Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006414.1 Hibiscus syriacus cultivar Beakdansim tig00015469_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: 56831
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2622 original size:35 final size:38
Alignment explanation
Indices: 2548--2637 Score: 132
Period size: 35 Copynumber: 2.4 Consensus size: 38
2538 CATGCAAAAT
*
2548 ATACTTGCAAATTAATTTAAATATTAATATGCTCAGTC
1 ATACTTACAAATTAATTTAAATATTAATATGCTCAGTC
*
2586 ATACTTACAAATTAATTT-AATATT-A-ATGCTTAGTC
1 ATACTTACAAATTAATTTAAATATTAATATGCTCAGTC
*
2621 ATGCTTACAAATTAATT
1 ATACTTACAAATTAATT
2638 ACATGTTTAC
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
35 25 0.51
36 1 0.02
37 6 0.12
38 17 0.35
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.41
Consensus pattern (38 bp):
ATACTTACAAATTAATTTAAATATTAATATGCTCAGTC
Found at i:17414 original size:95 final size:95
Alignment explanation
Indices: 17241--17498 Score: 362
Period size: 95 Copynumber: 2.7 Consensus size: 95
17231 TATAATATTA
*
17241 TATATATATA-AATAAAGCTTGAGCTGTCCCTCTAAAGCAATTGGTTAAACGCCCCAGA-TTTAT
1 TATA-ATATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCC-GACTTTAT
17304 GGATAAGATTCAGCTAGCCTAATAAAGGTGAT
64 GGATAAGATTCAGCTAGCCTAATAAAGGTGAT
*
17336 TATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGG
1 TATAATATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGG
* * *
17401 ATAATATTCAGCTAGCCTGATAATGGTGAT
66 ATAAGATTCAGCTAGCCTAATAAAGGTGAT
* * * *
17431 TATAATATCTACAACGATA--TTGAACTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTA
1 TATAATA--TACAA-TAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTA
17494 TGGAT
63 TGGAT
17499 TCAGCTAGCT
Statistics
Matches: 148, Mismatches: 10, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
94 7 0.05
95 88 0.59
96 46 0.31
97 5 0.03
98 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Consensus pattern (95 bp):
TATAATATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGG
ATAAGATTCAGCTAGCCTAATAAAGGTGAT
Found at i:18771 original size:84 final size:84
Alignment explanation
Indices: 18630--19418 Score: 885
Period size: 84 Copynumber: 9.4 Consensus size: 84
18620 ACTATCGCAA
* * * * *
18630 CATAACTCAAGGCTAGAAGGGTTAT-TTGCCAACAAAAAACATTTGAGTTCGACTACGCTCAGCT
1 CATAACTCAAGGCTAGAAGGGTTATCTT-TCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCT
*
18694 CCAAGGCATATCATTTGCAG
65 CCAAGGCACATCATTTGCAG
*
18714 CATAACTCAAGGCTAGAAGGGTTATCTTTCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTT
1 CATAACTCAAGGCTAGAAGGGTTATCTTTCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTC
*
18779 CAAGGCACATCATTTGCAA
66 CAAGGCACATCATTTGCAG
* * * * * *
18798 CATAACTCAAGGCAAGAAGGGCTAT-TTTCCAAACACAGACCTTCAAGTTTGACTACGCTCTA-C
1 CATAACTCAAGGCTAGAAGGGTTATCTTT-CAACCAAAGACCTTCGAGTTCGACTACGCTC-AGC
18861 TCCAAGGCACATCATTTGCAG
64 TCCAAGGCACATCATTTGCAG
** * *
18882 CATAACTCAAGGCTAGAAATGTTATCTGTT-AACAAAAGACCTTCGAGTTCGACTACGCTCAACT
1 CATAACTCAAGGCTAGAAGGGTTATCT-TTCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCT
*
18946 CCAAGGCATATCATTTGCAG
65 CCAAGGCACATCATTTGCAG
* * * *
18966 CATAGCTCAAGGCTAGAAGGGTTATC-TGCCACCAAAAGACCTTCGAGTTTGACTACGCTCAGCT
1 CATAACTCAAGGCTAGAAGGGTTATCTTTCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCT
19030 CCAAGGCACATCATTTGCAG
65 CCAAGGCACATCATTTGCAG
** *
19050 CATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCAACTACGCTCAGCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTTTCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* *
19115 CAAGGTACATCATTTTCAG
66 CAAGGCACATCATTTGCAG
* * * *
19134 CATAGA-TCAAGGCTAGAAGGGCTATC-TGCCACCAAAAGACCTTCGAGTTCGACAACGCTCAGC
1 CATA-ACTCAAGGCTAGAAGGGTTATCTTTCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGC
* *
19197 TCCAAGGCATATTATTTGCAG
64 TCCAAGGCACATCATTTGCAG
* * * * * *
19218 TATAACTCAATGCTAGAAGGGTTATCTTCCAACTAAAGACCTTCGAGTTCAACTACGCTTAGCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTTTCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* *
19283 TAAGGCACATCATTTGCAA
66 CAAGGCACATCATTTGCAG
* * * * * * * * *
19302 CATAGCTCAAGGCAAAAATGGCTAT-TTGTCAA-CAAAGACCTTCGAGTTCAATTTCACTCAGCT
1 CATAACTCAAGGCTAGAAGGGTTATCTT-TCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCT
* ** *
19365 CAAAGGCACGCCATTTTACAG
65 CCAAGGCACATCA-TTTGCAG
* * * * * *
19386 CGTAGCTCAAGGCAAAAAGGGCTATCTGTCAAC
1 CATAACTCAAGGCTAGAAGGGTTATCTTTCAAC
19419 AAAATTATCG
Statistics
Matches: 601, Mismatches: 87, Indels: 33
0.83 0.12 0.05
Matches are distributed among these distances:
82 1 0.00
83 49 0.08
84 535 0.89
85 14 0.02
86 2 0.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.24
Consensus pattern (84 bp):
CATAACTCAAGGCTAGAAGGGTTATCTTTCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTC
CAAGGCACATCATTTGCAG
Found at i:19092 original size:252 final size:250
Alignment explanation
Indices: 18630--19422 Score: 1032
Period size: 252 Copynumber: 3.1 Consensus size: 250
18620 ACTATCGCAA
* * * *
18630 CATAACTCAAGGCTAGAAGGGTTATTTGCCAACAAAAAACATTTGAGTTCGACTACGCTCAGCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
*
18695 CAAGGCATATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTTTCAACCAAAGACCTTCGA
66 CAAGGCATATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATC-TTCCACCAAAGACCTTCGA
*
18760 GTTCGACTACGCTCAGCTTCAAGGCACATCATTTGCAACATAACTCAAGGCAAGAAGGGCTATTT
130 GTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCAAGAAGGGCTATTT
* * * **
18825 TCCAAACACAGACCTTCAAGTTTGACTACGCTCTA-CTCCAAGGCACATCATTTGCAG
195 GCC-AACAAAGACCTTCGAGTTCAACTACGCTC-AGCTCCAAGGCACATCATTTGCAG
** ** *
18882 CATAACTCAAGGCTAGAAATGTTATCTGTTAACAAAAGACCTTCGAGTTCGACTACGCTCAACTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* *
18947 CAAGGCATATCATTTGCAGCATAGCTCAAGGCTAGAAGGGTTATCTGCCACCAAAAGACCTTCGA
66 CAAGGCATATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTTCCACC-AAAGACCTTCGA
* * * * *
19012 GTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCT
130 GTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCAAGAAGGGCTATTT
* *
19077 GCCAACCAAAGACCTTCGAGTTCAACTACGCTCAGCTCCAAGGTACATCATTTTCAG
195 GCCAA-CAAAGACCTTCGAGTTCAACTACGCTCAGCTCCAAGGCACATCATTTGCAG
* * *
19134 CATAGA-TCAAGGCTAGAAGGGCTATCTGCCACCAAAAGACCTTCGAGTTCGACAACGCTCAGCT
1 CATA-ACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCT
* * * *
19198 CCAAGGCATATTATTTGCAGTATAACTCAATGCTAGAAGGGTTATCTTCCAACTAAAGACCTTCG
65 CCAAGGCATATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTTCC-ACCAAAGACCTTCG
* * * * * *
19263 AGTTCAACTACGCTTAGCTCTAAGGCACATCATTTGCAACATAGCTCAAGGCAAAAATGGCTATT
129 AGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCAAGAAGGGCTATT
* * * * * ** *
19328 TGTCAACAAAGACCTTCGAGTTCAATTTCACTCAGCTCAAAGGCACGCCATTTTACAG
194 TGCCAACAAAGACCTTCGAGTTCAACTACGCTCAGCTCCAAGGCACATCA-TTTGCAG
* * * * * *
19386 CGTAGCTCAAGGCAAAAAGGGCTATCTGTCAACAAAA
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAA
19423 TTATCGAGTT
Statistics
Matches: 469, Mismatches: 65, Indels: 14
0.86 0.12 0.03
Matches are distributed among these distances:
251 45 0.10
252 421 0.90
253 3 0.01
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.24
Consensus pattern (250 bp):
CATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
CAAGGCATATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTTCCACCAAAGACCTTCGAG
TTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCAAGAAGGGCTATTTG
CCAACAAAGACCTTCGAGTTCAACTACGCTCAGCTCCAAGGCACATCATTTGCAG
Found at i:20022 original size:13 final size:15
Alignment explanation
Indices: 20006--20042 Score: 51
Period size: 13 Copynumber: 2.5 Consensus size: 15
19996 TGCTATATAA
20006 TATATTTATAA-AT-
1 TATATTTATAATATG
20019 TATATTATATAATATG
1 TATATT-TATAATATG
20035 TATATTTA
1 TATATTTA
20043 CATTGAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 6 0.29
14 5 0.24
15 4 0.19
16 6 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
TATATTTATAATATG
Found at i:21064 original size:17 final size:16
Alignment explanation
Indices: 21039--21138 Score: 52
Period size: 17 Copynumber: 6.4 Consensus size: 16
21029 TTTTTTAATT
* *
21039 TTTACTTTTTTGTTTTA
1 TTTA-TTTTTTCTTTGA
21056 TTTCATTTTTTCTTTGA
1 TTT-ATTTTTTCTTTGA
*
21073 TTTA-TTTTCCTTT--
1 TTTATTTTTTCTTTGA
* *
21086 TTTCTTATTT-TTT-A
1 TTTATTTTTTCTTTGA
*
21100 TTTATTCTTT-TTT-A
1 TTTATTTTTTCTTTGA
*
21114 TTACATTTTTTCTTTTGA
1 TT-TATTTTTTC-TTTGA
21132 TTTATTT
1 TTTATTT
21139 AATGTATTTT
Statistics
Matches: 65, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
13 6 0.09
14 17 0.26
15 14 0.22
16 1 0.02
17 23 0.35
18 4 0.06
ACGTcount: A:0.13, C:0.09, G:0.03, T:0.75
Consensus pattern (16 bp):
TTTATTTTTTCTTTGA
Found at i:21086 original size:22 final size:21
Alignment explanation
Indices: 21047--21138 Score: 88
Period size: 22 Copynumber: 4.6 Consensus size: 21
21037 TTTTTACTTT
*
21047 TTTGTTTTATTTCATTTTTTC
1 TTTGATTTATTTCATTTTTTC
*
21068 TTTGATTTATTTTCCTTTTTTC
1 TTTGATTTA-TTTCATTTTTTC
*
21090 -TT-ATTT-TTT-ATTTATTC
1 TTTGATTTATTTCATTTTTTC
*
21107 TTT--TTTATTACATTTTTTC
1 TTTGATTTATTTCATTTTTTC
21126 TTTTGATTTATTT
1 -TTTGATTTATTT
21139 AATGTATTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
17 9 0.16
18 7 0.12
19 7 0.12
20 7 0.12
21 10 0.18
22 17 0.30
ACGTcount: A:0.13, C:0.09, G:0.03, T:0.75
Consensus pattern (21 bp):
TTTGATTTATTTCATTTTTTC
Found at i:21122 original size:24 final size:23
Alignment explanation
Indices: 21073--21122 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
21063 TTTTCTTTGA
* **
21073 TTTATTTTCCTTTTTTCTTATTT
1 TTTATTTTCCTTTTTTATTACAT
*
21096 TTTATTTATTCTTTTTTATTACAT
1 TTTATTT-TCCTTTTTTATTACAT
21120 TTT
1 TTT
21123 TTCTTTTGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTATTTTCCTTTTTTATTACAT
Found at i:21136 original size:36 final size:37
Alignment explanation
Indices: 21096--21166 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
21086 TTTCTTATTT
* *
21096 TTTATTTATTCT-TTTTTATTACATTTTTTCTTTTGA
1 TTTATTTAATCTATTTTTATTACATTTTTCCTTTTGA
* **
21132 TTTATTTAATGTATTTTTATTTTATTTTTCCTTTT
1 TTTATTTAATCTATTTTTATTACATTTTTCCTTTT
21167 TCCTTTTTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 10 0.34
37 19 0.66
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.73
Consensus pattern (37 bp):
TTTATTTAATCTATTTTTATTACATTTTTCCTTTTGA
Found at i:21149 original size:37 final size:35
Alignment explanation
Indices: 21083--21166 Score: 87
Period size: 36 Copynumber: 2.3 Consensus size: 35
21073 TTTATTTTCC
* *
21083 TTTTTTCTTATTTTTTATTTATTCTTTTTTATTACA
1 TTTTTTCTT-TTATTTATTTAATCTTTTTTATTACA
* **
21119 TTTTTTCTTTTGATTTATTTAATGTATTTTTATTTTA
1 TTTTTTCTTTT-ATTTATTTAATCT-TTTTTATTACA
*
21156 TTTTTCCTTTT
1 TTTTTTCTTTT
21167 TCCTTTTTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
35 2 0.05
36 19 0.47
37 19 0.47
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.75
Consensus pattern (35 bp):
TTTTTTCTTTTATTTATTTAATCTTTTTTATTACA
Found at i:21152 original size:58 final size:56
Alignment explanation
Indices: 21030--21154 Score: 137
Period size: 58 Copynumber: 2.2 Consensus size: 56
21020 CTTAAAATAT
* * ** *
21030 TTTTTAATTTTTACTTTTTTGTTTTATTTCATTTTTTCTTTGATTTATTTTCCTTT
1 TTTTTATTTTTTACTTTTTTGTTTTATTACATTTTTTCTTTGATTTATTTTAATTA
*
21086 TTTCTTATTTTTTA-TTTATTCTTTTTTATTACATTTTTTCTTTTGATTTA-TTTAATGTA
1 TTT-TTATTTTTTACTTT-TT-TGTTTTATTACATTTTTTC-TTTGATTTATTTTAAT-TA
21145 TTTTTATTTT
1 TTTTTATTTT
21155 ATTTTTCCTT
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
56 6 0.10
57 11 0.19
58 28 0.48
59 13 0.22
ACGTcount: A:0.15, C:0.07, G:0.03, T:0.74
Consensus pattern (56 bp):
TTTTTATTTTTTACTTTTTTGTTTTATTACATTTTTTCTTTGATTTATTTTAATTA
Found at i:21154 original size:6 final size:6
Alignment explanation
Indices: 21143--21245 Score: 52
Period size: 6 Copynumber: 17.2 Consensus size: 6
21133 TTATTTAATG
* * * *
21143 TATTTT TA-TTT TATTTT TCCTTTT TCCTTTT TGATTTT GATTTT GA-TTT
1 TATTTT TATTTT TATTTT T-ATTTT T-ATTTT T-ATTTT TATTTT TATTTT
* * * * * *
21192 TCTTTT TCTTTT GA--TT TATTAT TATTTT TATTTT TATTTT CATTCT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT
21238 TATGTTT T
1 TAT-TTT T
21246 TTCTTTGATT
Statistics
Matches: 76, Mismatches: 15, Indels: 11
0.75 0.15 0.11
Matches are distributed among these distances:
4 3 0.04
5 8 0.11
6 46 0.61
7 19 0.25
ACGTcount: A:0.14, C:0.08, G:0.05, T:0.74
Consensus pattern (6 bp):
TATTTT
Found at i:21225 original size:45 final size:49
Alignment explanation
Indices: 21170--21259 Score: 116
Period size: 45 Copynumber: 1.9 Consensus size: 49
21160 TCCTTTTTCC
* *
21170 TTTTTGATTTTGATTTTGATT-TTCT-TTTTCT-TTTGATTTATTATTA
1 TTTTTGATTTTGATTTTCATTCTTATGTTTTCTCTTTGATTTATTATTA
* *
21216 TTTTT-ATTTTTATTTTCATTCTTATGTTTTTTCTTTGATTTATT
1 TTTTTGATTTTGATTTTCATTCTTATGTTTTCTCTTTGATTTATT
21260 TAAATATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
45 13 0.35
46 8 0.22
47 5 0.14
48 11 0.30
ACGTcount: A:0.14, C:0.06, G:0.07, T:0.73
Consensus pattern (49 bp):
TTTTTGATTTTGATTTTCATTCTTATGTTTTCTCTTTGATTTATTATTA
Found at i:26028 original size:110 final size:110
Alignment explanation
Indices: 25835--26051 Score: 389
Period size: 110 Copynumber: 2.0 Consensus size: 110
25825 CTCTAGAAAA
*
25835 AAGTGAATGCTGTCTCGTTTTGTGAAGTGAGATGAAAAGGTTCGAGCACCGTGTATGTTAAGTAT
1 AAGTGAATGCTGTCTCGTTTTGTGAAGTGAGATGAAAAGGTTCGAGCACCGTATATGTTAAGTAT
*
25900 GAATGTTCATTATTAAATAATCAAGAGTTTTTTTAACATATAAAG
66 GAATGTTCATTATTAAATAATCAAGAATTTTTTTAACATATAAAG
* *
25945 AAGTGAATGCTGTCTCGTTTTGTGAAGTGAGATGGAAAGGTTCGAGCACCGTATATGTTATGTAT
1 AAGTGAATGCTGTCTCGTTTTGTGAAGTGAGATGAAAAGGTTCGAGCACCGTATATGTTAAGTAT
*
26010 GAATGTTCATTGTTAAATAATCAAGAATTTTTTTAACATATA
66 GAATGTTCATTATTAAATAATCAAGAATTTTTTTAACATATA
26052 TTATCTTATA
Statistics
Matches: 102, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
110 102 1.00
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.36
Consensus pattern (110 bp):
AAGTGAATGCTGTCTCGTTTTGTGAAGTGAGATGAAAAGGTTCGAGCACCGTATATGTTAAGTAT
GAATGTTCATTATTAAATAATCAAGAATTTTTTTAACATATAAAG
Found at i:26839 original size:15 final size:15
Alignment explanation
Indices: 26802--26841 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
26792 TTATAGATAG
* *
26802 ATTAATACTTCATAT
1 ATTAATAGTTAATAT
26817 ATTAATAGTTAATAT
1 ATTAATAGTTAATAT
26832 ATTAATAGTT
1 ATTAATAGTT
26842 GGGGGCATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (15 bp):
ATTAATAGTTAATAT
Found at i:27104 original size:18 final size:19
Alignment explanation
Indices: 27065--27104 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
27055 ATATTAATAG
*
27065 TTAATTTTTTATAAGTTGTT
1 TTAATTTATTATAAG-TGTT
27085 TTAATTTATTATAA-TGTT
1 TTAATTTATTATAAGTGTT
27103 TT
1 TT
27105 TAACTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
20 13 0.68
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (19 bp):
TTAATTTATTATAAGTGTT
Found at i:34278 original size:15 final size:15
Alignment explanation
Indices: 34258--34300 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
34248 AGAGGTGGCT
**
34258 GAAGAAGAAGACGAG
1 GAAGAAGAAGAAAAG
34273 GAAGAAGAAGAAAAG
1 GAAGAAGAAGAAAAG
*
34288 GAAGAAAAAGAAA
1 GAAGAAGAAGAAA
34301 TACTCCGGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (15 bp):
GAAGAAGAAGAAAAG
Found at i:37911 original size:29 final size:29
Alignment explanation
Indices: 37878--37955 Score: 120
Period size: 29 Copynumber: 2.7 Consensus size: 29
37868 TAAATTGATA
* *
37878 TCATTACTTACATCATTTAATTAAAGATG
1 TCATTGCTTACATCATTTAAGTAAAGATG
*
37907 TCATTGCTTACATCATTTAAGTAATGATG
1 TCATTGCTTACATCATTTAAGTAAAGATG
37936 TCATTGCTTACATCAATTTA
1 TCATTGCTTACATC-ATTTA
37956 GTTAGGTGAG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 40 0.89
30 5 0.11
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.42
Consensus pattern (29 bp):
TCATTGCTTACATCATTTAAGTAAAGATG
Found at i:42659 original size:29 final size:29
Alignment explanation
Indices: 42624--42704 Score: 135
Period size: 29 Copynumber: 2.8 Consensus size: 29
42614 AAACTAAATT
* *
42624 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
42653 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
42682 GATGTCATTGCTTACATCATTTA
1 GATGTCATTGCTTACATCATTTA
42705 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Done.