Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002918.1 Hibiscus syriacus cultivar Beakdansim tig00006032_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: 87305
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:5415 original size:207 final size:207
Alignment explanation
Indices: 5060--5473 Score: 765
Period size: 207 Copynumber: 2.0 Consensus size: 207
5050 ATATCATATT
* * **
5060 GAAGAATTGAAGGCACAATTGGCTAGGGAATTTGAAATGAAGGACTTGGGATCAGCAAACAAGAT
1 GAAGAATTGAAGGCACAACTGGCTAGGGAATTTGAAATGAAGGACGTGGGATCAAAAAACAAGAT
*
5125 TCTAGGGATACAAATTCACCGAGACAGAAGTAATAGGAAGATTTGGCTTTCACAAAAGAATTACT
66 TATAGGGATACAAATTCACCGAGACAGAAGTAATAGGAAGATTTGGCTTTCACAAAAGAATTACT
5190 TGAAGAAGATATTGTCACGATTTAGCATGCAAGATTATAAGCCAATTTCTACCCCTCTTCCTATT
131 TGAAGAAGATATTGTCACGATTTAGCATGCAAGATTATAAGCCAATTTCTACCCCTCTTCCTATT
5255 AACTTCAAATTA
196 AACTTCAAATTA
5267 GAAGAATTGAAGGCACAACTGGCTAGGGAATTTGAAATGAAGGACGTGGGATCAAAAAACAAGAT
1 GAAGAATTGAAGGCACAACTGGCTAGGGAATTTGAAATGAAGGACGTGGGATCAAAAAACAAGAT
5332 TATAGGGATACAAATTCACCGAGACAGAAGTAATAGGAAGATTTGGCTTTCACAAAAGAATTACT
66 TATAGGGATACAAATTCACCGAGACAGAAGTAATAGGAAGATTTGGCTTTCACAAAAGAATTACT
* *
5397 TGAAGAAGATCTTGTCACGATTTAGCATGCAAGATTGTAAGCCAATTTCTACCCCTCTTCCTATT
131 TGAAGAAGATATTGTCACGATTTAGCATGCAAGATTATAAGCCAATTTCTACCCCTCTTCCTATT
5462 AACTTCAAATTA
196 AACTTCAAATTA
5474 TCCTCCAGTA
Statistics
Matches: 200, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
207 200 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (207 bp):
GAAGAATTGAAGGCACAACTGGCTAGGGAATTTGAAATGAAGGACGTGGGATCAAAAAACAAGAT
TATAGGGATACAAATTCACCGAGACAGAAGTAATAGGAAGATTTGGCTTTCACAAAAGAATTACT
TGAAGAAGATATTGTCACGATTTAGCATGCAAGATTATAAGCCAATTTCTACCCCTCTTCCTATT
AACTTCAAATTA
Found at i:12228 original size:86 final size:85
Alignment explanation
Indices: 12087--12690 Score: 693
Period size: 85 Copynumber: 7.1 Consensus size: 85
12077 ACAAATGTCG
* * * *
12087 ATATCTATAGCGGCATTTTTGGAATAAACACCGCAATAGGTCGAGATTTATAGCGATATTTTTGG
1 ATATCTATAGCGGCATTTTTGGAACAAACACCGCAAAAGGTCGAGATCTATAGCGACATTTTTGG
12152 AACAAACGCCGCAGAAGGTC
66 AACAAACGCCGCAGAAGGTC
* * * * * *
12172 GATATATATAGCGGCGTTTTTGGAACAAATACTGCAATAGGTCGAGATCTATAGCGAAATTTTTG
1 -ATATCTATAGCGGCATTTTTGGAACAAACACCGCAAAAGGTCGAGATCTATAGCGACATTTTTG
*
12237 GAACAAAAGCCGCAGAAGGTC
65 GAACAAACGCCGCAGAAGGTC
* *
12258 TATATCTATAGCGGCATTTTTGGAACAAACATCGCAAAAGGTTGAGATCTATAGCGACATTTTTG
1 -ATATCTATAGCGGCATTTTTGGAACAAACACCGCAAAAGGTCGAGATCTATAGCGACATTTTTG
12323 GAACAAACGCCGCAGAAGGTC
65 GAACAAACGCCGCAGAAGGTC
* *
12344 ATATCTATAGCGGCATTTTTGGAACAAACATCGCAAAAGGTTGAGATCTATAGCGACATTTTTGG
1 ATATCTATAGCGGCATTTTTGGAACAAACACCGCAAAAGGTCGAGATCTATAGCGACATTTTTGG
12409 AACAAACGCCGCAGAAGGTC
66 AACAAACGCCGCAGAAGGTC
* * * * *
12429 ATATCTATAGCGGC-GTTTTGGAACAAACGCCGGAAAAGGTC-ATAACTATAGC-AGCATTTTTG
1 ATATCTATAGCGGCATTTTTGGAACAAACACCGCAAAAGGTCGAGATCTATAGCGA-CATTTTTG
* * **
12491 GAACAAATGCCGCAAAATATC
65 GAACAAACGCCGCAGAAGGTC
* * * * * **
12512 ATATCTATAGTGGCATTTTTGGAACAAACGCCACAAAAGGTC-ATAACTATAGCGGTATTTTTGG
1 ATATCTATAGCGGCATTTTTGGAACAAACACCGCAAAAGGTCGAGATCTATAGCGACATTTTTGG
* *
12576 AACAAACGCCGCAAAAGATC
66 AACAAACGCCGCAGAAGGTC
* * * * * * * *
12596 GAGATCTATAACAG-AGTTTTGGGAACAAACGCCGCAAAAGGT-TAGATCTATAGATG-CGTTTT
1 -ATATCTATAGCGGCA-TTTTTGGAACAAACACCGCAAAAGGTCGAGATCTATAG-CGACATTTT
* * *
12658 TGGAACAAACGTC-TAAAAGGTC
63 TGGAACAAACGCCGCAGAAGGTC
*
12680 AAATCTATAGC
1 ATATCTATAGC
12691 CGCTAATTAC
Statistics
Matches: 458, Mismatches: 53, Indels: 17
0.87 0.10 0.03
Matches are distributed among these distances:
82 1 0.00
83 56 0.12
84 91 0.20
85 156 0.34
86 154 0.34
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (85 bp):
ATATCTATAGCGGCATTTTTGGAACAAACACCGCAAAAGGTCGAGATCTATAGCGACATTTTTGG
AACAAACGCCGCAGAAGGTC
Found at i:12363 original size:42 final size:42
Alignment explanation
Indices: 12087--12690 Score: 620
Period size: 43 Copynumber: 14.3 Consensus size: 42
12077 ACAAATGTCG
* * *
12087 ATATCTATAGCGGCATTTTTGGAATAAACACCGCAATAGGTC
1 ATATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTC
* * ** *
12129 GAGATTTATAGCGATATTTTTGGAACAAACGCCGCAGAAGGTC
1 -ATATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTC
* * ** * *
12172 GATATATATAGCGGCGTTTTTGGAACAAATACTGCAATAGGTC
1 -ATATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTC
* ** * *
12215 GAGATCTATAGCGAAATTTTTGGAACAAAAGCCGCAGAAGGTC
1 -ATATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTC
** *
12258 TATATCTATAGCGGCATTTTTGGAACAAACATCGCAAAAGGTTG
1 -ATATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGG-TC
* * *
12302 AGATCTATAGCGACATTTTTGGAACAAACGCCGCAGAAGGTC
1 ATATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTC
** *
12344 ATATCTATAGCGGCATTTTTGGAACAAACATCGCAAAAGGTTG
1 ATATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGG-TC
* * *
12387 AGATCTATAGCGACATTTTTGGAACAAACGCCGCAGAAGGTC
1 ATATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTC
* *
12429 ATATCTATAGCGGC-GTTTTGGAACAAACGCCGGAAAAGGTC
1 ATATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTC
* * * **
12470 ATAACTATAGCAGCATTTTTGGAACAAATGCCGCAAAATATC
1 ATATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTC
* *
12512 ATATCTATAGTGGCATTTTTGGAACAAACGCCACAAAAGGTC
1 ATATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTC
* * *
12554 ATAACTATAGCGGTATTTTTGGAACAAACGCCGCAAAAGATC
1 ATATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTC
* * * * *
12596 GAGATCTATAACAG-AGTTTTGGGAACAAACGCCGCAAAAGGTT
1 -ATATCTATAGCGGCA-TTTTTGGAACAAACGCCGCAAAAGGTC
* ** * * *
12639 AGATCTATAGATGCGTTTTTGGAACAAACGTC-TAAAAGGTC
1 ATATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTC
*
12680 AAATCTATAGC
1 ATATCTATAGC
12691 CGCTAATTAC
Statistics
Matches: 459, Mismatches: 96, Indels: 14
0.81 0.17 0.02
Matches are distributed among these distances:
41 52 0.11
42 169 0.37
43 237 0.52
44 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (42 bp):
ATATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTC
Found at i:16462 original size:2 final size:2
Alignment explanation
Indices: 16455--16520 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
16445 CTTAAAAATA
16455 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16497 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
16521 GTATTTAGAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18194 original size:24 final size:25
Alignment explanation
Indices: 18166--18213 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
18156 TATTATTATT
18166 TTAATAAAAATAT-ATTTATTTAAA
1 TTAATAAAAATATAATTTATTTAAA
*
18190 TTAATAAAAATATAATTTTTTTAA
1 TTAATAAAAATATAATTTATTTAA
18214 CGAATAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TTAATAAAAATATAATTTATTTAAA
Found at i:18219 original size:24 final size:24
Alignment explanation
Indices: 18168--18221 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
18158 TTATTATTTT
**
18168 AATAAAAATATATTTATTTAAATT
1 AATAAAAATATATTTATTTAAACG
*
18192 AATAAAAATATAATTT-TTTTAACG
1 AATAAAAATAT-ATTTATTTAAACG
18216 AATAAA
1 AATAAA
18222 GAAAATACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (24 bp):
AATAAAAATATATTTATTTAAACG
Found at i:19316 original size:16 final size:17
Alignment explanation
Indices: 19295--19326 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
19285 TCTCCAGCCC
19295 TCATCTCTA-CTCTACA
1 TCATCTCTATCTCTACA
19311 TCATCTCTATCTCTAC
1 TCATCTCTATCTCTAC
19327 TCTAAAGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.22, C:0.38, G:0.00, T:0.41
Consensus pattern (17 bp):
TCATCTCTATCTCTACA
Found at i:19474 original size:15 final size:17
Alignment explanation
Indices: 19443--19474 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
19433 ATGTATTTTT
19443 ATCTATCTTGCAATTTA
1 ATCTATCTTGCAATTTA
19460 ATCTA-CTTG-AATTTA
1 ATCTATCTTGCAATTTA
19475 TTATATTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (17 bp):
ATCTATCTTGCAATTTA
Found at i:29038 original size:28 final size:28
Alignment explanation
Indices: 29001--29070 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
28991 TACTTTCTTT
*
29001 TTTTCCTTTTTCTTTAACTTCGAGTAACG
1 TTTT-CTTTTTCTTTAACTTCGAGTAACA
29030 TTTTCTTTTTCTTTAACTTCGAGTAACA
1 TTTTCTTTTTCTTTAACTTCGAGTAACA
*
29058 TTTTCTTCTTCTT
1 TTTTCTTTTTCTT
29071 CTTCTCCTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 35 0.90
29 4 0.10
ACGTcount: A:0.16, C:0.20, G:0.07, T:0.57
Consensus pattern (28 bp):
TTTTCTTTTTCTTTAACTTCGAGTAACA
Found at i:33139 original size:17 final size:17
Alignment explanation
Indices: 33113--33146 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
33103 TGTTAAATTC
* *
33113 ATATTTAAAATTTAAAA
1 ATATTAAAAATATAAAA
33130 ATATTAAAAATATAAAA
1 ATATTAAAAATATAAAA
33147 CTCCTAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATATTAAAAATATAAAA
Found at i:34195 original size:18 final size:17
Alignment explanation
Indices: 34172--34210 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
34162 CCTAAGGGTA
34172 ATAATATAATTTTTACAT
1 ATAATAT-ATTTTTACAT
*
34190 ATAATATTTTTTTACAT
1 ATAATATATTTTTACAT
34207 ATAA
1 ATAA
34211 AGTTTGGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (17 bp):
ATAATATATTTTTACAT
Found at i:46689 original size:16 final size:16
Alignment explanation
Indices: 46670--46703 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
46660 CAATATACGA
46670 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
46686 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
46702 AT
1 AT
46704 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:46774 original size:16 final size:18
Alignment explanation
Indices: 46742--46775 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
46732 ATATAATGTA
46742 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
46760 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
46776 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:47293 original size:23 final size:21
Alignment explanation
Indices: 47267--47313 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
47257 GTGTCACCAA
*
47267 TAACATATGTCATGATCATGTGT
1 TAACACATGTCA-GATCATG-GT
*
47290 TAACACATGTCAGATCCTGGT
1 TAACACATGTCAGATCATGGT
47311 TAA
1 TAA
47314 ATGATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 6 0.27
23 11 0.50
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (21 bp):
TAACACATGTCAGATCATGGT
Found at i:47444 original size:130 final size:130
Alignment explanation
Indices: 47240--47487 Score: 433
Period size: 130 Copynumber: 1.9 Consensus size: 130
47230 AATTTTCTTC
* *
47240 TAATTAGGTGGTGACATGTGTCACCAATAACATATGTCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATGTCATGATCATGTGCTAACACATGTCAGAT
** *
47305 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* *
47370 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATGTCATGATCATGTGCTAACACATGTCAGAT
47435 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
47488 TATATAAATA
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 111 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATGTCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:47936 original size:35 final size:35
Alignment explanation
Indices: 47885--47958 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
47875 AATTGAATTT
* * * * *
47885 AATTGAATTATTTTGGAATTTAGTGTTTAGAATGA
1 AATTAAATTACTTTGGAAATTAGGGTTTAAAATGA
*
47920 AATTAAATTACTTTGGAAATTGGGGTTTAAAATGA
1 AATTAAATTACTTTGGAAATTAGGGTTTAAAATGA
47955 AATT
1 AATT
47959 GAGGACTGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.38, C:0.01, G:0.19, T:0.42
Consensus pattern (35 bp):
AATTAAATTACTTTGGAAATTAGGGTTTAAAATGA
Found at i:63129 original size:29 final size:31
Alignment explanation
Indices: 63069--63166 Score: 105
Period size: 31 Copynumber: 3.2 Consensus size: 31
63059 GTTATTAAAA
*
63069 TATATATT-TTACAATAAATAATATAATTTAT
1 TATATATTATTAAAATAAATAATATAA-TTAT
*
63100 TATATATTATTAAAATAGA-AATATAA-TAT
1 TATATATTATTAAAATAAATAATATAATTAT
*
63129 TATATATTATTATAATATAATTAA-ATATATTAT
1 TATATATTATTA-AA-ATAAATAATATA-ATTAT
63162 TATAT
1 TATAT
63167 CACTAAAAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
29 15 0.26
30 2 0.04
31 21 0.37
32 11 0.19
33 8 0.14
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (31 bp):
TATATATTATTAAAATAAATAATATAATTAT
Found at i:63593 original size:22 final size:23
Alignment explanation
Indices: 63568--63621 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
63558 TGATATCGTA
* * *
63568 TTAAATATTAT-TGTTTAAAAAT
1 TTAAATATTATAAGTTCAAAAAG
*
63590 TTAAAAATTATAAGTTCAAAAAG
1 TTAAATATTATAAGTTCAAAAAG
63613 TTAAATATT
1 TTAAATATT
63622 TAAATATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.43
Consensus pattern (23 bp):
TTAAATATTATAAGTTCAAAAAG
Found at i:71035 original size:32 final size:32
Alignment explanation
Indices: 70983--71058 Score: 116
Period size: 32 Copynumber: 2.4 Consensus size: 32
70973 CTTTATTTTG
** *
70983 TTCGGGTCGGGTCGGGTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTCGAATTTTTTAAATGTGATA
*
71015 TTCGAGTCGGGTCGAATTTTTTAAATGTGATA
1 TTCGGGTCGGGTCGAATTTTTTAAATGTGATA
71047 TTCGGGTCGGGT
1 TTCGGGTCGGGT
71059 TTAGGGTGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.16, C:0.11, G:0.34, T:0.39
Consensus pattern (32 bp):
TTCGGGTCGGGTCGAATTTTTTAAATGTGATA
Found at i:79878 original size:20 final size:21
Alignment explanation
Indices: 79831--79879 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
79821 GAAGCATGGC
*
79831 TGTTTTGTTTGTTTTAAACTG
1 TGTTTAGTTTGTTTTAAACTG
79852 TGTTTAGTTTGTTTTAAACTG
1 TGTTTAGTTTGTTTTAAACTG
79873 -GTTTAGT
1 TGTTTAGT
79880 GTAAGAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.16, C:0.04, G:0.20, T:0.59
Consensus pattern (21 bp):
TGTTTAGTTTGTTTTAAACTG
Found at i:80143 original size:58 final size:58
Alignment explanation
Indices: 80074--80238 Score: 154
Period size: 58 Copynumber: 2.8 Consensus size: 58
80064 AACTATATTC
* *
80074 CTCATTTTAAATT-GATCTTTAAACTTTTGAATATTCTAATTTCATCTCTAAATTATGA
1 CTCATTTTAAATTAG-TCCTTAAACTTTTGAATATTCTAATTTCATCCCTAAATTATGA
* * * * **
80132 CTCATTTTAAATTAGTCCTTAAATTTTTGTATATTTTAATTTTATCCCTAAACCATGA
1 CTCATTTTAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATCCCTAAATTATGA
* * * * * *
80190 ATCTATTTCTAAGA-TGGTCCCTAAACTTTTAAATATTTTAGTTTCATCC
1 CTC-ATTT-TAA-ATTAGTCCTTAAACTTTTGAATATTCTAATTTCATCC
80239 AAATATGTAA
Statistics
Matches: 87, Mismatches: 16, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
58 50 0.57
59 5 0.06
60 31 0.36
61 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (58 bp):
CTCATTTTAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATCCCTAAATTATGA
Found at i:86401 original size:24 final size:24
Alignment explanation
Indices: 86373--86430 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
86363 ATTATATATA
* *
86373 TTATTATTAGTTTATT-TATAGGT
1 TTATTATTAGTTAATTAAATAGGT
86396 TGTATTATT-GTTAATTAAATAGGT
1 T-TATTATTAGTTAATTAAATAGGT
*
86420 TAATTATTAGT
1 TTATTATTAGT
86431 GCGAGTGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 13 0.45
24 16 0.55
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (24 bp):
TTATTATTAGTTAATTAAATAGGT
Done.