Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000652.1 Hibiscus syriacus cultivar Beakdansim tig00001261_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: 60747
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:4944 original size:16 final size:16
Alignment explanation
Indices: 4920--4980 Score: 104
Period size: 16 Copynumber: 3.8 Consensus size: 16
4910 TAATAAATAA
4920 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
4936 ACAAACATAAACGAAC
1 ACGAACATAAACGAAC
*
4952 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
4968 ACGAACATAAACG
1 ACGAACATAAACG
4981 TTGGAGACCC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.57, C:0.23, G:0.11, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:8202 original size:16 final size:16
Alignment explanation
Indices: 8178--8208 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
8168 TTTTAATTTT
*
8178 TTTTTGAGTTCAAGCC
1 TTTTCGAGTTCAAGCC
8194 TTTTCGAGTTCAAGC
1 TTTTCGAGTTCAAGC
8209 TTACTTTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (16 bp):
TTTTCGAGTTCAAGCC
Found at i:9165 original size:17 final size:16
Alignment explanation
Indices: 9138--9176 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
9128 TAAAAAGAGA
* *
9138 AAAATATTAATATAAT
1 AAAATAATAATAAAAT
9154 AATAATAATAATAAAAT
1 AA-AATAATAATAAAAT
9171 AAAATA
1 AAAATA
9177 GATACCAAAG
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAATAATAATAAAAT
Found at i:11388 original size:33 final size:33
Alignment explanation
Indices: 11346--11412 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
11336 TACCCTTAAT
*
11346 ATTTTTGTCAGCAACTACCAAATCAATATGCCA
1 ATTTTTGTCAGCAACTACCAAACCAATATGCCA
*
11379 ATTTTTGTCATCAACTACCAAACCAATATGCCA
1 ATTTTTGTCAGCAACTACCAAACCAATATGCCA
11412 A
1 A
11413 ATTCCAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.37, C:0.25, G:0.07, T:0.30
Consensus pattern (33 bp):
ATTTTTGTCAGCAACTACCAAACCAATATGCCA
Found at i:20765 original size:31 final size:32
Alignment explanation
Indices: 20730--20793 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
20720 TCACCCAACC
* * *
20730 AATTAATATAATAGCTTAATTGGTA-TAATTT
1 AATTAATAGAAGAGCATAATTGGTATTAATTT
*
20761 AATTAATAGAAGAGCATATTTGGTATTAATTT
1 AATTAATAGAAGAGCATAATTGGTATTAATTT
20793 A
1 A
20794 TGAATTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 21 0.75
32 7 0.25
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (32 bp):
AATTAATAGAAGAGCATAATTGGTATTAATTT
Found at i:24256 original size:102 final size:103
Alignment explanation
Indices: 24140--24345 Score: 310
Period size: 102 Copynumber: 2.0 Consensus size: 103
24130 ACGCAGTTGA
24140 AGAAAAAATTAGGCAATTTGATCCAAGAGGGCAAAATGTGCA-TAGTGTTCTCAAACCAGATGAA
1 AGAAAAAA-TAGGCAATTTGATCCAAGAGGGCAAAATGTGCAGT-GTGTTCTCAAACCAGATGAA
24204 GACGAGCT-TGTAGATGTACATACAAGTACTGATGCTGAAG
64 GACG-GCTGTGTAGATGTACATACAAGTACTGATGCTGAAG
* *
24244 AGAAAAAA-AGGCAATTTGATCCAAGAGGGCAACATGTGCAGTGTGTTCTCAAACCGGATGAAGA
1 AGAAAAAATAGGCAATTTGATCCAAGAGGGCAAAATGTGCAGTGTGTTCTCAAACCAGATGAAGA
* * * *
24308 TGGGTGTGTAGCTGTACATATAAGTACTGATGCTGAAG
66 CGGCTGTGTAGATGTACATACAAGTACTGATGCTGAAG
24346 CCAAGTTGGA
Statistics
Matches: 94, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
101 2 0.02
102 83 0.88
103 1 0.01
104 8 0.09
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.23
Consensus pattern (103 bp):
AGAAAAAATAGGCAATTTGATCCAAGAGGGCAAAATGTGCAGTGTGTTCTCAAACCAGATGAAGA
CGGCTGTGTAGATGTACATACAAGTACTGATGCTGAAG
Found at i:24593 original size:18 final size:18
Alignment explanation
Indices: 24566--24607 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
24556 TTTTTGGGCA
*
24566 TTTTTGTTTG-GTTTTAT
1 TTTTTCTTTGAGTTTTAT
24583 GTTTTTCTTTGATGTTTTAT
1 -TTTTTCTTTGA-GTTTTAT
24603 TTTTT
1 TTTTT
24608 AGTCTTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 9 0.43
19 5 0.24
20 7 0.33
ACGTcount: A:0.07, C:0.02, G:0.14, T:0.76
Consensus pattern (18 bp):
TTTTTCTTTGAGTTTTAT
Found at i:25138 original size:156 final size:153
Alignment explanation
Indices: 24859--25310 Score: 556
Period size: 156 Copynumber: 2.9 Consensus size: 153
24849 TTAAGTTGTA
* *
24859 ATTTCTATTTACATCCATCATATTTTGTAGGGGGA--G--GATTTAAATACTGCTGAGACTAAGG
1 ATTTCTATTTATATCCATCATATTTTGTAGAGGGATTGCTGATTTAAATACTGCTGAGACTAA-G
* * * * *
24920 GTGATGCCTCAGTAGCCCTTTCACAA-GCATTGCAAGAAAAGGTTTCAGATGTTTATTCTGTCTA
65 GTGATGCCTCAGAAGCCCTTGCA-AAGGCATTGCAAGAAAAGGTTTTAGACGTTTCTTCTGTCTA
* *
24984 TGGTTTGGTTTCTGGTAAATTATAT
129 TGGTCTGGTTTCTGGTAAATTATAC
*
25009 ATTTCTATTTATATCCATCATATTTTGTAGAGGGATTTGCTCGATTCAAATACTGCTGAGACTAC
1 ATTTCTATTTATATCCATCATATTTTGTAGAGGGA-TTGCT-GATTTAAATACTGCTGAGACTA-
** * * *
25074 ACTTAATGCCTCAGAAGCCCTTGCAAAGGCATTGGAAGAAAAGGTTTTAGACGTTTCTTTTGTCT
63 AGGTGATGCCTCAGAAGCCCTTGCAAAGGCATTGCAAGAAAAGGTTTTAGACGTTTCTTCTGTCT
* *
25139 GTGGTCTGGTTTCTGGTAATTTATAC
128 ATGGTCTGGTTTCTGGTAAATTATAC
* *
25165 ATATCTATTTATATCCATCATATTTTGTAGAGGG-TCATGCTGGATTTAAATACTGCCGAGACTA
1 ATTTCTATTTATATCCATCATATTTTGTAGAGGGAT--TGCT-GATTTAAATACTGCTGAGACT-
* * *
25229 AAGGTGATGCCTCAGAAGCCCTTGCACAGGCATTACAAGAAAAGGTTTTAGACGTTTCTTCTATC
62 AAGGTGATGCCTCAGAAGCCCTTGCAAAGGCATTGCAAGAAAAGGTTTTAGACGTTTCTTCTGTC
* **
25294 CATAATCTGGTTTCTGG
127 TATGGTCTGGTTTCTGG
25311 AAGTTCATAC
Statistics
Matches: 258, Mismatches: 33, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
150 33 0.13
153 1 0.00
154 1 0.00
155 2 0.01
156 219 0.85
157 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (153 bp):
ATTTCTATTTATATCCATCATATTTTGTAGAGGGATTGCTGATTTAAATACTGCTGAGACTAAGG
TGATGCCTCAGAAGCCCTTGCAAAGGCATTGCAAGAAAAGGTTTTAGACGTTTCTTCTGTCTATG
GTCTGGTTTCTGGTAAATTATAC
Found at i:27716 original size:31 final size:31
Alignment explanation
Indices: 27639--27708 Score: 122
Period size: 31 Copynumber: 2.3 Consensus size: 31
27629 ATTATATAAA
27639 TTGGGGGATCATATTGAAAACGGACTAAATG
1 TTGGGGGATCATATTGAAAACGGACTAAATG
* *
27670 TTGGGGGATCATATTGAAAATGGATTAAATG
1 TTGGGGGATCATATTGAAAACGGACTAAATG
27701 TTGGGGGA
1 TTGGGGGA
27709 CTGTATTGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.33, C:0.06, G:0.33, T:0.29
Consensus pattern (31 bp):
TTGGGGGATCATATTGAAAACGGACTAAATG
Found at i:29680 original size:31 final size:31
Alignment explanation
Indices: 29645--29705 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
29635 AATACAGTCC
*
29645 CCCAACATTTAGTCCGTTTTCAATATGGTCT
1 CCCAACATTTAGTCCGTTTGCAATATGGTCT
*
29676 CCCAACATTTATTCCGTTTGCAATATGGTC
1 CCCAACATTTAGTCCGTTTGCAATATGGTC
29706 CCCGACGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (31 bp):
CCCAACATTTAGTCCGTTTGCAATATGGTCT
Found at i:32499 original size:18 final size:18
Alignment explanation
Indices: 32476--32514 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
32466 ATATATTTGT
32476 CGAATAAATACTCATATC
1 CGAATAAATACTCATATC
*
32494 CGAATAAATACTCGTATC
1 CGAATAAATACTCATATC
32512 CGA
1 CGA
32515 TACTTACACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.23, G:0.10, T:0.26
Consensus pattern (18 bp):
CGAATAAATACTCATATC
Found at i:34656 original size:27 final size:27
Alignment explanation
Indices: 34603--34656 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
34593 GGGTCAAACC
* *
34603 AAGTATTTAGTTATTTTATTATTACTT
1 AAGTATTTAGTTATTTCATTATCACTT
34630 AAGTATTTAGTTA-TTCATCTATCACTT
1 AAGTATTTAGTTATTTCAT-TATCACTT
34657 TAGTTTCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.54
Consensus pattern (27 bp):
AAGTATTTAGTTATTTCATTATCACTT
Found at i:38954 original size:14 final size:14
Alignment explanation
Indices: 38935--38975 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
38925 TAGGCAATAT
*
38935 TGGAATATGCATTC
1 TGGAATATACATTC
38949 TGGAATATACATTC
1 TGGAATATACATTC
*
38963 CGGAATATACATT
1 TGGAATATACATT
38976 TGCATTCTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (14 bp):
TGGAATATACATTC
Found at i:40678 original size:35 final size:35
Alignment explanation
Indices: 40625--40738 Score: 167
Period size: 35 Copynumber: 3.3 Consensus size: 35
40615 TCGTCTATAG
* *
40625 TAGAAC-GAAGGGAGGCATCGCACTTTCGATTCAAG
1 TAGAACGGAA-GGAAGCATCGCACTTTCGATTCAAC
* * *
40660 AAGAACGGAAGGAAGCATCGCACGTTCGATTCAAT
1 TAGAACGGAAGGAAGCATCGCACTTTCGATTCAAC
40695 TAGAACGGAAGGAAGCATCGCACTTTCGATTCAAC
1 TAGAACGGAAGGAAGCATCGCACTTTCGATTCAAC
40730 TAGAACGGA
1 TAGAACGGA
40739 TGATTTACTA
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
35 68 0.96
36 3 0.04
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.18
Consensus pattern (35 bp):
TAGAACGGAAGGAAGCATCGCACTTTCGATTCAAC
Found at i:40860 original size:14 final size:14
Alignment explanation
Indices: 40841--40881 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
40831 GGGAGAATAT
*
40841 TGGAATATGCATTA
1 TGGAATATACATTA
*
40855 TGGAATATACATTC
1 TGGAATATACATTA
*
40869 CGGAATATACATT
1 TGGAATATACATT
40882 TGCATTCTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (14 bp):
TGGAATATACATTA
Found at i:46082 original size:20 final size:20
Alignment explanation
Indices: 46057--46107 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
46047 GCGAAATAAA
46057 AATCGCAATGCAA-TCTCCAG
1 AATCGCAATGCAATTC-CCAG
*
46077 AATCGCAAAT-CAGTTCCCAG
1 AATCGC-AATGCAATTCCCAG
46097 AATCGCAATGC
1 AATCGCAATGC
46108 GATAGTACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 3 0.11
20 19 0.70
21 5 0.19
ACGTcount: A:0.35, C:0.29, G:0.16, T:0.20
Consensus pattern (20 bp):
AATCGCAATGCAATTCCCAG
Found at i:46144 original size:21 final size:21
Alignment explanation
Indices: 46120--46187 Score: 136
Period size: 21 Copynumber: 3.2 Consensus size: 21
46110 TAGTACAAAT
46120 TCGCATTGCGATTTTCCATAA
1 TCGCATTGCGATTTTCCATAA
46141 TCGCATTGCGATTTTCCATAA
1 TCGCATTGCGATTTTCCATAA
46162 TCGCATTGCGATTTTCCATAA
1 TCGCATTGCGATTTTCCATAA
46183 TCGCA
1 TCGCA
46188 ACGCGAATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.37
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCATAA
Found at i:46151 original size:42 final size:42
Alignment explanation
Indices: 46097--46193 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
46087 CAGTTCCCAG
46097 AATCGCAATGCGATAGTACA-AATTCGCATTGCGATTTTCCAT
1 AATCGCAATGCGATAGTACATAA-TCGCATTGCGATTTTCCAT
* ** *
46139 AATCGCATTGCGATTTTCCATAATCGCATTGCGATTTTCCAT
1 AATCGCAATGCGATAGTACATAATCGCATTGCGATTTTCCAT
*
46181 AATCGCAACGCGA
1 AATCGCAATGCGA
46194 ATATGAAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
42 46 0.96
43 2 0.04
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (42 bp):
AATCGCAATGCGATAGTACATAATCGCATTGCGATTTTCCAT
Found at i:46193 original size:21 final size:21
Alignment explanation
Indices: 46127--46215 Score: 99
Period size: 21 Copynumber: 4.3 Consensus size: 21
46117 AATTCGCATT
**
46127 GCGATTTTCCATAATCGCATT
1 GCGATTTTCCATAATCGCAAC
**
46148 GCGATTTTCCATAATCGCATT
1 GCGATTTTCCATAATCGCAAC
46169 GCGATTTTCCATAATCGCAAC
1 GCGATTTTCCATAATCGCAAC
* * * *
46190 GCGAATAT-GAAAATCGCAAC
1 GCGATTTTCCATAATCGCAAC
46210 GCGATT
1 GCGATT
46216 CTGACTATCG
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
20 15 0.25
21 46 0.75
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (21 bp):
GCGATTTTCCATAATCGCAAC
Found at i:46266 original size:20 final size:20
Alignment explanation
Indices: 46222--46428 Score: 156
Period size: 20 Copynumber: 10.4 Consensus size: 20
46212 GATTCTGACT
* *
46222 ATCGCAATGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
*
46243 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
46263 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
*
46284 ATCGTAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
46304 ATCGCAACGAC-AATACATAAA
1 ATCGCAACG-CGTATCCGT-AA
* *
46325 ATCGCAATGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
46345 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
46365 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
**
46385 ATCGCAACGATTA-CC-TAA
1 ATCGCAACGCGTATCCGTAA
**
46403 ATCGCAACGATTA-CC-TAA
1 ATCGCAACGCGTATCCGTAA
46421 ATCGCAAC
1 ATCGCAAC
46429 TCATTCTATC
Statistics
Matches: 152, Mismatches: 28, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
18 29 0.19
19 2 0.01
20 74 0.49
21 47 0.31
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:46267 original size:41 final size:41
Alignment explanation
Indices: 46237--46394 Score: 264
Period size: 41 Copynumber: 3.9 Consensus size: 41
46227 AATGAGTATC
46237 CGTAAAATCGCAATGCGTATCCGTAAATCGCAACGACAATA
1 CGTAAAATCGCAATGCGTATCCGTAAATCGCAACGACAATA
* *
46278 CGTAAAATCGTAACGCGTATCCGTAAATCGCAACGACAATA
1 CGTAAAATCGCAATGCGTATCCGTAAATCGCAACGACAATA
* * *
46319 CATAAAATCGCAATGCGTATCTGTAAATCGCAACGAGAATA
1 CGTAAAATCGCAATGCGTATCCGTAAATCGCAACGACAATA
46360 CGT-AAATCGCAATGCGTATCCGTAAATCGCAACGA
1 CGTAAAATCGCAATGCGTATCCGTAAATCGCAACGA
46395 TTACCTAAAT
Statistics
Matches: 108, Mismatches: 9, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
40 31 0.29
41 77 0.71
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (41 bp):
CGTAAAATCGCAATGCGTATCCGTAAATCGCAACGACAATA
Found at i:46405 original size:18 final size:18
Alignment explanation
Indices: 46382--46428 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
46372 TGCGTATCCG
46382 TAAATCGCAACGATTACC
1 TAAATCGCAACGATTACC
46400 TAAATCGCAACGATTACC
1 TAAATCGCAACGATTACC
46418 TAAATCGCAAC
1 TAAATCGCAAC
46429 TCATTCTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.40, C:0.28, G:0.11, T:0.21
Consensus pattern (18 bp):
TAAATCGCAACGATTACC
Found at i:47115 original size:20 final size:20
Alignment explanation
Indices: 47078--47165 Score: 100
Period size: 20 Copynumber: 4.8 Consensus size: 20
47068 GCAACGAGAG
*
47078 AATCGCAATTCG-AAATGAA
1 AATCGCAATGCGAAAATGAA
47097 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCGAAAATGAA
*
47117 AATCGCAA--CG--AGTG--
1 AATCGCAATGCGAAAATGAA
47131 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCGAAAATGAA
*
47151 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
47166 TTACGTTGCA
Statistics
Matches: 58, Mismatches: 4, Indels: 13
0.77 0.05 0.17
Matches are distributed among these distances:
14 8 0.14
16 5 0.09
18 5 0.09
19 11 0.19
20 29 0.50
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (20 bp):
AATCGCAATGCGAAAATGAA
Found at i:47206 original size:33 final size:33
Alignment explanation
Indices: 47169--47329 Score: 207
Period size: 33 Copynumber: 4.8 Consensus size: 33
47159 CGCGAAATTA
**
47169 CGTTGCAATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCAATAGTCATTTCGCATTGCGATTCTCT
*
47202 CGTTGCGATAGTCATTTCGCATTGCGATTCTCT
1 CGTTGCAATAGTCATTTCGCATTGCGATTCTCT
47235 CGTTG-AGATAGTCATTTCGCATTGCGATTCTCT
1 CGTTGCA-ATAGTCATTTCGCATTGCGATTCTCT
* ** *
47268 CGTTGCGATTTTTATTTCGCATTGCGATTCTCT
1 CGTTGCAATAGTCATTTCGCATTGCGATTCTCT
* * *
47301 CGTTACGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCAATAGTCATTT-CGCATTGCGAT
47330 AGTCTGTTCT
Statistics
Matches: 112, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
33 102 0.91
34 10 0.09
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.42
Consensus pattern (33 bp):
CGTTGCAATAGTCATTTCGCATTGCGATTCTCT
Found at i:47209 original size:14 final size:14
Alignment explanation
Indices: 47190--47277 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 14
47180 TCATTTCGCA
47190 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
47204 TTGCGATAGTCATTTCG
1 TTGCGAT--TC-TCTCG
47221 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
* *
47237 TTGAGATAGTCATTTCG
1 TTGCGAT--TC-TCTCG
47254 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
47270 TTGCGATT
1 TTGCGATT
47278 TTTATTTCGC
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 21 0.36
16 12 0.21
17 12 0.21
19 13 0.22
ACGTcount: A:0.15, C:0.23, G:0.22, T:0.41
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:47228 original size:19 final size:17
Alignment explanation
Indices: 47179--47297 Score: 76
Period size: 17 Copynumber: 7.2 Consensus size: 17
47169 CGTTGCAATT
47179 TTCATTTCGCATTGCGA
1 TTCATTTCGCATTGCGA
*
47196 TTC-TCTCG--TTGCGA
1 TTCATTTCGCATTGCGA
47210 TAGTCATTTCGCATTGCGA
1 T--TCATTTCGCATTGCGA
* *
47229 TTC-TCTCG--TTGAGA
1 TTCATTTCGCATTGCGA
47243 TAGTCATTTCGCATTGCGA
1 T--TCATTTCGCATTGCGA
*
47262 TTC-TCTCG--TTGCGA
1 TTCATTTCGCATTGCGA
*
47276 TTTTTATTTCGCATTGCGA
1 --TTCATTTCGCATTGCGA
47295 TTC
1 TTC
47298 TCTCGTTACG
Statistics
Matches: 77, Mismatches: 10, Indels: 30
0.66 0.09 0.26
Matches are distributed among these distances:
14 19 0.25
16 18 0.23
17 21 0.27
19 19 0.25
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (17 bp):
TTCATTTCGCATTGCGA
Found at i:47250 original size:66 final size:66
Alignment explanation
Indices: 47180--47329 Score: 239
Period size: 66 Copynumber: 2.3 Consensus size: 66
47170 GTTGCAATTT
47180 TCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTCGCATTGCGATTCTCTCGTTGA-GAT
1 TCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTCGCATTGCGATTCTCTCGTT-ACGAT
47244 AG
65 AG
** *
47246 TCATTTCGCATTGCGATTCTCTCGTTGCGATTTTTATTTCGCATTGCGATTCTCTCGTTACGATA
1 TCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTCGCATTGCGATTCTCTCGTTACGATA
47311 G
66 G
*
47312 TCATTTCCGCGTTGCGAT
1 TCATTT-CGCATTGCGAT
47330 AGTCTGTTCT
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
65 1 0.01
66 67 0.86
67 10 0.13
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
TCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTCGCATTGCGATTCTCTCGTTACGATA
G
Found at i:47450 original size:14 final size:14
Alignment explanation
Indices: 47431--47467 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
47421 CATCAATTAA
47431 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
47445 ACAAATCATCTTTT
1 ACAAATCAACATTT
47459 ACAAATCAA
1 ACAAATCAA
47468 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:48916 original size:42 final size:42
Alignment explanation
Indices: 48837--48918 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
48827 CCTCTTCAAC
* *
48837 GATGACAGTGGCCTCTTGAACAATAGGAGATGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACAATAGGAGAGGACTCTTGAGG
* * * *
48879 GATGATAGGGGCCTCTTGAACGATAGGGGAGGCCTCTTGA
1 GATGACAGGGGCCTCTTGAACAATAGGAGAGGACTCTTGA
48919 ACGATTACAG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.26, C:0.17, G:0.34, T:0.23
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACAATAGGAGAGGACTCTTGAGG
Found at i:49397 original size:94 final size:94
Alignment explanation
Indices: 49276--49598 Score: 558
Period size: 94 Copynumber: 3.4 Consensus size: 94
49266 TTCAATGACA
*
49276 ACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGATAAAACAAAGA
1 ACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGA
49341 CAAATATTAACTTCACAGTGTTAAAGAAT
66 CAAATATTAACTTCACAGTGTTAAAGAAT
49370 ACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGA
1 ACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGA
49435 CAAATATTAACTTCACAGTGTTAAAGAAT
66 CAAATATTAACTTCACAGTGTTAAAGAAT
*
49464 ACACAGTTTAGCAGAATTGGCAGCAACCGAATAAATTTAC-TTCAACCAAAAGACAAAACAAAAG
1 ACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAAC-AAAG
*
49528 ACAAATACTAACTTCACAGTGTTAAAGAAT
65 ACAAATATTAACTTCACAGTGTTAAAGAAT
* * ** *
49558 AAACAGTTTAGCAGTATTGGCAGCAACTAAATAAATTTACT
1 ACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
49599 AAGCAATCTA
Statistics
Matches: 220, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
93 19 0.09
94 201 0.91
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (94 bp):
ACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGA
CAAATATTAACTTCACAGTGTTAAAGAAT
Found at i:51348 original size:20 final size:19
Alignment explanation
Indices: 51299--51353 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
51289 TTAAATGAAA
*
51299 ATCGCAACGAGAGAATGACT
1 ATCGCAACGCGA-AATGACT
51319 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
51339 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
51354 AAAAATCGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 5 0.15
20 26 0.79
21 2 0.06
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:51413 original size:33 final size:33
Alignment explanation
Indices: 51365--51445 Score: 117
Period size: 33 Copynumber: 2.5 Consensus size: 33
51355 AAAATCGCAA
**
51365 TGCGATTTTGGTTTCGCGTTACGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTACGATTATCTCGT
* *
51398 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTACGATTATCTCGT
*
51431 TGCAATTTTCATTTC
1 TGCGATTTTCATTTC
51446 TCTCGTTGCG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.12, C:0.21, G:0.20, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTACGATTATCTCGT
Found at i:51448 original size:21 final size:21
Alignment explanation
Indices: 51422--51485 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
51412 CGCGTTGCGA
*
51422 TTCTCTCGTTGCAATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
51443 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
51464 TT-TCGT-GTTGCGATTTTCAT
1 TTCTC-TCGTTGCGATTTTCAT
51484 TT
1 TT
51486 TCATGTTACA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
20 16 0.43
21 21 0.57
ACGTcount: A:0.12, C:0.20, G:0.16, T:0.52
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:51475 original size:20 final size:20
Alignment explanation
Indices: 51450--51492 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
51440 CATTTCTCTC
*
51450 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCAT
**
51470 GTTGCGATTTTCATTTTCAT
1 GTTGCGATAGTCATTTTCAT
51490 GTT
1 GTT
51493 ACAATTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.51
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCAT
Found at i:51499 original size:20 final size:20
Alignment explanation
Indices: 51460--51500 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
51450 GTTGCGATAG
* * *
51460 TCATTTTCGTGTTGCGATTT
1 TCATTTTCATGTTACAATTT
51480 TCATTTTCATGTTACAATTT
1 TCATTTTCATGTTACAATTT
51500 T
1 T
51501 AAGTTTAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.56
Consensus pattern (20 bp):
TCATTTTCATGTTACAATTT
Found at i:52082 original size:20 final size:20
Alignment explanation
Indices: 52057--52270 Score: 234
Period size: 20 Copynumber: 10.6 Consensus size: 20
52047 CTTTAAAAAT
52057 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
52077 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
52097 TGTCGTTACGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
52118 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
52138 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
52158 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
52178 CTCGTTGCGATTTACTGATA
1 CGCGTTGCGATTTACGGATA
*
52198 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
52218 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
52239 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
52260 CTCGTTGCGAT
1 CGCGTTGCGAT
52271 AGTCAGAATC
Statistics
Matches: 158, Mismatches: 29, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
20 107 0.68
21 51 0.32
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:52265 original size:41 final size:41
Alignment explanation
Indices: 52059--52270 Score: 338
Period size: 41 Copynumber: 5.2 Consensus size: 41
52049 TTAAAAATCG
*
52059 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
52100 CGTTACGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
52140 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
52180 CGTTGCGATTTACTGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
52221 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
52262 CGTTGCGAT
1 CGTTGCGAT
52271 AGTCAGAATC
Statistics
Matches: 158, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 75 0.47
41 83 0.53
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:52349 original size:21 final size:21
Alignment explanation
Indices: 52320--52367 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
52310 TTTTCATATT
* *
52320 CGCATTGCGATTCTAGTAAAG
1 CGCAATGCGATTCTAGAAAAG
*
52341 CGCAATGCGATTCTGGAAAAG
1 CGCAATGCGATTCTAGAAAAG
52362 CGCAAT
1 CGCAAT
52368 ACGAATTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (21 bp):
CGCAATGCGATTCTAGAAAAG
Found at i:54258 original size:20 final size:20
Alignment explanation
Indices: 54233--54272 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
54223 AGCAACAGAA
*
54233 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
54253 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
54273 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:54315 original size:20 final size:21
Alignment explanation
Indices: 54286--54325 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
54276 TAATAGAATA
54286 AAAAATTGAT-TCTATCTAATT
1 AAAAATTGATCT-TATCTAATT
54307 AAAAA-TGATCTTATCTAAT
1 AAAAATTGATCTTATCTAAT
54326 AACTAATAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (21 bp):
AAAAATTGATCTTATCTAATT
Found at i:54367 original size:20 final size:21
Alignment explanation
Indices: 54337--54377 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
54327 ACTAATAGAA
*
54337 TAAAGACTGATTCTATCTAAT
1 TAAAGACTGATCCTATCTAAT
54358 TAAA-ACTGATCCTATCTAAT
1 TAAAGACTGATCCTATCTAAT
54378 ATTTAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (21 bp):
TAAAGACTGATCCTATCTAAT
Found at i:54374 original size:52 final size:51
Alignment explanation
Indices: 54229--54378 Score: 246
Period size: 53 Copynumber: 2.9 Consensus size: 51
54219 AATTAGCAAC
54229 AGAATAAAAATGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAATAAAAATGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
*
54280 AGAATAAAAAATTGATTCTATCTAATTAAAAATGATCTTATCTAATAACTAAT
1 AGAAT-AAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
* *
54333 AGAATAAAGACTGATTCTATCTAATTAAAACTGATCCTATCTAATA
1 AGAATAAA-AATGATTCTATCTAATTAAAAATGATCCTATCTAATA
54379 TTTAATTTAG
Statistics
Matches: 92, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
51 5 0.05
52 41 0.45
53 46 0.50
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.34
Consensus pattern (51 bp):
AGAATAAAAATGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
Found at i:59003 original size:49 final size:49
Alignment explanation
Indices: 58910--59044 Score: 188
Period size: 48 Copynumber: 2.8 Consensus size: 49
58900 AATTAGCAAC
58910 AGAATAAAAA-TGATTCTATCTAATTAAAA--ATCATATCTAATAACTAAT
1 AGAATAAAAACTGATTCTATCTAATTAAAATGATCATATC--ATAACTAAT
*
58958 AGAATAAAAAACTGATTCTATCTAATTAAAATGATCCTATC-TAACTAAT
1 AGAAT-AAAAACTGATTCTATCTAATTAAAATGATCATATCATAACTAAT
*
59007 AGAATAAAGACTGATTCTATCTAATTAAAACTGATCAT
1 AGAATAAAAACTGATTCTATCTAATTAAAA-TGATCAT
59045 CTAATATTTA
Statistics
Matches: 79, Mismatches: 3, Indels: 9
0.87 0.03 0.10
Matches are distributed among these distances:
48 29 0.37
49 24 0.30
50 19 0.24
52 7 0.09
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.33
Consensus pattern (49 bp):
AGAATAAAAACTGATTCTATCTAATTAAAATGATCATATCATAACTAAT
Found at i:59048 original size:18 final size:21
Alignment explanation
Indices: 59011--59049 Score: 57
Period size: 18 Copynumber: 2.0 Consensus size: 21
59001 ACTAATAGAA
59011 TAAAGACTGATTCTATCTAAT
1 TAAAGACTGATTCTATCTAAT
59032 TAAA-ACTGA-TC-ATCTAAT
1 TAAAGACTGATTCTATCTAAT
59050 ATTTAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 2 0.11
20 5 0.28
21 4 0.22
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (21 bp):
TAAAGACTGATTCTATCTAAT
Found at i:59767 original size:42 final size:45
Alignment explanation
Indices: 59680--59768 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 45
59670 TCAATGTCGG
59680 ATTCGTTTCGGATGATTAGTAGAATAGCCCAATGGCTTTAGCAGCT
1 ATTCGTTTCGGATGATTA-TAGAATAGCCCAATGGCTTTAGCAGCT
59726 ATTCGTTTCGGATGA-T-TAGAATAG-CCAATGGCTTTAGCAGCT
1 ATTCGTTTCGGATGATTATAGAATAGCCCAATGGCTTTAGCAGCT
59768 A
1 A
59769 AAGATAAAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
42 19 0.44
43 8 0.19
45 1 0.02
46 15 0.35
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.33
Consensus pattern (45 bp):
ATTCGTTTCGGATGATTATAGAATAGCCCAATGGCTTTAGCAGCT
Done.