TGTTTTCTTAATTGTTTT
1 TGTTTTCTCAAATGTTTT
70751 GATCAGATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.08, G:0.11, T:0.66
Consensus pattern (20 bp):
TGTTTTCTCAAATGTTTTAT
Done.