Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000804.1 Hibiscus syriacus cultivar Beakdansim tig00001561_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: 85694
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:6192 original size:16 final size:16
Alignment explanation
Indices: 6173--6205 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
6163 TTAAAAATAA
6173 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
6189 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
6205 A
1 A
6206 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:6284 original size:10 final size:10
Alignment explanation
Indices: 6269--6342 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
6259 CATTTAATAA
6269 ATAAACGAAC
1 ATAAACGAAC
6279 ATAAACGAAC
1 ATAAACGAAC
6289 AT----GAAC
1 ATAAACGAAC
6295 ATAAACGAAC
1 ATAAACGAAC
** *
6305 A-GGAC-ATAA
1 ATAAACGA-AC
6314 ATGAACACGAAC
1 AT-AA-ACGAAC
6326 ATAAACGAAC
1 ATAAACGAAC
6336 ATAAACG
1 ATAAACG
6343 TTGGAGACCC
Statistics
Matches: 49, Mismatches: 6, Indels: 18
0.67 0.08 0.25
Matches are distributed among these distances:
6 6 0.12
8 1 0.02
9 4 0.08
10 30 0.61
11 2 0.04
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.19, G:0.14, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:6296 original size:16 final size:16
Alignment explanation
Indices: 6275--6337 Score: 92
Period size: 16 Copynumber: 4.0 Consensus size: 16
6265 ATAAATAAAC
6275 GAACATAAACGAACAT
1 GAACATAAACGAACAT
6291 GAACATAAACGAACA-
1 GAACATAAACGAACAT
* * *
6306 GGACATAAATGAACAC
1 GAACATAAACGAACAT
6322 GAACATAAACGAACAT
1 GAACATAAACGAACAT
6338 AAACGTTGGA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
15 13 0.32
16 28 0.68
ACGTcount: A:0.56, C:0.19, G:0.14, T:0.11
Consensus pattern (16 bp):
GAACATAAACGAACAT
Found at i:6312 original size:31 final size:31
Alignment explanation
Indices: 6277--6336 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
6267 AAATAAACGA
*
6277 ACATAAACGAACATGAACATAAACGAACAGG
1 ACATAAACGAACACGAACATAAACGAACAGG
*
6308 ACATAAATGAACACGAACATAAACGAACA
1 ACATAAACGAACACGAACATAAACGAACA
6337 TAAACGTTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.57, C:0.20, G:0.13, T:0.10
Consensus pattern (31 bp):
ACATAAACGAACACGAACATAAACGAACAGG
Found at i:7098 original size:14 final size:14
Alignment explanation
Indices: 7081--7136 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
7071 AATGAACATA
*
7081 AACGAACATAATCG
1 AACGAACATAACCG
7095 AACGAACAT-A---
1 AACGAACATAACCG
*
7105 AACGAACATAACCA
1 AACGAACATAACCG
7119 AACGAACATAACCG
1 AACGAACATAACCG
7133 AACG
1 AACG
7137 TTCACGAACG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:7101 original size:24 final size:24
Alignment explanation
Indices: 7061--7135 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
7051 GATTGTGTTA
*
7061 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
7085 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
* * *
7109 AACATAACCAAACGAACATAACCG
1 AACATAATCGAACGAACATAAACG
7133 AAC
1 AAC
7136 GTTCACGAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 3 0.07
24 43 0.93
ACGTcount: A:0.56, C:0.21, G:0.11, T:0.12
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:30125 original size:5 final size:5
Alignment explanation
Indices: 30115--30140 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
30105 CATAGAATAT
30115 TTTAA TTTAA TTTAA TTTAA TTTAA T
1 TTTAA TTTAA TTTAA TTTAA TTTAA T
30141 CATAATTGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTAA
Found at i:41609 original size:18 final size:18
Alignment explanation
Indices: 41581--41618 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
41571 TACATATACA
41581 ATTTTAAAAATT-ATTTT
1 ATTTTAAAAATTAATTTT
41598 ATTTTAAAAAATTAATTTT
1 ATTTT-AAAAATTAATTTT
41617 AT
1 AT
41619 AAATAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.26
18 7 0.37
19 7 0.37
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTTAAAAATTAATTTT
Found at i:42344 original size:5 final size:5
Alignment explanation
Indices: 42336--42414 Score: 67
Period size: 5 Copynumber: 16.2 Consensus size: 5
42326 TTATAAATTC
* * * *
42336 TATAT TATAA TATAT TATAATT TATAT TATA- TAAAT TATAC TATA- TAAAT
1 TATAT TATAT TATAT TAT-A-T TATAT TATAT TATAT TATAT TATAT TATAT
*
42386 TATAT TATA- TA-AT TATAT TATAT AATAT T
1 TATAT TATAT TATAT TATAT TATAT TATAT T
42415 TGTCCAAGAA
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
3 1 0.02
4 10 0.17
5 42 0.71
6 2 0.03
7 4 0.07
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (5 bp):
TATAT
Found at i:42345 original size:14 final size:12
Alignment explanation
Indices: 42326--42407 Score: 78
Period size: 14 Copynumber: 6.4 Consensus size: 12
42316 TTTTTATTTT
42326 TTATAAATTCTATA
1 TTATAAA-T-TATA
42340 TTAT-AA-TATA
1 TTATAAATTATA
*
42350 TTATAATTTATA
1 TTATAAATTATA
42362 TTATATAAATTATA
1 -T-TATAAATTATA
42376 CTATATAAATTATA
1 -T-TATAAATTATA
42390 TTATATAATTATA
1 TTATA-AATTATA
42403 TTATA
1 TTATA
42408 TAATATTTGT
Statistics
Matches: 60, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
10 8 0.13
11 1 0.02
12 8 0.13
13 16 0.27
14 27 0.45
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (12 bp):
TTATAAATTATA
Found at i:42353 original size:24 final size:22
Alignment explanation
Indices: 42326--42375 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 22
42316 TTTTTATTTT
*
42326 TTATAAATTCTATATTATAATATA
1 TTATAAATT-TATATTAT-ATAAA
42350 TTAT-AATTTATATTATATAAA
1 TTATAAATTTATATTATATAAA
42371 TTATA
1 TTATA
42376 CTATATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 8 0.33
22 8 0.33
23 4 0.17
24 4 0.17
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATAAATTTATATTATATAAA
Found at i:42391 original size:28 final size:27
Alignment explanation
Indices: 42327--42410 Score: 95
Period size: 28 Copynumber: 3.2 Consensus size: 27
42317 TTTTATTTTT
*
42327 TATAAATTCTA-TATTATAA-TATA-T-
1 TATAAATTATATTA-TATAATTATACTA
*
42351 TATAATTTATATTATATAAATTATACTA
1 TATAAATTATATTATAT-AATTATACTA
*
42379 TATAAATTATATTATATAATTATATTA
1 TATAAATTATATTATATAATTATACTA
42406 TATAA
1 TATAA
42411 TATTTGTCCA
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
24 12 0.24
25 4 0.08
26 4 0.08
27 15 0.29
28 16 0.31
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (27 bp):
TATAAATTATATTATATAATTATACTA
Found at i:46155 original size:24 final size:23
Alignment explanation
Indices: 46127--46193 Score: 68
Period size: 25 Copynumber: 2.9 Consensus size: 23
46117 ATATAATATA
46127 ATTTTATATATATTAACTTAAAAT
1 ATTTT-TATATATTAACTTAAAAT
46151 A-TTTT-TATATTAACTTATTAAAT
1 ATTTTTATATATTAACTTA--AAAT
*
46174 ATATTTTA-CTATTAACTTAA
1 AT-TTTTATATATTAACTTAA
46194 TTTAAAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
21 12 0.32
22 1 0.03
23 9 0.24
24 1 0.03
25 14 0.38
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTTTTATATATTAACTTAAAAT
Found at i:46159 original size:21 final size:22
Alignment explanation
Indices: 46135--46193 Score: 84
Period size: 21 Copynumber: 2.6 Consensus size: 22
46125 TAATTTTATA
46135 TATATTAACTTAAAATAT-TTT
1 TATATTAACTTAAAATATATTT
46156 TATATTAACTTATTAAATATATTT
1 TATATTAACTTA--AAATATATTT
46180 TACTATTAACTTAA
1 TA-TATTAACTTAA
46194 TTTAAAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
21 12 0.35
23 7 0.21
24 5 0.15
25 10 0.29
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (22 bp):
TATATTAACTTAAAATATATTT
Found at i:46177 original size:25 final size:26
Alignment explanation
Indices: 46139--46213 Score: 84
Period size: 25 Copynumber: 2.9 Consensus size: 26
46129 TTTATATATA
*
46139 TTAACTTAAAATATTTTTATATTAAC
1 TTAATTTAAAATATTTTTATATTAAC
46165 TT-A-TT-AAATATATTTTACTATTAAC
1 TTAATTTAAAATAT-TTTTA-TATTAAC
*
46190 TTAATTTAAAAATATTTTTTTATT
1 TTAATTT-AAAATATTTTTATATT
46214 TTCATTTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
23 6 0.14
24 7 0.17
25 10 0.24
26 3 0.07
27 6 0.14
28 4 0.10
29 6 0.14
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (26 bp):
TTAATTTAAAATATTTTTATATTAAC
Found at i:46205 original size:27 final size:24
Alignment explanation
Indices: 46135--46207 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 24
46125 TAATTTTATA
*
46135 TATATTAACTTA--AAATAT-TTT
1 TATATTAACTTATTAAAAATATTT
*
46156 TATATTAACTTATTAAATATATTT
1 TATATTAACTTATTAAAAATATTT
46180 TACTATTAACTTAATTTAAAAATATTT
1 TA-TATTAACTT-A-TTAAAAATATTT
46207 T
1 T
46208 TTTATTTTCA
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
21 12 0.27
23 6 0.13
24 5 0.11
25 9 0.20
26 1 0.02
27 12 0.27
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.52
Consensus pattern (24 bp):
TATATTAACTTATTAAAAATATTT
Found at i:46225 original size:24 final size:25
Alignment explanation
Indices: 46190--46246 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 25
46180 TACTATTAAC
**
46190 TTAATTTAAAAATAT-TTTTTTATT
1 TTAATTTAAAAATATATAATTTATT
*
46214 TTCATTTAAAAATATATAATTTATT
1 TTAATTTAAAAATATATAATTTATT
46239 TTAATTTA
1 TTAATTTA
46247 TTAAAAGTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 14 0.50
25 14 0.50
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
TTAATTTAAAAATATATAATTTATT
Found at i:46621 original size:10 final size:10
Alignment explanation
Indices: 46601--46632 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
46591 TTAAATAGAT
46601 ATTATTTTAAA
1 ATTA-TTTAAA
46612 ATTATTTAAA
1 ATTATTTAAA
46622 ATTATTTAAA
1 ATTATTTAAA
46632 A
1 A
46633 GAATTCTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 17 0.81
11 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
ATTATTTAAA
Found at i:47168 original size:13 final size:13
Alignment explanation
Indices: 47150--47175 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
47140 CGGGTCGGGT
47150 TGATCAAAATAGA
1 TGATCAAAATAGA
47163 TGATCAAAATAGA
1 TGATCAAAATAGA
47176 AATAAGACAT
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:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (13 bp):
TGATCAAAATAGA
Found at i:49826 original size:27 final size:26
Alignment explanation
Indices: 49761--49850 Score: 78
Period size: 26 Copynumber: 3.4 Consensus size: 26
49751 ATAAATTCAT
* *
49761 AATATTTTATATATATTAACTTTAAGA
1 AATATTTTAT-TATAATAAATTTAAGA
*
49788 AATATTTT-TTATAATAAATTATTAGA
1 AATATTTTATTATAATAAATT-TAAGA
* *
49814 TATATTTTATTATTAACTTAA-TTAA-A
1 AATATTTTATTA-TAA-TAAATTTAAGA
49840 AATATTTTATT
1 AATATTTTATT
49851 TTATTTTAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
25 9 0.17
26 23 0.44
27 13 0.25
28 4 0.08
29 3 0.06
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
AATATTTTATTATAATAAATTTAAGA
Found at i:49864 original size:26 final size:26
Alignment explanation
Indices: 49815--49886 Score: 85
Period size: 25 Copynumber: 2.8 Consensus size: 26
49805 ATTATTAGAT
**
49815 ATATTTTATTATTAACTTAA-TTAAAA
1 ATATTTTATT-TTATTTTAATTTAAAA
49841 ATATTTTATTTTATTTTAATTTAAAA
1 ATATTTTATTTTATTTTAATTTAAAA
* *
49867 ATA-TATATTTTATTCTAATT
1 ATATTTTATTTTATTTTAATT
49887 GGTGGAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
25 22 0.54
26 19 0.46
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (26 bp):
ATATTTTATTTTATTTTAATTTAAAA
Found at i:49984 original size:28 final size:28
Alignment explanation
Indices: 49944--50012 Score: 120
Period size: 28 Copynumber: 2.5 Consensus size: 28
49934 TAACCGAATG
*
49944 GTGACACATGACACGCCACGTGGTACCA
1 GTGACACATGACACGCCACGTGGTACAA
49972 GTGACACATGACACGCCACGTGGTACAA
1 GTGACACATGACACGCCACGTGGTACAA
*
50000 ATGACACATGACA
1 GTGACACATGACA
50013 TCATTTTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.33, C:0.29, G:0.23, T:0.14
Consensus pattern (28 bp):
GTGACACATGACACGCCACGTGGTACAA
Found at i:50361 original size:16 final size:17
Alignment explanation
Indices: 50342--50381 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
50332 AGGGAAAATA
50342 TGAAAAATCAAA-AAGT
1 TGAAAAATCAAATAAGT
*
50358 TGAAAAGTCAAATAAGT
1 TGAAAAATCAAATAAGT
*
50375 GGAAAAA
1 TGAAAAA
50382 ATTAATTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.60, C:0.05, G:0.17, T:0.17
Consensus pattern (17 bp):
TGAAAAATCAAATAAGT
Found at i:52260 original size:37 final size:37
Alignment explanation
Indices: 52210--52284 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
52200 GAATGATGTA
52210 AAAGGTGTCAGTCTCACCTCTGACATTAAACAGTCAT
1 AAAGGTGTCAGTCTCACCTCTGACATTAAACAGTCAT
52247 AAAGGTGTCAGTCTCACCTCTGACATTAAACAGTCAT
1 AAAGGTGTCAGTCTCACCTCTGACATTAAACAGTCAT
52284 A
1 A
52285 CTCTCGATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (37 bp):
AAAGGTGTCAGTCTCACCTCTGACATTAAACAGTCAT
Found at i:53359 original size:37 final size:38
Alignment explanation
Indices: 53317--53400 Score: 136
Period size: 38 Copynumber: 2.2 Consensus size: 38
53307 TTTATTTTGT
53317 TCGGGTCGGG-TTTTTTAAGTGTGATATTCAGGTC-GAG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCAG-G
*
53354 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAGG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCAGG
53392 TCGGGTCGG
1 TCGGGTCGG
53401 ATTTGGGTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
37 10 0.23
38 33 0.75
39 1 0.02
ACGTcount: A:0.13, C:0.12, G:0.38, T:0.37
Consensus pattern (38 bp):
TCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCAGG
Found at i:53522 original size:21 final size:18
Alignment explanation
Indices: 53498--53545 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 18
53488 TCTATATATA
53498 ATTTTTTTCAATTAAATCAAT
1 ATTTTTTTCAA-TAAA--AAT
*
53519 ATTTTTATTGAATAAAAAT
1 ATTTTT-TTCAATAAAAAT
53538 ATTTTTTT
1 ATTTTTTT
53546 TATTATTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.08
19 9 0.36
21 10 0.40
22 4 0.16
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (18 bp):
ATTTTTTTCAATAAAAAT
Found at i:53898 original size:16 final size:18
Alignment explanation
Indices: 53877--53922 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
53867 TATGAAATTG
53877 GATTCCAATTCC-T-ACA
1 GATTCCAATTCCTTCACA
53893 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
*
53911 GATTCTAATTCC
1 GATTCCAATTCC
53923 CTCATAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 12 0.44
17 1 0.04
18 14 0.52
ACGTcount: A:0.28, C:0.30, G:0.07, T:0.35
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:56346 original size:16 final size:16
Alignment explanation
Indices: 56312--56374 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
56302 TTTCATATCA
* *
56312 GGTTAAATTTGATTCG
1 GGTTAAATTCGGTTCG
*
56328 GGTTAAATTCGGTTTG
1 GGTTAAATTCGGTTCG
**
56344 GGTTACTTTCGGTTCG
1 GGTTAAATTCGGTTCG
**
56360 GGTTACTTTCGGTTC
1 GGTTAAATTCGGTTC
56375 AGATTACTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.14, C:0.13, G:0.29, T:0.44
Consensus pattern (16 bp):
GGTTAAATTCGGTTCG
Found at i:56360 original size:32 final size:32
Alignment explanation
Indices: 56324--56407 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 32
56314 TTAAATTTGA
* ** *
56324 TTCGGGTTAAATTCGGTTTGGGTTACTTTCGG
1 TTCGGGTTAATTTCGGTTCAGATTACTTTCGG
* *
56356 TTCGGGTTACTTTCGGTTCAGATTACTTTTGG
1 TTCGGGTTAATTTCGGTTCAGATTACTTTCGG
* *
56388 TTCAGGTTAATTTCGATTCA
1 TTCGGGTTAATTTCGGTTCA
56408 TGTTGCTTTT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.15, C:0.14, G:0.25, T:0.45
Consensus pattern (32 bp):
TTCGGGTTAATTTCGGTTCAGATTACTTTCGG
Found at i:56381 original size:16 final size:16
Alignment explanation
Indices: 56344--56407 Score: 83
Period size: 16 Copynumber: 4.0 Consensus size: 16
56334 ATTCGGTTTG
*
56344 GGTTACTTTCGGTTCG
1 GGTTACTTTCGGTTCA
56360 GGTTACTTTCGGTTCA
1 GGTTACTTTCGGTTCA
* *
56376 GATTACTTTTGGTTCA
1 GGTTACTTTCGGTTCA
* *
56392 GGTTAATTTCGATTCA
1 GGTTACTTTCGGTTCA
56408 TGTTGCTTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.45
Consensus pattern (16 bp):
GGTTACTTTCGGTTCA
Found at i:56417 original size:32 final size:32
Alignment explanation
Indices: 56346--56420 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
56336 TCGGTTTGGG
* * * *
56346 TTACTTTCGGTTCGGGTTACTTTCGGTTCAGA
1 TTACTTTTGGTTCAGGTTAATTTCGATTCAGA
56378 TTACTTTTGGTTCAGGTTAATTTCGATTCATG-
1 TTACTTTTGGTTCAGGTTAATTTCGATTCA-GA
*
56410 TTGCTTTTGGT
1 TTACTTTTGGT
56421 GGTTGTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 36 0.97
33 1 0.03
ACGTcount: A:0.13, C:0.15, G:0.23, T:0.49
Consensus pattern (32 bp):
TTACTTTTGGTTCAGGTTAATTTCGATTCAGA
Found at i:56478 original size:15 final size:15
Alignment explanation
Indices: 56458--56491 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
56448 ATACTAACTT
*
56458 ATAATTATAAATTTG
1 ATAATTATAAATTTA
56473 ATAATTATAAATTTA
1 ATAATTATAAATTTA
56488 ATAA
1 ATAA
56492 GAAATATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (15 bp):
ATAATTATAAATTTA
Found at i:60702 original size:16 final size:17
Alignment explanation
Indices: 60683--60719 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
60673 TGTTATTAAA
60683 CTGATA-TGATATTTAC
1 CTGATATTGATATTTAC
*
60699 CTGA-ATTGATATTTAT
1 CTGATATTGATATTTAC
60715 CTGAT
1 CTGAT
60720 TTATAAGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 1 0.06
16 17 0.94
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (17 bp):
CTGATATTGATATTTAC
Found at i:61010 original size:23 final size:24
Alignment explanation
Indices: 60980--61029 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
60970 TTTTTATTTA
60980 ATAATTAA-TTAATAA-TTT-AAAT
1 ATAATTAACTTAA-AATTTTAAAAT
61002 ATAATTTAACTTAAAATTTTAAAAT
1 ATAA-TTAACTTAAAATTTTAAAAT
61027 ATA
1 ATA
61030 TAAATGATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.17
23 6 0.25
24 7 0.29
25 7 0.29
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
ATAATTAACTTAAAATTTTAAAAT
Found at i:61410 original size:2 final size:2
Alignment explanation
Indices: 61403--61564 Score: 71
Period size: 2 Copynumber: 77.5 Consensus size: 2
61393 ATGTTTAATG
* * *
61403 AT AT AT AT AT AT AT AT AT AT AGT TT AT AT AGT TT AT AT AT AT CT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT
* * * *
61447 AGT TT AT AT AT TT AT AT -T AT AG AGT TT AT AT ACT CAT ACT -T AT
1 A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A-T -AT A-T AT AT
* * * * *
61490 AGT CT AT A- AT AT AA AT AT AT AA ACT AG AT AT AT AT AA ACT AT
1 A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT
* *
61532 AT AA ACT AT AT GT AT AT AT AT AT AT AT AT -T AT A
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A
61565 GTTCTTCTAA
Statistics
Matches: 117, Mismatches: 28, Indels: 30
0.67 0.16 0.17
Matches are distributed among these distances:
1 4 0.03
2 102 0.87
3 10 0.09
4 1 0.01
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:61432 original size:9 final size:9
Alignment explanation
Indices: 61418--61463 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 9
61408 TATATATATA
61418 TATATAGTT
1 TATATAGTT
61427 TATATAGTT
1 TATATAGTT
61436 TATATA---
1 TATATAGTT
*
61442 TATCTAGTT
1 TATATAGTT
61451 TATATA-TT
1 TATATAGTT
61459 TATAT
1 TATAT
61464 TATAGAGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
6 5 0.16
8 7 0.22
9 20 0.62
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.57
Consensus pattern (9 bp):
TATATAGTT
Found at i:61441 original size:24 final size:23
Alignment explanation
Indices: 61404--61478 Score: 107
Period size: 24 Copynumber: 3.3 Consensus size: 23
61394 TGTTTAATGA
*
61404 TATATATATATATATATATAGTT
1 TATATATTTATATATATATAGTT
*
61427 TATATAGTTTATATATATCTAGTT
1 TATATA-TTTATATATATATAGTT
*
61451 TATATATTTATAT-TATAGAGTT
1 TATATATTTATATATATATAGTT
61473 TATATA
1 TATATA
61479 CTCATACTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
22 13 0.28
23 13 0.28
24 21 0.45
ACGTcount: A:0.39, C:0.01, G:0.07, T:0.53
Consensus pattern (23 bp):
TATATATTTATATATATATAGTT
Found at i:61521 original size:24 final size:24
Alignment explanation
Indices: 61494--61559 Score: 80
Period size: 24 Copynumber: 2.7 Consensus size: 24
61484 ACTTATAGTC
61494 TATAATATAAATATATAAACTAGA
1 TATAATATAAATATATAAACTAGA
*
61518 TAT-ATATAAACTATATAAACTATA
1 TATAATATAAA-TATATAAACTAGA
* *
61542 TGTATATATATATATATA
1 TATA-ATATAAATATATA
61560 TTATAGTTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 7 0.19
24 17 0.47
25 6 0.17
26 6 0.17
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (24 bp):
TATAATATAAATATATAAACTAGA
Found at i:61534 original size:9 final size:9
Alignment explanation
Indices: 61498--61542 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
61488 ATAGTCTATA
61498 ATATAAA-T
1 ATATAAACT
61506 ATATAAACT
1 ATATAAACT
*
61515 AGAT--A-T
1 ATATAAACT
61521 ATATAAACT
1 ATATAAACT
61530 ATATAAACT
1 ATATAAACT
61539 ATAT
1 ATAT
61543 GTATATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
6 4 0.13
7 1 0.03
8 8 0.26
9 18 0.58
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (9 bp):
ATATAAACT
Found at i:70955 original size:23 final size:23
Alignment explanation
Indices: 70925--71007 Score: 121
Period size: 23 Copynumber: 3.6 Consensus size: 23
70915 TCGTATAAAG
*
70925 GCACCGAAGTGCCACATAGAATT
1 GCACCGAAGTGCCACGTAGAATT
*
70948 GCACCGAAGTGCCTCGTAGAATT
1 GCACCGAAGTGCCACGTAGAATT
* *
70971 ACACCGAAGTGCCTCGTAGAATT
1 GCACCGAAGTGCCACGTAGAATT
*
70994 GCACCGTAGTGCCA
1 GCACCGAAGTGCCA
71008 TATAAGCTTG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.29, C:0.28, G:0.24, T:0.19
Consensus pattern (23 bp):
GCACCGAAGTGCCACGTAGAATT
Found at i:72672 original size:13 final size:14
Alignment explanation
Indices: 72642--72673 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
72632 GATATGTATC
72642 TTTTATTTTATTAA
1 TTTTATTTTATTAA
72656 -TTTATTTT-TTAA
1 TTTTATTTTATTAA
72668 TTTTAT
1 TTTTAT
72674 AAAAGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTATTTTATTAA
Found at i:72720 original size:15 final size:15
Alignment explanation
Indices: 72682--72720 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
72672 ATAAAAGAAA
*
72682 AAATATAAATTTTAT
1 AAATAAAAATTTTAT
* *
72697 GAATTAAAATTTTAT
1 AAATAAAAATTTTAT
72712 AAATAAAAA
1 AAATAAAAA
72721 ATATAAATTA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
AAATAAAAATTTTAT
Found at i:75906 original size:20 final size:20
Alignment explanation
Indices: 75881--75937 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
75871 TAAAAAAATG
*
75881 TGTAGTATCGATACTCTAGT
1 TGTAGTATCGATACCCTAGT
75901 TGTAGTATCGATACCCTAG-
1 TGTAGTATCGATACCCTAGT
*
75920 GGTCAAGTATCGATACCC
1 TGT--AGTATCGATACCC
75938 CTATGAGTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 2 0.06
20 18 0.55
21 13 0.39
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (20 bp):
TGTAGTATCGATACCCTAGT
Found at i:76636 original size:17 final size:18
Alignment explanation
Indices: 76616--76653 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
76606 TTTTATTCTC
76616 TTCATATTC-TCATTCCT
1 TTCATATTCTTCATTCCT
* *
76633 TTCATTTTCTTCATTCTT
1 TTCATATTCTTCATTCCT
76651 TTC
1 TTC
76654 CATTCTATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.61
Consensus pattern (18 bp):
TTCATATTCTTCATTCCT
Found at i:84362 original size:16 final size:17
Alignment explanation
Indices: 84343--84383 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
84333 TTTATAAAAT
84343 AATATTATAATT-TATA
1 AATATTATAATTCTATA
*
84359 AATATTAAAATTCTATA
1 AATATTATAATTCTATA
*
84376 ATTATTAT
1 AATATTAT
84384 TATAATCATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
AATATTATAATTCTATA
Done.