Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002099.1 Hibiscus syriacus cultivar Beakdansim tig00004284_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: 78696
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:12666 original size:13 final size:11
Alignment explanation
Indices: 12625--12709 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
12615 ACAATCTGTC
12625 CATCACCATTAT
1 CATCACCA-TAT
*
12637 CA-CGCCTATAT
1 CATCACC-ATAT
12648 CATCACCATAGT
1 CATCACCATA-T
12660 CCATCACCATTAT
1 -CATCACCA-TAT
*
12673 CA-CGCCTATAT
1 CATCACC-ATAT
12684 CATCACCATATT
1 CATCACCATA-T
12696 CCATCACCATAT
1 -CATCACCATAT
12708 CA
1 CA
12710 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:12669 original size:36 final size:36
Alignment explanation
Indices: 12622--12726 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
12612 GATACAATCT
12622 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
12658 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
12694 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
12727 ACTTATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:13093 original size:35 final size:37
Alignment explanation
Indices: 13042--13117 Score: 111
Period size: 35 Copynumber: 2.1 Consensus size: 37
13032 TTTGAGAATT
*
13042 TGGTAATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTAATGATATAGGCGTGATAATGGAAGATGGACTA
* *
13077 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTAATGATATAGGCGTGATAATGGAAGATGGACTA
13114 TGGT
1 TGGT
13118 TATGGAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 20 0.56
36 4 0.11
37 12 0.33
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.32
Consensus pattern (37 bp):
TGGTAATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:17354 original size:13 final size:13
Alignment explanation
Indices: 17319--17359 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
17309 TGCTGCAACA
17319 AAAGCAACAAAAAG
1 AAAG-AACAAAAAG
*
17333 --AGAAAAAAAAG
1 AAAGAACAAAAAG
17344 AAAGAACAAAAAG
1 AAAGAACAAAAAG
17357 AAA
1 AAA
17360 AAGAAAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
11 8 0.35
12 2 0.09
13 13 0.57
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAGAACAAAAAG
Found at i:17362 original size:6 final size:6
Alignment explanation
Indices: 17327--17385 Score: 70
Period size: 6 Copynumber: 10.2 Consensus size: 6
17317 CAAAAGCAAC
* *
17327 AAAAAG AGAAA- AAAAAG AAAGAAC AAAAAG AAAAAG -AAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG
17374 -AAAAG AAAAAG A
1 AAAAAG AAAAAG A
17386 CTCCTACATC
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 14 0.31
6 26 0.58
7 5 0.11
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:17366 original size:5 final size:5
Alignment explanation
Indices: 17333--17382 Score: 52
Period size: 5 Copynumber: 10.2 Consensus size: 5
17323 CAACAAAAAG
*
17333 AGAAA A-AAA AG-AA AGAAC A-AAA AGAAAA AGAAA AGAAAA AGAAA AGAAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AG-AAA AGAAA AG-AAA AGAAA AGAAA
17382 A
1 A
17383 AGACTCCTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
4 11 0.29
5 17 0.45
6 10 0.26
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:17384 original size:11 final size:11
Alignment explanation
Indices: 17328--17385 Score: 73
Period size: 11 Copynumber: 5.1 Consensus size: 11
17318 AAAAGCAACA
17328 AAAAGAGAAAA-
1 AAAAGA-AAAAG
*
17339 AAAAGAAAGAACA
1 AAAAGAAA-AA-G
17352 AAAAGAAAAAG
1 AAAAGAAAAAG
17363 AAAAGAAAAAG
1 AAAAGAAAAAG
17374 AAAAGAAAAAG
1 AAAAGAAAAAG
17385 A
1 A
17386 CTCCTACATC
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
10 2 0.05
11 31 0.72
12 2 0.05
13 8 0.19
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:17384 original size:22 final size:24
Alignment explanation
Indices: 17319--17385 Score: 86
Period size: 24 Copynumber: 2.8 Consensus size: 24
17309 TGCTGCAACA
17319 AAAGCAACAAAAAGAGAAAA-AAAAG
1 AAAG-AACAAAAAGA-AAAAGAAAAG
17344 AAAGAACAAAAAGAAAAAGAAAAG
1 AAAGAACAAAAAGAAAAAGAAAAG
*
17368 AAA-AA-GAAAAGAAAAAGA
1 AAAGAACAAAAAGAAAAAGA
17386 CTCCTACATC
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
22 12 0.30
23 6 0.15
24 18 0.45
25 4 0.10
ACGTcount: A:0.79, C:0.04, G:0.16, T:0.00
Consensus pattern (24 bp):
AAAGAACAAAAAGAAAAAGAAAAG
Found at i:40638 original size:27 final size:27
Alignment explanation
Indices: 40590--40651 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
40580 ATTCATCTTG
*
40590 AAAAAAAAAGAGAATTCCAAAAATTAA
1 AAAAAAAAACAGAATTCCAAAAATTAA
* **
40617 AAAAAAAAACA-AATTCCGAAAATTTT
1 AAAAAAAAACAGAATTCCAAAAATTAA
40643 AAAAAAAAA
1 AAAAAAAAA
40652 GAAAAAAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 21 0.68
27 10 0.32
ACGTcount: A:0.71, C:0.08, G:0.05, T:0.16
Consensus pattern (27 bp):
AAAAAAAAACAGAATTCCAAAAATTAA
Found at i:52142 original size:13 final size:11
Alignment explanation
Indices: 52122--52278 Score: 106
Period size: 11 Copynumber: 13.2 Consensus size: 11
52112 AATATAGGCG
52122 TGATATGGTGA
1 TGATATGGTGA
52133 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
52146 TGATATAGGCG-
1 TGATAT-GGTGA
52157 TGATAATGGTGA
1 TGAT-ATGGTGA
52169 TGGACTATGGTGA
1 T-GA-TATGGTGA
*
52182 TGATATAGGCG-
1 TGATAT-GGTGA
52193 TGATAATGGTGA
1 TGAT-ATGGTGA
52205 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
52218 TGATATAGGCG-
1 TGATAT-GGTGA
52229 TGATAATGGTGA
1 TGAT-ATGGTGA
52241 TGGACTATGGTGA
1 T-GA-TATGGTGA
*
52254 TGATATAGGCG-
1 TGATAT-GGTGA
52265 TGATAATGGTGA
1 TGAT-ATGGTGA
52277 TG
1 TG
52279 GACAGATTGT
Statistics
Matches: 118, Mismatches: 8, Indels: 39
0.72 0.05 0.24
Matches are distributed among these distances:
11 43 0.36
12 32 0.27
13 39 0.33
14 4 0.03
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:52178 original size:36 final size:36
Alignment explanation
Indices: 52105--52281 Score: 320
Period size: 36 Copynumber: 4.9 Consensus size: 36
52095 ATTTATAAGT
* *
52105 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
52140 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
52176 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
52212 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
52248 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
52282 AGATTGTATC
Statistics
Matches: 137, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.15
36 117 0.85
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:52274 original size:23 final size:24
Alignment explanation
Indices: 52105--52278 Score: 102
Period size: 23 Copynumber: 7.3 Consensus size: 24
52095 ATTTATAAGT
* *
52105 TGGTGATAATATA-GGCG-TGATA
1 TGGTGATGATATAGGGTGATGATA
*
52127 TGGTGATGGA-ATATGGTGATGATA
1 TGGTGAT-GATATAGGGTGATGATA
* *
52151 TAGGCG-TGATA-ATGGTGATGGACTA
1 T-GGTGATGATATAGGGTGAT-GA-TA
52176 TGGTGATGATATAGGCGTGAT-A-A
1 TGGTGATGATATAGG-GTGATGATA
*
52199 TGGTGATGGA-ATATGGTGATGATA
1 TGGTGAT-GATATAGGGTGATGATA
* *
52223 TAGGCG-TGATA-ATGGTGATGGACTA
1 T-GGTGATGATATAGGGTGAT-GA-TA
52248 TGGTGATGATATAGGCGTGAT-A-A
1 TGGTGATGATATAGG-GTGATGATA
52271 TGGTGATG
1 TGGTGATG
52279 GACAGATTGT
Statistics
Matches: 123, Mismatches: 9, Indels: 39
0.72 0.05 0.23
Matches are distributed among these distances:
22 15 0.12
23 46 0.37
24 24 0.20
25 24 0.20
26 4 0.03
27 10 0.08
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (24 bp):
TGGTGATGATATAGGGTGATGATA
Found at i:52666 original size:19 final size:20
Alignment explanation
Indices: 52619--52666 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
52609 GAAACCCCTT
**
52619 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
52639 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
52658 TGAAGATAC
1 TGAAAATAC
52667 GTGCTCTTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:57240 original size:16 final size:16
Alignment explanation
Indices: 57209--57255 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
57199 TGGTAATGAA
57209 ATAAGAAAAGATGAAA-G
1 ATAA-AAAA-ATGAAATG
*
57226 AATAAAGAAATGAAATG
1 -ATAAAAAAATGAAATG
57243 ATAAAAAAATGAA
1 ATAAAAAAATGAA
57256 GATAACTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 18 0.69
17 4 0.15
18 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (16 bp):
ATAAAAAAATGAAATG
Found at i:57901 original size:13 final size:11
Alignment explanation
Indices: 57881--58037 Score: 97
Period size: 11 Copynumber: 13.2 Consensus size: 11
57871 AATATAGGCG
57881 TGATATGGTGA
1 TGATATGGTGA
57892 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
57905 TGATATAGG-CA
1 TGATAT-GGTGA
57916 TGATAATGGTGA
1 TGAT-ATGGTGA
*
57928 TGGACTATGGCGA
1 T-GA-TATGGTGA
*
57941 TGATATAGGCG-
1 TGATAT-GGTGA
57952 TGATAATGGTGA
1 TGAT-ATGGTGA
57964 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
57977 TGATATAGGCG-
1 TGATAT-GGTGA
57988 TGATAATGGTGA
1 TGAT-ATGGTGA
58000 TGGACTATGGTGA
1 T-GA-TATGGTGA
*
58013 TGATATAGGCG-
1 TGATAT-GGTGA
58024 TGATAATGGTGA
1 TGAT-ATGGTGA
58036 TG
1 TG
58038 GACAGATTGT
Statistics
Matches: 118, Mismatches: 8, Indels: 39
0.72 0.05 0.24
Matches are distributed among these distances:
11 43 0.36
12 33 0.28
13 38 0.32
14 4 0.03
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:57937 original size:36 final size:36
Alignment explanation
Indices: 57864--58040 Score: 302
Period size: 36 Copynumber: 4.9 Consensus size: 36
57854 ATTTATAAGT
* *
57864 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
57899 TGGTGATGATATAGGCATGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
* *
57935 TGGCGATGATATAGGCGTGATAATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
57971 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
58007 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
58041 AGATTGTATC
Statistics
Matches: 133, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
35 19 0.14
36 114 0.86
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:58033 original size:23 final size:24
Alignment explanation
Indices: 57864--58037 Score: 93
Period size: 23 Copynumber: 7.3 Consensus size: 24
57854 ATTTATAAGT
* *
57864 TGGTGATAATATA-GGCG-TGATA
1 TGGTGATGATATAGGGTGATGATA
*
57886 TGGTGATGGA-ATATGGTGATGATA
1 TGGTGAT-GATATAGGGTGATGATA
* *
57910 TAGG-CATGATA-ATGGTGATGGACTA
1 T-GGTGATGATATAGGGTGAT-GA-TA
*
57935 TGGCGATGATATAGGCGTGAT-A-A
1 TGGTGATGATATAGG-GTGATGATA
*
57958 TGGTGATGGA-ATATGGTGATGATA
1 TGGTGAT-GATATAGGGTGATGATA
* *
57982 TAGGCG-TGATA-ATGGTGATGGACTA
1 T-GGTGATGATATAGGGTGAT-GA-TA
58007 TGGTGATGATATAGGCGTGAT-A-A
1 TGGTGATGATATAGG-GTGATGATA
58030 TGGTGATG
1 TGGTGATG
58038 GACAGATTGT
Statistics
Matches: 122, Mismatches: 10, Indels: 39
0.71 0.06 0.23
Matches are distributed among these distances:
22 15 0.12
23 45 0.37
24 24 0.20
25 24 0.20
26 4 0.03
27 10 0.08
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (24 bp):
TGGTGATGATATAGGGTGATGATA
Found at i:58425 original size:19 final size:20
Alignment explanation
Indices: 58378--58428 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
58368 GAAACCCCTT
**
58378 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
58398 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
58417 TGAAGATACATG
1 TGAAAATACATG
58429 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:62759 original size:18 final size:18
Alignment explanation
Indices: 62736--62778 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
62726 CCTTATTAAG
62736 GATGAAGGATAATTCAAA
1 GATGAAGGATAATTCAAA
62754 GATGAAGGATAATTCAAA
1 GATGAAGGATAATTCAAA
62772 GATGAAG
1 GATGAAG
62779 AAATGGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.49, C:0.05, G:0.26, T:0.21
Consensus pattern (18 bp):
GATGAAGGATAATTCAAA
Found at i:62834 original size:13 final size:12
Alignment explanation
Indices: 62815--62902 Score: 62
Period size: 11 Copynumber: 7.3 Consensus size: 12
62805 ATATAGGCGT
62815 GATATGGTGATG
1 GATATGGTGATG
62827 GAATATGGTGAT-
1 G-ATATGGTGATG
*
62839 GATATAGGCG-T-
1 GATAT-GGTGATG
62850 GATATTGGTGATG
1 GATA-TGGTGATG
62863 GACTATGGTGAT-
1 GA-TATGGTGATG
*
62875 GATATAGGCG-T-
1 GATAT-GGTGATG
62886 GATAATGGTGATG
1 GAT-ATGGTGATG
62899 GATA
1 GATA
62903 AAATGTATCT
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
11 22 0.35
12 16 0.26
13 22 0.35
14 2 0.03
ACGTcount: A:0.28, C:0.03, G:0.36, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:62870 original size:36 final size:35
Alignment explanation
Indices: 62797--62900 Score: 172
Period size: 36 Copynumber: 2.9 Consensus size: 35
62787 ATTTATAAGT
*
62797 TGGTGATAATATAGGCGTGATATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATATGGTGATGGAATA
*
62832 TGGTGATGATATAGGCGTGATATTGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATA-TGGTGATGGAATA
62868 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATGATATAGGCGTGAT-ATGGTGATGGA
62901 TAAAATGTAT
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
35 21 0.32
36 43 0.66
37 1 0.02
ACGTcount: A:0.28, C:0.04, G:0.37, T:0.32
Consensus pattern (35 bp):
TGGTGATGATATAGGCGTGATATGGTGATGGAATA
Found at i:66257 original size:18 final size:20
Alignment explanation
Indices: 66225--66263 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
66215 GGATAATAAT
66225 ATAAGTAATGAAAATAAATA
1 ATAAGTAATGAAAATAAATA
66245 ATAAG-AATG-AAATAAATA
1 ATAAGTAATGAAAATAAATA
66263 A
1 A
66264 ATAAAAAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.53
19 4 0.21
20 5 0.26
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAAATAAATA
Found at i:66266 original size:19 final size:21
Alignment explanation
Indices: 66219--66267 Score: 68
Period size: 19 Copynumber: 2.4 Consensus size: 21
66209 AATAAAGGAT
66219 AATAATATAAGTAATGAAAATA
1 AATAA-ATAAGTAATGAAAATA
66241 AAT-AATAAG-AATG-AAATA
1 AATAAATAAGTAATGAAAATA
66259 AATAAATAA
1 AATAAATAA
66268 AAAGAGAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 8 0.31
19 9 0.35
20 5 0.19
21 1 0.04
22 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (21 bp):
AATAAATAAGTAATGAAAATA
Found at i:71524 original size:18 final size:16
Alignment explanation
Indices: 71486--71528 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 16
71476 CTTTTTGAAC
71486 TTCTCTT-TTTCTTTT
1 TTCTCTTCTTTCTTTT
71501 TT-TCTTCTTTCTGATTT
1 TTCTCTTCTTTCT--TTT
71518 TTCTCTTCTTT
1 TTCTCTTCTTT
71529 TTGCACTCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.17
15 7 0.29
17 5 0.21
18 8 0.33
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.74
Consensus pattern (16 bp):
TTCTCTTCTTTCTTTT
Found at i:75445 original size:18 final size:18
Alignment explanation
Indices: 75422--75466 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
75412 CCTTGTTGAG
*
75422 GATGAAGGATAATTCAAA
1 GATGAAGAATAATTCAAA
75440 GATGAAGAATAATTCAAA
1 GATGAAGAATAATTCAAA
75458 GATGAAGAA
1 GATGAAGAA
75467 ATGGAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.53, C:0.04, G:0.22, T:0.20
Consensus pattern (18 bp):
GATGAAGAATAATTCAAA
Found at i:75520 original size:13 final size:12
Alignment explanation
Indices: 75501--75565 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
75491 ATATAGGCGT
75501 GATATGGTGATG
1 GATATGGTGATG
75513 GAATATGGTGAT-
1 G-ATATGGTGATG
*
75525 GATATAGGCG-T-
1 GATAT-GGTGATG
75536 GATAATGGTGATG
1 GAT-ATGGTGATG
75549 GACTATGGTGAT-
1 GA-TATGGTGATG
75561 GATAT
1 GATAT
75566 AGGCGTTATA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 10 0.22
13 20 0.44
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:75556 original size:36 final size:36
Alignment explanation
Indices: 75483--75586 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
75473 ATTTATAAGT
* *
75483 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
75518 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
75554 TGGTGATGATATAGGCGTTATAAT-GTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
75587 AGATTATCTT
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 29 0.45
36 36 0.55
ACGTcount: A:0.29, C:0.05, G:0.35, T:0.32
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Done.