Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005627.1 Hibiscus syriacus cultivar Beakdansim tig00013110_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: 70913
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:3253 original size:18 final size:18
Alignment explanation
Indices: 3230--3264 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3220 TCGAGTTAAT
3230 TTTGTATAAGATTTATAA
1 TTTGTATAAGATTTATAA
*
3248 TTTGTATACGATTTATA
1 TTTGTATAAGATTTATA
3265 TTTTTTTATG
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:0.34, C:0.03, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGTATAAGATTTATAA
Found at i:3913 original size:199 final size:199
Alignment explanation
Indices: 3351--4559 Score: 2149
Period size: 197 Copynumber: 6.1 Consensus size: 199
3341 TTAAGGGTCA
* * *
3351 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
3416 AATAAAGTGTCG--CCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
3478 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
3543 AATG
196 AATG
* *
3547 TGTCGACACTAATATAG-TTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
3611 AATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
3675 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
3740 AATG
196 AATG
3744 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
3809 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
3874 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
3939 AATG
196 AATG
* *
3943 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
4008 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* *
4073 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGG-TTTATAAGA-AATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
4136 AATG
196 AATG
*
4140 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
4205 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACCC-AAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
4268 TAATATGTAATTTTTCAATCTAACC-GTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
4332 AATG
196 AATG
4336 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
* *
4401 CATAAAGTGTCGATCCATATATAAAACGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
4466 TAATATGTAA-TTTTCAATCTAACCGGTACAATAATACC-GTTTTATGAGAGAAT--GTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
4527 AATG
196 AATG
*
4531 TGTCGACACTAATATATTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
4560 CTAATTTAAA
Statistics
Matches: 983, Mismatches: 21, Indels: 19
0.96 0.02 0.02
Matches are distributed among these distances:
194 15 0.02
195 142 0.14
196 147 0.15
197 294 0.30
198 107 0.11
199 278 0.28
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (199 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATG
Found at i:6031 original size:18 final size:18
Alignment explanation
Indices: 6008--6075 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 18
5998 ATCGGTCGCA
6008 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* *
6026 GAAGATGACGATGATGATGAT
1 GAAGATGA--A-GCTGACGAT
*
6047 GATGACGATGAAGCTGGCGAT
1 GA--A-GATGAAGCTGACGAT
6068 GAAGATGA
1 GAAGATGA
6076 TGACGATGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 13 0.33
19 1 0.03
20 1 0.03
21 17 0.44
22 1 0.03
23 1 0.03
24 5 0.13
ACGTcount: A:0.37, C:0.09, G:0.35, T:0.19
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:6032 original size:6 final size:6
Alignment explanation
Indices: 6008--6099 Score: 67
Period size: 6 Copynumber: 15.3 Consensus size: 6
5998 ATCGGTCGCA
* * * * * *
6008 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* ** * * * *
6056 GAAGCT GGCGAT GAAGAT GATGAC GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
6100 TGATCCAAAC
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:6043 original size:3 final size:3
Alignment explanation
Indices: 6023--6103 Score: 72
Period size: 3 Copynumber: 27.0 Consensus size: 3
6013 TGAAGCTGAC
* * * * * ** *
6023 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
6071 GAT GAT GAC GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
6104 CCAAACAAGT
Statistics
Matches: 59, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.36, C:0.06, G:0.35, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:6058 original size:42 final size:42
Alignment explanation
Indices: 6008--6099 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
5998 ATCGGTCGCA
*
6008 GAAGATGAAGCTGACGATGAAGATGACGATGATGATGATGAT
1 GAAGATGAAGCTGACGATGAAGATGACGACGATGATGATGAT
* * *
6050 GACGATGAAGCTGGCGATGAAGATGATGACGATGATGATGAT
1 GAAGATGAAGCTGACGATGAAGATGACGACGATGATGATGAT
6092 GAAGATGA
1 GAAGATGA
6100 TGATCCAAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.21
Consensus pattern (42 bp):
GAAGATGAAGCTGACGATGAAGATGACGACGATGATGATGAT
Found at i:6086 original size:12 final size:12
Alignment explanation
Indices: 6008--6103 Score: 84
Period size: 12 Copynumber: 8.0 Consensus size: 12
5998 ATCGGTCGCA
* *
6008 GAAGATGAAGCT
1 GAAGATGATGAT
* *
6020 GACGATGAAGAT
1 GAAGATGATGAT
*
6032 GACGATGATGAT
1 GAAGATGATGAT
* *
6044 GATGATGACGAT
1 GAAGATGATGAT
* **
6056 GAAGCTGGCGAT
1 GAAGATGATGAT
*
6068 GAAGATGATGAC
1 GAAGATGATGAT
*
6080 GATGATGATGAT
1 GAAGATGATGAT
6092 GAAGATGATGAT
1 GAAGATGATGAT
6104 CCAAACAAGT
Statistics
Matches: 69, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 69 1.00
ACGTcount: A:0.36, C:0.07, G:0.34, T:0.22
Consensus pattern (12 bp):
GAAGATGATGAT
Found at i:6103 original size:18 final size:18
Alignment explanation
Indices: 6011--6103 Score: 78
Period size: 18 Copynumber: 5.2 Consensus size: 18
6001 GGTCGCAGAA
* * *
6011 GATGAAGCTGACGATGAA
1 GATGAAGATGAAGATGAT
* *
6029 GATGACGATGATGATGAT
1 GATGAAGATGAAGATGAT
* * **
6047 GATGACGATGAAGCTGGC
1 GATGAAGATGAAGATGAT
* *
6065 GATGAAGATGATGACGAT
1 GATGAAGATGAAGATGAT
*
6083 GATGATGATGAAGATGAT
1 GATGAAGATGAAGATGAT
6101 GAT
1 GAT
6104 CCAAACAAGT
Statistics
Matches: 58, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 58 1.00
ACGTcount: A:0.35, C:0.08, G:0.34, T:0.23
Consensus pattern (18 bp):
GATGAAGATGAAGATGAT
Found at i:7779 original size:184 final size:184
Alignment explanation
Indices: 7470--8324 Score: 1640
Period size: 184 Copynumber: 4.7 Consensus size: 184
7460 CTTTCAACAT
**
7470 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
7535 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
7600 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
7654 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
7719 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
7784 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
7838 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
7903 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
7968 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
8022 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
8087 GGTCTACAA-CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
8151 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* *
8205 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
*
8270 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
8325 CCATTTAAAA
Statistics
Matches: 663, Mismatches: 7, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
183 180 0.27
184 483 0.73
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (184 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:10943 original size:23 final size:23
Alignment explanation
Indices: 10880--10944 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
10870 ATAGGTAAAC
* *
10880 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCCCTT
**
10903 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCCCTT
10926 ATATAATGTAATAGGTATC
1 ATATAATGTAATAGGTATC
10945 TATCTCGCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCCCTT
Found at i:11169 original size:18 final size:18
Alignment explanation
Indices: 11148--11184 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
11138 GTAATTGGAG
11148 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
11166 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
11184 T
1 T
11185 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:11192 original size:24 final size:24
Alignment explanation
Indices: 11140--11186 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
11130 TTTCATATGT
* *
11140 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
11164 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
11187 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:12868 original size:26 final size:29
Alignment explanation
Indices: 12815--12888 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 29
12805 ATAAATTTTT
* *
12815 TATTATATTATAATCATTTAATAGTTTAC
1 TATTTTATTATTATCATTTAATAGTTTAC
12844 TATTTTATTATTATCATTT-A-A-TTTAC
1 TATTTTATTATTATCATTTAATAGTTTAC
*
12870 TAATTTTCTTATTA-CATTT
1 T-ATTTTATTATTATCATTT
12889 TGCAGATATA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 11 0.27
27 12 0.29
28 1 0.02
29 17 0.41
ACGTcount: A:0.32, C:0.08, G:0.01, T:0.58
Consensus pattern (29 bp):
TATTTTATTATTATCATTTAATAGTTTAC
Found at i:12883 original size:27 final size:25
Alignment explanation
Indices: 12839--12888 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 25
12829 CATTTAATAG
12839 TTTACTATTTTATTATTATCATTTAA
1 TTTACTATTTTATTATTA-CATTTAA
*
12865 TTTACTAATTTTCTTATTACATTT
1 TTTACT-ATTTTATTATTACATTT
12889 TGCAGATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTACTATTTTATTATTACATTTAA
Found at i:13029 original size:24 final size:22
Alignment explanation
Indices: 13002--13055 Score: 54
Period size: 25 Copynumber: 2.3 Consensus size: 22
12992 TTGTGAACAT
* * *
13002 TTTATTTTTATTTTTTAGTATTA
1 TTTATTTTCAATTTTTA-TACTA
13025 GTTTATATTTCAATTTTTATACTA
1 -TTTAT-TTTCAATTTTTATACTA
13049 TTTATTT
1 TTTATTT
13056 AATTATGGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 2 0.08
23 5 0.19
24 9 0.35
25 10 0.38
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.69
Consensus pattern (22 bp):
TTTATTTTCAATTTTTATACTA
Found at i:15178 original size:13 final size:13
Alignment explanation
Indices: 15160--15185 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15150 GAATTGTAAC
15160 GTTTATATTTAAT
1 GTTTATATTTAAT
15173 GTTTATATTTAAT
1 GTTTATATTTAAT
15186 TATTTTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
GTTTATATTTAAT
Found at i:15198 original size:9 final size:9
Alignment explanation
Indices: 15184--15208 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
15174 TTTATATTTA
15184 ATTATTTTT
1 ATTATTTTT
15193 ATTATTTTT
1 ATTATTTTT
15202 ATTATTT
1 ATTATTT
15209 AGTTTGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
ATTATTTTT
Found at i:19400 original size:21 final size:23
Alignment explanation
Indices: 19374--19430 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 23
19364 ACCAAAAAAG
*
19374 GTAGTATCGGTACCAC-CACTAA
1 GTAGTATCGATACCACACACTAA
*
19396 G-AGTATCGATACTACTACACTAA
1 GTAGTATCGATACCAC-ACACTAA
19419 GTAGTATCGATA
1 GTAGTATCGATA
19431 TTGTATATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 12 0.40
22 1 0.03
23 7 0.23
24 10 0.33
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (23 bp):
GTAGTATCGATACCACACACTAA
Found at i:21134 original size:24 final size:26
Alignment explanation
Indices: 21077--21134 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
21067 AATATTAATT
*
21077 ATTATATTAAATAAATATCATAAAATA
1 ATTAT-TTAAATAAAAATCATAAAATA
*
21104 ATT-TTTAAATAAAAAT-TTAAAA-A
1 ATTATTTAAATAAAAATCATAAAATA
21127 ATTATTTA
1 ATTATTTA
21135 GGTGTACATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 4 0.14
24 9 0.32
25 11 0.39
26 1 0.04
27 3 0.11
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (26 bp):
ATTATTTAAATAAAAATCATAAAATA
Found at i:24482 original size:138 final size:138
Alignment explanation
Indices: 24234--24709 Score: 763
Period size: 138 Copynumber: 3.4 Consensus size: 138
24224 TTCAGGTGAA
* * *
24234 GGCGCGCTTTCCATTATTTTGTCAGAGAATATGTTAACATTGCCCTATTATGTCACTTATGTCCC
1 GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
*
24299 CCGAAGAACTATTCATGCCAATACCTATTATTTCTGAGGAGACTTGGCAAAGTGGTGAAGGCGCA
66 CCGAAGAACTATTCATGCCAATACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTGAAGGCGCA
24364 TTCCCGGG
131 TTCCCGGG
*
24372 GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCTC
1 GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
* * * * * *
24437 TCGGAGAACTATTTATGCCAATACCTATTATTTTTTAGGGGACTTGGCAAAGTGGTGAAGGCGCG
66 CCGAAGAACTATTCATGCCAATACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTGAAGGCGCA
24502 TTCCCGGG
131 TTCCCGGG
*
24510 GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGTCCTATTATGTCACTCATGTCCC
1 GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
* * ** * *
24575 CCGAAGAACTATTCATGTCAGTTTCTATTATTTCTGAAGGGACTTGGCAAAATGGTGAAGGCGCA
66 CCGAAGAACTATTCATGCCAATACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTGAAGGCGCA
24640 TTCCCGGG
131 TTCCCGGG
* * *
24648 GGCGCGCCTTCAATTATTTTGTCAGATAATATGTTATCATTGCCTTATTATGTCACTCATGT
1 GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
24710 GAAATTGGAT
Statistics
Matches: 309, Mismatches: 29, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
138 309 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.34
Consensus pattern (138 bp):
GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
CCGAAGAACTATTCATGCCAATACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTGAAGGCGCA
TTCCCGGG
Found at i:24780 original size:23 final size:23
Alignment explanation
Indices: 24754--24816 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
24744 ATGTGAAGTT
24754 TGAATAAATTGGATAAAATGTTA
1 TGAATAAATTGGATAAAATGTTA
*
24777 TGAATAAAATGGATAAAATGTTA
1 TGAATAAATTGGATAAAATGTTA
* *
24800 TGGATAAATTGAATAAA
1 TGAATAAATTGGATAAA
24817 TATGAAGTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.51, C:0.00, G:0.17, T:0.32
Consensus pattern (23 bp):
TGAATAAATTGGATAAAATGTTA
Found at i:24923 original size:14 final size:14
Alignment explanation
Indices: 24904--24934 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
24894 TGATAAGTTG
24904 GTTTTAATGTATAT
1 GTTTTAATGTATAT
24918 GTTTTAATGTATAT
1 GTTTTAATGTATAT
24932 GTT
1 GTT
24935 AAGGATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (14 bp):
GTTTTAATGTATAT
Found at i:25612 original size:21 final size:21
Alignment explanation
Indices: 25588--25660 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
25578 GGTGTCATAA
* *
25588 AACCTTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
25609 AA-CCTAGCGGGATAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
25630 AACCCTGAGGGCTAGGAATGT
1 AACCCTGCGGGCTAGGAATGT
25651 AACCCTGCGG
1 AACCCTGCGG
25661 AGATGGCATA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
20 2 0.05
21 39 0.89
22 3 0.07
ACGTcount: A:0.26, C:0.22, G:0.33, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:32446 original size:14 final size:13
Alignment explanation
Indices: 32427--32465 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
32417 ACATATTAAA
32427 TAATAAATATAAT
1 TAATAAATATAAT
*
32440 TATATAACTATAAT
1 TA-ATAAATATAAT
*
32454 TAAAAAATATAA
1 TAATAAATATAA
32466 ATTTGGGGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (13 bp):
TAATAAATATAAT
Found at i:33026 original size:15 final size:16
Alignment explanation
Indices: 33006--33044 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
32996 TAAAGTTTAA
33006 AATATA-TATTCAAAT
1 AATATATTATTCAAAT
33021 AATATATTCTATTCAAAT
1 AATATA-T-TATTCAAAT
33039 AATATA
1 AATATA
33045 CTTAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.29
18 15 0.71
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (16 bp):
AATATATTATTCAAAT
Found at i:33039 original size:30 final size:30
Alignment explanation
Indices: 33005--33063 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
32995 TTAAAGTTTA
33005 AAAT-ATATA-TTCAAATAATATATTCTATTC
1 AAATAATATACTT-AAA-AATATATTCTATTC
*
33035 AAATAATATACTTAAAAATATATTTTATT
1 AAATAATATACTTAAAAATATATTCTATT
33064 TTAAAGTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 16 0.62
31 8 0.31
32 2 0.08
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (30 bp):
AAATAATATACTTAAAAATATATTCTATTC
Found at i:34999 original size:12 final size:13
Alignment explanation
Indices: 34982--35010 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
34972 ACTCTACCTC
34982 GCATTACCTTA-T
1 GCATTACCTTATT
34994 GCATTACCTTATT
1 GCATTACCTTATT
35007 GCAT
1 GCAT
35011 ATGAAAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.41
Consensus pattern (13 bp):
GCATTACCTTATT
Found at i:49242 original size:28 final size:29
Alignment explanation
Indices: 49206--49267 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
49196 TTTATAGAGA
49206 AAATCACAT-T-TGGTTTTAAAATATATAT
1 AAATCACATATAT-GTTTTAAAATATATAT
*
49234 AAATGACATAATATGTTTTAAAATATATAT
1 AAATCACAT-ATATGTTTTAAAATATATAT
49264 AAAT
1 AAAT
49268 ATTTTATAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 8 0.27
30 21 0.70
31 1 0.03
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.40
Consensus pattern (29 bp):
AAATCACATATATGTTTTAAAATATATAT
Found at i:54676 original size:29 final size:30
Alignment explanation
Indices: 54643--54711 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
54633 TTAACAACGG
54643 GGTATTAAAATGAAAAAAA-TAAAACTTTA
1 GGTATTAAAATGAAAAAAATTAAAACTTTA
* ***
54672 GGTATGATTTTGAAAAAAATTAAAACTTTA
1 GGTATTAAAATGAAAAAAATTAAAACTTTA
* *
54702 GATACTAAAA
1 GGTATTAAAA
54712 CAAATAAAAA
Statistics
Matches: 29, Mismatches: 10, Indels: 1
0.73 0.25 0.03
Matches are distributed among these distances:
29 15 0.52
30 14 0.48
ACGTcount: A:0.54, C:0.04, G:0.12, T:0.30
Consensus pattern (30 bp):
GGTATTAAAATGAAAAAAATTAAAACTTTA
Found at i:57673 original size:29 final size:29
Alignment explanation
Indices: 57635--57703 Score: 111
Period size: 29 Copynumber: 2.4 Consensus size: 29
57625 TATTTAATAG
*
57635 GAATGTAAGATTACAATATTTGGTTGAAA
1 GAATATAAGATTACAATATTTGGTTGAAA
* *
57664 TAATATAAGATTACAATGTTTGGTTGAAA
1 GAATATAAGATTACAATATTTGGTTGAAA
57693 GAATATAAGAT
1 GAATATAAGAT
57704 AGAAAAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.43, C:0.03, G:0.19, T:0.35
Consensus pattern (29 bp):
GAATATAAGATTACAATATTTGGTTGAAA
Found at i:64693 original size:23 final size:22
Alignment explanation
Indices: 64657--64734 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
64647 TAGAGAGAAT
64657 CGATACCCCCTTGAAGGGGAAC
1 CGATACCCCCTTGAAGGGGAAC
*
64679 CGATTCCCCCTTTGAAGGGGAAC
1 CGATACCCCC-TTGAAGGGGAAC
* * *
64702 CGATTCCCCCCTGTAGGGGAAC
1 CGATACCCCCTTGAAGGGGAAC
64724 CGATACCCCCT
1 CGATACCCCCT
64735 GGGGTTCTGG
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
22 28 0.56
23 22 0.44
ACGTcount: A:0.22, C:0.36, G:0.24, T:0.18
Consensus pattern (22 bp):
CGATACCCCCTTGAAGGGGAAC
Found at i:66939 original size:13 final size:13
Alignment explanation
Indices: 66921--66948 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
66911 CACACTTATT
66921 TTAAAACACACAC
1 TTAAAACACACAC
66934 TTAAAACACACAC
1 TTAAAACACACAC
66947 TT
1 TT
66949 CTCCCCCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (13 bp):
TTAAAACACACAC
Found at i:69249 original size:20 final size:21
Alignment explanation
Indices: 69195--69257 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
69185 GATTCCCCTG
69195 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
69219 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
69239 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
69258 TGAACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Done.