Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007206.1 Hibiscus syriacus cultivar Beakdansim tig00019037_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: 48304
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:3583 original size:23 final size:23
Alignment explanation
Indices: 3555--3599 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3545 AATCTATGTA
3555 TTTTAAATACAACCACATTATAT
1 TTTTAAATACAACCACATTATAT
* *
3578 TTTTAAATACAATCATATTATA
1 TTTTAAATACAACCACATTATA
3600 ATTGAATTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.42
Consensus pattern (23 bp):
TTTTAAATACAACCACATTATAT
Found at i:4170 original size:18 final size:18
Alignment explanation
Indices: 4124--4173 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
4114 TCAAAATCTT
*
4124 ATAATTATTAAATTTAATAA
1 ATAA-TATTAAA-TAAATAA
* *
4144 ATAAAATTAAATAAATGA
1 ATAATATTAAATAAATAA
4162 ATAATATTAAAT
1 ATAATATTAAAT
4174 TATAACCGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 16 0.62
19 6 0.23
20 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
ATAATATTAAATAAATAA
Found at i:12700 original size:10 final size:9
Alignment explanation
Indices: 12681--12740 Score: 84
Period size: 10 Copynumber: 6.3 Consensus size: 9
12671 GGTCGGGTTG
*
12681 GGTCAGACC
1 GGTCAAACC
12690 GGTTCAAACC
1 GG-TCAAACC
12700 GGTCAAACC
1 GGTCAAACC
12709 GGTTCAAACC
1 GG-TCAAACC
12719 GGTCAAGACC
1 GGTCAA-ACC
12729 GGTCAAACC
1 GGTCAAACC
12738 GGT
1 GGT
12741 TTTCCAGCTG
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
9 21 0.45
10 26 0.55
ACGTcount: A:0.28, C:0.30, G:0.27, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:12709 original size:19 final size:19
Alignment explanation
Indices: 12681--12740 Score: 95
Period size: 19 Copynumber: 3.2 Consensus size: 19
12671 GGTCGGGTTG
*
12681 GGTCAGACCGGTTCAAACC
1 GGTCAAACCGGTTCAAACC
12700 GGTCAAACCGGTTCAAACC
1 GGTCAAACCGGTTCAAACC
12719 GGTCAAGACCGG-TCAAACC
1 GGTCAA-ACCGGTTCAAACC
12738 GGT
1 GGT
12741 TTTCCAGCTG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
19 34 0.87
20 5 0.13
ACGTcount: A:0.28, C:0.30, G:0.27, T:0.15
Consensus pattern (19 bp):
GGTCAAACCGGTTCAAACC
Found at i:15252 original size:32 final size:32
Alignment explanation
Indices: 15207--15273 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
15197 AACATGACGC
* *
15207 AAAATTAACCCCTTTCTGTAATATTTGAGTAT
1 AAAATTAACCCCTTTATGTAATATTTGACTAT
*
15239 AAAATTAATCCCTTTATGTAATATTTGACTAT
1 AAAATTAACCCCTTTATGTAATATTTGACTAT
15271 AAA
1 AAA
15274 GGTGTTCAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.40
Consensus pattern (32 bp):
AAAATTAACCCCTTTATGTAATATTTGACTAT
Found at i:20951 original size:19 final size:19
Alignment explanation
Indices: 20927--20978 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
20917 TTTATGAATG
20927 TGCATCGATGCACTACTAA
1 TGCATCGATGCACTACTAA
20946 TGCATCGATGCACTACTAA
1 TGCATCGATGCACTACTAA
20965 TGCATCGATGCACT
1 TGCATCGATGCACT
20979 CTTTTAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (19 bp):
TGCATCGATGCACTACTAA
Found at i:21426 original size:24 final size:24
Alignment explanation
Indices: 21399--21471 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 24
21389 ACATGCATAA
*
21399 GATATAT-ATATGTTCATGTGATAT
1 GATATATGATATG-ACATGTGATAT
*
21423 GATATGTGATATGACATGTGATAT
1 GATATATGATATGACATGTGATAT
* *
21447 GAGAACATGATATGA-A-GTGATAT
1 GA-TATATGATATGACATGTGATAT
21470 GA
1 GA
21472 GATACATGAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
23 9 0.21
24 19 0.45
25 14 0.33
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.36
Consensus pattern (24 bp):
GATATATGATATGACATGTGATAT
Found at i:21431 original size:12 final size:12
Alignment explanation
Indices: 21413--21448 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
21403 TATATATGTT
21413 CATGTGATATGA
1 CATGTGATATGA
*
21425 TATGTGATATGA
1 CATGTGATATGA
21437 CATGTGATATGA
1 CATGTGATATGA
21449 GAACATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:21470 original size:23 final size:26
Alignment explanation
Indices: 21413--21481 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
21403 TATATATGTT
**
21413 CATGTGATAT--GATATGTGATATGA
1 CATGTGATATGAGATACATGATATGA
21437 CATGTGATATGAGA-ACATGATATGA
1 CATGTGATATGAGATACATGATATGA
21462 -A-GTGATATGAGATACATGAT
1 CATGTGATATGAGATACATGAT
21482 CACAAGAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 18 0.45
25 9 0.22
26 2 0.05
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.32
Consensus pattern (26 bp):
CATGTGATATGAGATACATGATATGA
Found at i:22064 original size:17 final size:18
Alignment explanation
Indices: 22037--22073 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
22027 AAGTATGTAC
22037 TTGGTTATGT-ATAGAGTG
1 TTGGTTATGTAATA-AGTG
22055 TTGG-TATGTAATAAGTG
1 TTGGTTATGTAATAAGTG
22072 TT
1 TT
22074 AATTATGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (18 bp):
TTGGTTATGTAATAAGTG
Found at i:24285 original size:15 final size:15
Alignment explanation
Indices: 24265--24318 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 15
24255 TTCTGAAAAA
24265 TGAATTACTGGAATT
1 TGAATTACTGGAATT
*
24280 TGAATTACTAGAATT
1 TGAATTACTGGAATT
*
24295 GGATGAATTACTGAAATT
1 ---TGAATTACTGGAATT
24313 TGAATT
1 TGAATT
24319 CTGAAAAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 20 0.61
18 13 0.39
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.39
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:24330 original size:14 final size:15
Alignment explanation
Indices: 24257--24334 Score: 59
Period size: 15 Copynumber: 5.1 Consensus size: 15
24247 AATTGATTTT
24257 CTGAAAAATGAATTA
1 CTGAAAAATGAATTA
* **
24272 CTGGAATTTGAATTA
1 CTGAAAAATGAATTA
**
24287 CTAGAATTGGATGAATTA
1 CT-GAA--AAATGAATTA
**
24305 CTGAAATTTGAATT-
1 CTGAAAAATGAATTA
24319 CTGAAAAATGAATTA
1 CTGAAAAATGAATTA
24334 C
1 C
24335 ATTTCTGGAA
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 12 0.26
15 21 0.45
16 2 0.04
17 3 0.06
18 9 0.19
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (15 bp):
CTGAAAAATGAATTA
Found at i:24769 original size:19 final size:20
Alignment explanation
Indices: 24717--24769 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
24707 TTAAATATCT
24717 TTATTAAA-ATATTATTTAA
1 TTATTAAATATATTATTTAA
* *
24736 ATATATAAATAATATTA-TTCA
1 TTAT-TAAAT-ATATTATTTAA
24757 TTATTAAATATAT
1 TTATTAAATATAT
24770 AAAAAAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 6 0.21
22 6 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTAAATATATTATTTAA
Found at i:24770 original size:30 final size:29
Alignment explanation
Indices: 24725--24829 Score: 94
Period size: 29 Copynumber: 3.6 Consensus size: 29
24715 CTTTATTAAA
* *
24725 ATATTATTTAAATATATAAATAA-TATTAT
1 ATATTATTAAAATATA-AAAAAATTATTAT
24754 -TCATTATTAAATATATAAAAAAATTATTAT
1 AT-ATTATTAAA-ATATAAAAAAATTATTAT
24784 ATATTATTAAAATA-AAAATATAA-TATCT-T
1 ATATTATTAAAATATAAAA-A-AATTAT-TAT
*
24813 ATATTATTATAATATAA
1 ATATTATTAAAATATAA
24830 TTGATTATTT
Statistics
Matches: 65, Mismatches: 3, Indels: 15
0.78 0.04 0.18
Matches are distributed among these distances:
28 5 0.08
29 34 0.52
30 25 0.38
31 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (29 bp):
ATATTATTAAAATATAAAAAAATTATTAT
Found at i:25184 original size:42 final size:42
Alignment explanation
Indices: 25070--25186 Score: 164
Period size: 42 Copynumber: 2.8 Consensus size: 42
25060 AATTACATTC
* * *
25070 CGGAAAACCAATTACGTGAAACAAACA-TAGGAAGACATTTTT
1 CGGAAAACGAATTACGTGAAACAAACACGA-GAAAACATTTTT
* *
25112 CGGAAAACGAATTACGTGAAACAAATACGAGAAAATATTTTT
1 CGGAAAACGAATTACGTGAAACAAACACGAGAAAACATTTTT
*
25154 CGGAAAACGAATTACGTAAAACAAACACGAGAA
1 CGGAAAACGAATTACGTGAAACAAACACGAGAA
25187 TTCAGGAAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 66 0.99
43 1 0.01
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.19
Consensus pattern (42 bp):
CGGAAAACGAATTACGTGAAACAAACACGAGAAAACATTTTT
Found at i:25460 original size:15 final size:15
Alignment explanation
Indices: 25440--25490 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
25430 TTCCAGAAAA
25440 TGAATTACTGAAATT
1 TGAATTACTGAAATT
*
25455 TGAATTACTGGAAA-A
1 TGAATTACT-GAAATT
25470 TGAATTACT-AGAATT
1 TGAATTACTGA-AATT
25485 TGAATT
1 TGAATT
25491 CTGGAAAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 1 0.03
14 2 0.06
15 24 0.77
16 4 0.13
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (15 bp):
TGAATTACTGAAATT
Found at i:25504 original size:29 final size:30
Alignment explanation
Indices: 25435--25506 Score: 121
Period size: 30 Copynumber: 2.4 Consensus size: 30
25425 TGGTTTTCCA
25435 GAAAATGAATTACTGAAATTTGAATTACTG
1 GAAAATGAATTACTGAAATTTGAATTACTG
25465 GAAAATGAATTACT-AGAATTTGAATT-CTG
1 GAAAATGAATTACTGA-AATTTGAATTACTG
25494 GAAAATGAATTAC
1 GAAAATGAATTAC
25507 ATTTCTGGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
29 17 0.41
30 24 0.59
ACGTcount: A:0.44, C:0.07, G:0.17, T:0.32
Consensus pattern (30 bp):
GAAAATGAATTACTGAAATTTGAATTACTG
Found at i:25512 original size:20 final size:20
Alignment explanation
Indices: 25489--25538 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
25479 AGAATTTGAA
25489 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
25509 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
25529 TTCTGGAAAA
1 TTCTGGAAAA
25539 CATCTGGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:25930 original size:26 final size:24
Alignment explanation
Indices: 25863--25941 Score: 65
Period size: 29 Copynumber: 3.2 Consensus size: 24
25853 TCTTACTAAA
* *
25863 ATATTATTGAAATATAAAATATAT
1 ATATTATTAAAATAAAAAATATAT
25887 -TCATTATTAAATATATAAAAAATTATTAT
1 AT-ATTATT-AA-A-ATAAAAAA-TA-TAT
25916 ATATTATTAAAAT-AAAAATATA-
1 ATATTATTAAAATAAAAAATATAT
25938 ATAT
1 ATAT
25942 CTTATATTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
22 4 0.09
23 3 0.07
24 8 0.17
25 6 0.13
26 3 0.07
27 8 0.17
28 4 0.09
29 9 0.20
30 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (24 bp):
ATATTATTAAAATAAAAAATATAT
Found at i:25956 original size:52 final size:51
Alignment explanation
Indices: 25900--26009 Score: 118
Period size: 52 Copynumber: 2.1 Consensus size: 51
25890 TTATTAAATA
25900 TATAAAAAATT-ATTATATATTAT-TAA-AATAAAAATATAATATCTTATATTAT
1 TATAAAAAATTGATTAT-T-TTATATAATAATAAAAATATAATA--TTATATTAT
* * *
25952 TATAATATAATTGATTATTTTATATAATATTAAAAATTTAATATTATATTAT
1 TATAA-AAAATTGATTATTTTATATAATAATAAAAATATAATATTATATTAT
*
26004 TTTAAA
1 TATAAA
26010 TATTAATAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
51 1 0.02
52 22 0.44
53 9 0.18
54 18 0.36
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (51 bp):
TATAAAAAATTGATTATTTTATATAATAATAAAAATATAATATTATATTAT
Found at i:26008 original size:24 final size:23
Alignment explanation
Indices: 25971--26017 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
25961 ATTGATTATT
25971 TTATATAATATTAAAAATTTAATA
1 TTATATAATATTAAAAA-TTAATA
* * *
25995 TTATATTATTTTAAATATTAATA
1 TTATATAATATTAAAAATTAATA
26018 AATATATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTATATAATATTAAAAATTAATA
Found at i:26289 original size:42 final size:41
Alignment explanation
Indices: 26230--26339 Score: 193
Period size: 42 Copynumber: 2.6 Consensus size: 41
26220 TACATTCCGG
26230 AAAACGAATTACGTGAAACAAACACGGAAAAACGTTTTCCAA
1 AAAACGAATTACGTGAAACAAACACGG-AAAACGTTTTCCAA
*
26272 AAAACGAATTACGTGAAACAAACACAGGAAAACGTTTTCCGA
1 AAAACGAATTACGTGAAACAAACAC-GGAAAACGTTTTCCAA
26314 AAAACGAATTACGTGAAACAAACACG
1 AAAACGAATTACGTGAAACAAACACG
26340 AGAATTCAGT
Statistics
Matches: 66, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
41 1 0.02
42 63 0.95
43 2 0.03
ACGTcount: A:0.50, C:0.19, G:0.15, T:0.15
Consensus pattern (41 bp):
AAAACGAATTACGTGAAACAAACACGGAAAACGTTTTCCAA
Found at i:27044 original size:56 final size:56
Alignment explanation
Indices: 26958--27071 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
26948 GGACGGTGAG
26958 TGGAGCAAAATCTGAAATTATTCCTCCATAGATTCTACTGCTTGACACGATAGTAA
1 TGGAGCAAAATCTGAAATTATTCCTCCATAGATTCTACTGCTTGACACGATAGTAA
27014 TGGAGCAAAATCTGAAATTATTCCTCCATAGATTCTACTGCTTGACACGATAGTAA
1 TGGAGCAAAATCTGAAATTATTCCTCCATAGATTCTACTGCTTGACACGATAGTAA
27070 TG
1 TG
27072 TTTTTTAAAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (56 bp):
TGGAGCAAAATCTGAAATTATTCCTCCATAGATTCTACTGCTTGACACGATAGTAA
Found at i:39222 original size:18 final size:18
Alignment explanation
Indices: 39199--39238 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
39189 GACATTGTTT
39199 TCTTGTTTCTTGCCTAAC
1 TCTTGTTTCTTGCCTAAC
39217 TCTTGTTTCTTGCCTAAC
1 TCTTGTTTCTTGCCTAAC
39235 TCTT
1 TCTT
39239 CCAAGAAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.10, C:0.28, G:0.10, T:0.53
Consensus pattern (18 bp):
TCTTGTTTCTTGCCTAAC
Found at i:40227 original size:22 final size:22
Alignment explanation
Indices: 40202--40247 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
40192 GTTTACAAAT
* *
40202 AGGGAATCGATTCCCCTACTAC
1 AGGGAACCGATTCCACTACTAC
*
40224 AGGGAACCGATTCCACTGCTAC
1 AGGGAACCGATTCCACTACTAC
40246 AG
1 AG
40248 TACTTCCGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (22 bp):
AGGGAACCGATTCCACTACTAC
Found at i:40797 original size:21 final size:21
Alignment explanation
Indices: 40748--40811 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
40738 ATATGAAATT
*
40748 TTGTCCCGAAGGACCTGTGAA
1 TTGTCCCGAAGGACCTATGAA
*
40769 TATGTCCCGAAGGACCTATGAG
1 T-TGTCCCGAAGGACCTATGAA
40791 TTGTCCCGAAGGACCTATGAA
1 TTGTCCCGAAGGACCTATGAA
40812 ACCCTCGACT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
21 20 0.51
22 19 0.49
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAA
Found at i:46628 original size:22 final size:24
Alignment explanation
Indices: 46600--46647 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
46590 TGTCCGGACA
*
46600 TCTATTA-AAAATAACATA-TCAT
1 TCTATTACAAAAGAACATACTCAT
46622 TCTATTAGCAAAAGAACATACTCAT
1 TCTATTA-CAAAAGAACATACTCAT
46647 T
1 T
46648 ACCATACCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
24 10 0.45
25 5 0.23
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (24 bp):
TCTATTACAAAAGAACATACTCAT
Found at i:47052 original size:22 final size:22
Alignment explanation
Indices: 47027--47072 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
47017 GTTTACAAAT
47027 AGGGAATCGATTCCCCTGCTAC
1 AGGGAATCGATTCCCCTGCTAC
47049 AGGGAATCGATTCCCCTGCTAC
1 AGGGAATCGATTCCCCTGCTAC
47071 AG
1 AG
47073 TACTGCTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.24, C:0.30, G:0.24, T:0.22
Consensus pattern (22 bp):
AGGGAATCGATTCCCCTGCTAC
Found at i:47080 original size:11 final size:11
Alignment explanation
Indices: 47064--47098 Score: 70
Period size: 11 Copynumber: 3.2 Consensus size: 11
47054 ATCGATTCCC
47064 CTGCTACAGTA
1 CTGCTACAGTA
47075 CTGCTACAGTA
1 CTGCTACAGTA
47086 CTGCTACAGTA
1 CTGCTACAGTA
47097 CT
1 CT
47099 TCCGTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (11 bp):
CTGCTACAGTA
Found at i:47626 original size:21 final size:21
Alignment explanation
Indices: 47577--47640 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
47567 ATATGAAATT
*
47577 TTGTCCCGAAGGACCTGTGAA
1 TTGTCCCGAAGGACCTATGAA
*
47598 TATGTCCCGAAGGACCTATGAG
1 T-TGTCCCGAAGGACCTATGAA
47620 TTGTCCCGAAGGACCTATGAA
1 TTGTCCCGAAGGACCTATGAA
47641 ACCCTCGACT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
21 20 0.51
22 19 0.49
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAA
Done.