Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005828.1 Hibiscus syriacus cultivar Beakdansim tig00013665_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: 86090
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:2332 original size:45 final size:47
Alignment explanation
Indices: 2210--2337 Score: 154
Period size: 48 Copynumber: 2.8 Consensus size: 47
2200 ATATAAATTT
* *
2210 CTTACC-TTTTATCCCATAAGCTCATAAGCTTATTTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTACCAAAATA
* ** *
2256 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTTTCAATATA
1 CTTACCATTT-AATTCCATAAGCTCATAAGCTTATTTTTACCAAAATA
* *
2304 CTTGCCA-TT-ATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTT
2338 GCATGGTTAC
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
45 23 0.32
46 6 0.08
47 5 0.07
48 37 0.52
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (47 bp):
CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTACCAAAATA
Found at i:6278 original size:17 final size:17
Alignment explanation
Indices: 6258--6318 Score: 74
Period size: 17 Copynumber: 3.6 Consensus size: 17
6248 CAAGTGAAAT
6258 ATTTTTTT-TCATTTCTC
1 ATTTTTTTCTCATTT-TC
6275 ATTTTTTTCTC-TATTT-
1 ATTTTTTTCTCAT-TTTC
6291 ATTTTCTTTCTCATTTTC
1 ATTTT-TTTCTCATTTTC
6309 ATTTTTTTCT
1 ATTTTTTTCT
6319 TCTTCGTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
16 5 0.13
17 24 0.62
18 10 0.26
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTTTTCTCATTTTC
Found at i:6281 original size:16 final size:15
Alignment explanation
Indices: 6260--6307 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
6250 AGTGAAATAT
6260 TTTTTTTCATTTCTCA
1 TTTTTTTC-TTTCTCA
6276 TTTTTTTC--TCT-A
1 TTTTTTTCTTTCTCA
6288 TTTATTTTCTTTCTCA
1 TTT-TTTTCTTTCTCA
6304 TTTT
1 TTTT
6308 CATTTTTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
12 4 0.14
13 8 0.29
15 4 0.14
16 12 0.43
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTTTTCTTTCTCA
Found at i:6329 original size:33 final size:32
Alignment explanation
Indices: 6259--6361 Score: 102
Period size: 33 Copynumber: 3.1 Consensus size: 32
6249 AAGTGAAATA
* **
6259 TTTT-TTTTCATTTCTCATTTTTTTCTCTATTTA
1 TTTTCTTTTCATTT-TCATTTTTTTCT-TCTTCG
6292 TTTTCTTTCTCATTTTCATTTTTTTCTTCTTCG
1 TTTTCTTT-TCATTTTCATTTTTTTCTTCTTCG
*
6325 TTTTCGTTTTCGTTTTC-TATTTTTTCTTCTTCTG
1 TTTTC-TTTTCATTTTCAT-TTTTTTCTTCTTC-G
6359 TTT
1 TTT
6362 GTTTTTCTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
32 1 0.02
33 32 0.52
34 22 0.36
35 6 0.10
ACGTcount: A:0.07, C:0.17, G:0.04, T:0.72
Consensus pattern (32 bp):
TTTTCTTTTCATTTTCATTTTTTTCTTCTTCG
Found at i:9265 original size:48 final size:45
Alignment explanation
Indices: 9204--9324 Score: 134
Period size: 48 Copynumber: 2.6 Consensus size: 45
9194 TTCTTACCTT
*
9204 TTATCCCATAAGCTCATAAGCTTATTTTTACCAAAATACTTACCA
1 TTATTCCATAAGCTCATAAGCTTATTTTTACCAAAATACTTACCA
* ** * *
9249 TTTAAATTCCATAAGCTCGTAAGCTTATTTTTTTTCAATATACTTGCCA
1 -TT--ATTCCATAAGCTCATAAGCTTA-TTTTTACCAAAATACTTACCA
**
9298 TTATTCTGTAAGCTCATAAGCTTATTT
1 TTATTCCATAAGCTCATAAGCTTATTT
9325 GCATGGTTAC
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
45 3 0.05
46 21 0.33
48 22 0.35
49 17 0.27
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.42
Consensus pattern (45 bp):
TTATTCCATAAGCTCATAAGCTTATTTTTACCAAAATACTTACCA
Found at i:9322 original size:46 final size:48
Alignment explanation
Indices: 9196--9324 Score: 140
Period size: 46 Copynumber: 2.8 Consensus size: 48
9186 ATATAAATTT
* *
9196 CTTACC-TTTTATCCCATAAGCTCATAAGCTTA-TTTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTACCAAAATA
* ** *
9242 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTTTTCAATATA
1 CTTACCATTT-AATTCCATAAGCTCATAAGCTTATTTTTTACCAAAATA
* **
9291 CTTGCCA-TT-ATTCTGTAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTT
9325 GCATGGTTAC
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
46 28 0.40
47 3 0.04
48 22 0.31
49 17 0.24
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (48 bp):
CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTACCAAAATA
Found at i:13664 original size:14 final size:14
Alignment explanation
Indices: 13645--13679 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
13635 GTTCTCGTCC
13645 AGCAAAAACAATTA
1 AGCAAAAACAATTA
13659 AGCAAAAACAATTA
1 AGCAAAAACAATTA
*
13673 AACAAAA
1 AGCAAAA
13680 TAAACGAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.69, C:0.14, G:0.06, T:0.11
Consensus pattern (14 bp):
AGCAAAAACAATTA
Found at i:18010 original size:13 final size:13
Alignment explanation
Indices: 17992--18017 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17982 CGGCTATGGG
17992 GAAAATGAAGAAA
1 GAAAATGAAGAAA
18005 GAAAATGAAGAAA
1 GAAAATGAAGAAA
18018 TGAGAGAGAA
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:0.69, C:0.00, G:0.23, T:0.08
Consensus pattern (13 bp):
GAAAATGAAGAAA
Found at i:18052 original size:27 final size:28
Alignment explanation
Indices: 18015--18082 Score: 97
Period size: 26 Copynumber: 2.5 Consensus size: 28
18005 GAAAATGAAG
18015 AAATGAGAGAGAAAAAAGAAAAAGTTACA
1 AAATGAGAGAGAAAAAAGAAAAAGTTA-A
*
18044 AAA-GA-AGAG-AAAAAGAAAAGGTTAA
1 AAATGAGAGAGAAAAAAGAAAAAGTTAA
18069 AAATGAGAGAGAAA
1 AAATGAGAGAGAAA
18083 TGAGTGATAG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
25 4 0.11
26 16 0.46
27 8 0.23
28 4 0.11
29 3 0.09
ACGTcount: A:0.66, C:0.01, G:0.24, T:0.09
Consensus pattern (28 bp):
AAATGAGAGAGAAAAAAGAAAAAGTTAA
Found at i:18359 original size:23 final size:23
Alignment explanation
Indices: 18324--18368 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
18314 AGTATGGTCC
18324 CTACAAATCAAAACAAAAATTAT
1 CTACAAATCAAAACAAAAATTAT
*
18347 CTACAAAAT-AAAATAAAAATTA
1 CTAC-AAATCAAAACAAAAATTA
18369 AAAATAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.64, C:0.13, G:0.00, T:0.22
Consensus pattern (23 bp):
CTACAAATCAAAACAAAAATTAT
Found at i:18372 original size:7 final size:6
Alignment explanation
Indices: 18351--18387 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
18341 AATTATCTAC
18351 AAAAT- AAAATA AAAATTA AAAATA AAAAT- AAAATA AA
1 AAAATA AAAATA AAAA-TA AAAATA AAAATA AAAATA AA
18388 GGAAAGATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
5 10 0.34
6 13 0.45
7 6 0.21
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:18372 original size:13 final size:11
Alignment explanation
Indices: 18351--18387 Score: 56
Period size: 11 Copynumber: 3.2 Consensus size: 11
18341 AATTATCTAC
18351 AAAATAAAATA
1 AAAATAAAATA
18362 AAAATTAAAAATA
1 AAAA-T-AAAATA
18375 AAAATAAAATA
1 AAAATAAAATA
18386 AA
1 AA
18388 GGAAAGATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 12 0.50
12 2 0.08
13 10 0.42
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:26165 original size:2 final size:2
Alignment explanation
Indices: 26158--26183 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
26148 TGGGTTTTAA
26158 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
26184 GTGGGGTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26253 original size:18 final size:19
Alignment explanation
Indices: 26232--26285 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 19
26222 GAAAGAATGG
26232 GAGAAAAAGAAGAAA-AAA
1 GAGAAAAAGAAGAAAGAAA
26250 GAG-AAAAG-AGAAAGAAA
1 GAGAAAAAGAAGAAAGAAA
26267 GAAGAAGAATAGAAGAAAG
1 G-AGAA-AA-AGAAGAAAG
26286 TTAAAGTCAG
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
16 5 0.17
17 9 0.30
18 5 0.17
19 1 0.03
20 2 0.07
21 2 0.07
22 6 0.20
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (19 bp):
GAGAAAAAGAAGAAAGAAA
Found at i:26625 original size:37 final size:37
Alignment explanation
Indices: 26584--26664 Score: 126
Period size: 37 Copynumber: 2.2 Consensus size: 37
26574 TTTCACTTGT
* *
26584 TTAAATTAAATTAGTTACTTGGTAGATTATTTTTAGA
1 TTAAATTAAATTAGTTACTTAGTAGATTATTTTTAAA
*
26621 TTAAATTAAATTAGTTATTTAGTAGATTATTTTTAAA
1 TTAAATTAAATTAGTTACTTAGTAGATTATTTTTAAA
*
26658 TTGAATT
1 TTAAATT
26665 CGTTATAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.37, C:0.01, G:0.11, T:0.51
Consensus pattern (37 bp):
TTAAATTAAATTAGTTACTTAGTAGATTATTTTTAAA
Found at i:27009 original size:20 final size:21
Alignment explanation
Indices: 26968--27019 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
26958 GGTAATAGTG
*
26968 TTATTATTATTTAATAAAATA
1 TTATAATTATTTAATAAAATA
*
26989 TTATAATTATTT-ATTAAATA
1 TTATAATTATTTAATAAAATA
* *
27009 TCATAAATATT
1 TTATAATTATT
27020 AATGTTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATAATTATTTAATAAAATA
Found at i:28045 original size:14 final size:14
Alignment explanation
Indices: 28011--28038 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28001 TATTTTTTAT
28011 TTAATTTAAATTAA
1 TTAATTTAAATTAA
28025 TTAATTTAAATTAA
1 TTAATTTAAATTAA
28039 GTTATTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAATTTAAATTAA
Found at i:28881 original size:21 final size:21
Alignment explanation
Indices: 28852--28893 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28842 TCCAGGAGGG
28852 ATGGAAGAGCAAAGTGGTGGA
1 ATGGAAGAGCAAAGTGGTGGA
* **
28873 ATGGGAGAGCATGGTGGTGGA
1 ATGGAAGAGCAAAGTGGTGGA
28894 CATAAATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.05, G:0.48, T:0.17
Consensus pattern (21 bp):
ATGGAAGAGCAAAGTGGTGGA
Found at i:29609 original size:30 final size:28
Alignment explanation
Indices: 29575--29667 Score: 96
Period size: 30 Copynumber: 3.1 Consensus size: 28
29565 AATTTTAAAA
*
29575 GTTAAGATGAGATAAAATATATATTTTTAT
1 GTTAA-ATAAGATAAAATATATATTTTT-T
*
29605 GTTAAATAAGAAAAAAATTATATATTTTTT
1 GTTAAATAAG-ATAAAA-TATATATTTTTT
* * *
29635 ATTAAATAACAGTAAAATATATATTTATT
1 GTTAAATAAGA-TAAAATATATATTTTTT
29664 GTTA
1 GTTA
29668 TTTGATAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
29 19 0.36
30 23 0.43
31 11 0.21
ACGTcount: A:0.47, C:0.01, G:0.09, T:0.43
Consensus pattern (28 bp):
GTTAAATAAGATAAAATATATATTTTTT
Found at i:29655 original size:29 final size:30
Alignment explanation
Indices: 29586--29660 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
29576 TTAAGATGAG
* *
29586 ATAAAATATATATTTTTATGTTAAATAAGA
1 ATAAAATATATATTTTTATATTAAATAACA
*
29616 AAAAAATTATATATTTTT-TATTAAATAACA
1 ATAAAA-TATATATTTTTATATTAAATAACA
*
29646 GTAAAATATATATTT
1 ATAAAATATATATTT
29661 ATTGTTATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 9 0.23
30 19 0.49
31 11 0.28
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (30 bp):
ATAAAATATATATTTTTATATTAAATAACA
Found at i:29786 original size:34 final size:34
Alignment explanation
Indices: 29748--29818 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
29738 TATACTAAAA
* *
29748 ATACATAAATTATTATTAAATAAAGTTAATTATT
1 ATACATAAATTACTATAAAATAAAGTTAATTATT
* * *
29782 ATACATAAATTGCTATAAAATCAGGTTAATTATT
1 ATACATAAATTACTATAAAATAAAGTTAATTATT
29816 ATA
1 ATA
29819 AGATCAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.41
Consensus pattern (34 bp):
ATACATAAATTACTATAAAATAAAGTTAATTATT
Found at i:33886 original size:27 final size:25
Alignment explanation
Indices: 33834--33903 Score: 99
Period size: 27 Copynumber: 2.8 Consensus size: 25
33824 ACATATTATA
33834 TGGCACTACGGTGC--AATTCTACG
1 TGGCACTACGGTGCAAAATTCTACG
*
33857 TGGCACTTCGGTGGACAAAATTCTACG
1 TGGCACTACGGT-G-CAAAATTCTACG
33884 TGGCACTACGGTGCAAAATT
1 TGGCACTACGGTGCAAAATT
33904 TATATGAGCT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.27
24 1 0.02
25 8 0.20
26 1 0.02
27 20 0.49
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (25 bp):
TGGCACTACGGTGCAAAATTCTACG
Found at i:35287 original size:18 final size:18
Alignment explanation
Indices: 35260--35306 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
35250 ATGTCAAAAT
*
35260 GGTATTGGTACTGAAGTG
1 GGTATCGGTACTGAAGTG
*
35278 TGTATCGGTACTGAAGTG
1 GGTATCGGTACTGAAGTG
35296 GGTATCGGTAC
1 GGTATCGGTAC
35307 CATAGAAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.21, C:0.11, G:0.36, T:0.32
Consensus pattern (18 bp):
GGTATCGGTACTGAAGTG
Found at i:36053 original size:23 final size:22
Alignment explanation
Indices: 36004--36078 Score: 80
Period size: 23 Copynumber: 3.4 Consensus size: 22
35994 GTCGAGGGTT
* *
36004 CTATGTGGTCCTTCGGGATAAA
1 CTATGTGGTCCTTTGGGACAAA
*
36026 TCTATGTGGTCCTTTTGGACAAA
1 -CTATGTGGTCCTTTGGGACAAA
* *
36049 CCTATATGGTCATTTGGGACAAA
1 -CTATGTGGTCCTTTGGGACAAA
36072 -TATGTGG
1 CTATGTGG
36079 CACTTCGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 6 0.14
23 38 0.86
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (22 bp):
CTATGTGGTCCTTTGGGACAAA
Found at i:40414 original size:9 final size:9
Alignment explanation
Indices: 40393--40436 Score: 63
Period size: 9 Copynumber: 4.8 Consensus size: 9
40383 AAGGAAAAAT
40393 ATAAATAAAA
1 ATAAAT-AAA
40403 ATAAATAAA
1 ATAAATAAA
40412 ATAAATAAA
1 ATAAATAAA
40421 AT-AATAATA
1 ATAAATAA-A
40430 ATAAATA
1 ATAAATA
40437 GTAAAAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
8 5 0.16
9 17 0.53
10 10 0.31
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (9 bp):
ATAAATAAA
Found at i:40592 original size:16 final size:16
Alignment explanation
Indices: 40571--40604 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
40561 ATATACATCC
* *
40571 TAAAAATAATAAAATA
1 TAAAAAGAAGAAAATA
40587 TAAAAAGAAGAAAATA
1 TAAAAAGAAGAAAATA
40603 TA
1 TA
40605 TATAAATGTA
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:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (16 bp):
TAAAAAGAAGAAAATA
Found at i:49814 original size:20 final size:20
Alignment explanation
Indices: 49789--49828 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
49779 TTTTGGTGCA
49789 GAGGGAA-TCGATCCCCCCTT
1 GAGGGAACT-GATCCCCCCTT
*
49809 GAGGGAACTGATTCCCCCTT
1 GAGGGAACTGATCCCCCCTT
49829 TGAAGGGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.20, C:0.33, G:0.25, T:0.23
Consensus pattern (20 bp):
GAGGGAACTGATCCCCCCTT
Found at i:49826 original size:21 final size:23
Alignment explanation
Indices: 49791--49850 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
49781 TTGGTGCAGA
*
49791 GGGAATCGA-TCCCCCCTTG-A-
1 GGGAACCGATTCCCCCCTTGAAG
* *
49811 GGGAACTGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCTTGAAG
49834 GGGAACCGATTCCCCCC
1 GGGAACCGATTCCCCCC
49851 ACAGGGGAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 7 0.22
21 9 0.28
22 1 0.03
23 15 0.47
ACGTcount: A:0.20, C:0.35, G:0.25, T:0.20
Consensus pattern (23 bp):
GGGAACCGATTCCCCCCTTGAAG
Found at i:49876 original size:20 final size:21
Alignment explanation
Indices: 49832--49871 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
49822 CCCCCTTTGA
*
49832 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
49853 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
49872 TAGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:58558 original size:123 final size:122
Alignment explanation
Indices: 58340--58588 Score: 392
Period size: 123 Copynumber: 2.0 Consensus size: 122
58330 GTACGTGTTC
* * *
58340 GTTTGTTGAGCATGAATTTCTTTTTACATTGCACTTTTGCTCAAGTTTGACCATTGAATGGTGAT
1 GTTTGTTGAACATGAATTTCTTTGTACATTGCACTTTTGCTCAAATTTGACCATTGAATGGTGAT
* * *
58405 ACATAGGGTACATACTGAATTAATGCTGGGGTAGAATATCTGTATCAATCAATCTTT
66 ACATAGGGTACAGACTGAATTAATGATGGGGTAGAATATCTGTATCAATCAATCTTG
*
58462 GTTTGTTGAACATGAATTTCTTTGTACATTTGCACTTTTGCT-AAATTTAGATCATTGAATGGTG
1 GTTTGTTGAACATGAATTTCTTTGTACA-TTGCACTTTTGCTCAAATTT-GACCATTGAATGGTG
* *
58526 ATACATAGGGTACAGACTGAATTAATGATGGGGTAGAATATTTGTATCATTCAATCTTG
64 ATACATAGGGTACAGACTGAATTAATGATGGGGTAGAATATCTGTATCAATCAATCTTG
58585 GTTT
1 GTTT
58589 CCTAGATGTT
Statistics
Matches: 116, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
122 31 0.27
123 85 0.73
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (122 bp):
GTTTGTTGAACATGAATTTCTTTGTACATTGCACTTTTGCTCAAATTTGACCATTGAATGGTGAT
ACATAGGGTACAGACTGAATTAATGATGGGGTAGAATATCTGTATCAATCAATCTTG
Found at i:58630 original size:21 final size:22
Alignment explanation
Indices: 58590--58636 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
58580 TCTTGGTTTC
58590 CTAGATGTTAGTGGCAATCCAG
1 CTAGATGTTAGTGGCAATCCAG
58612 CTAGATG-TAG-GGACAATCCAG
1 CTAGATGTTAGTGG-CAATCCAG
58633 CTAG
1 CTAG
58637 CTTGTGCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 2 0.08
21 15 0.62
22 7 0.29
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (22 bp):
CTAGATGTTAGTGGCAATCCAG
Found at i:58867 original size:36 final size:36
Alignment explanation
Indices: 58820--58970 Score: 194
Period size: 36 Copynumber: 4.2 Consensus size: 36
58810 TCTAGTTTAA
*
58820 AAAAGCAGCCATGTGAGTTATGAACTTATCTATTAG
1 AAAAGAAGCCATGTGAGTTATGAACTTATCTATTAG
*
58856 AAAAGAAGCCATGTGAGTTATGAGCTTATCTATTAG
1 AAAAGAAGCCATGTGAGTTATGAACTTATCTATTAG
* ** *
58892 AGAAGTGGCCATGTGAGTTATGAGCTTATCTATTAG
1 AAAAGAAGCCATGTGAGTTATGAACTTATCTATTAG
* ** * *
58928 AGAAGTGGCCATGTGAGTTATGAACCTATCTATTGG
1 AAAAGAAGCCATGTGAGTTATGAACTTATCTATTAG
*
58964 AATAGAA
1 AAAAGAA
58971 TTTAATATCA
Statistics
Matches: 103, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 103 1.00
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (36 bp):
AAAAGAAGCCATGTGAGTTATGAACTTATCTATTAG
Found at i:58944 original size:72 final size:72
Alignment explanation
Indices: 58827--58961 Score: 216
Period size: 72 Copynumber: 1.9 Consensus size: 72
58817 TAAAAAAGCA
* *
58827 GCCATGTGAGTTATGAACTTATCTATTAGAAAAGAAGCCATGTGAGTTATGAGCTTATCTATTAG
1 GCCATGTGAGTTATGAACTTATCTATTAGAAAAGAAGCCATGTGAGTTATGAACCTATCTATTAG
58892 AGAAGTG
66 AGAAGTG
* * **
58899 GCCATGTGAGTTATGAGCTTATCTATTAGAGAAGTGGCCATGTGAGTTATGAACCTATCTATT
1 GCCATGTGAGTTATGAACTTATCTATTAGAAAAGAAGCCATGTGAGTTATGAACCTATCTATT
58962 GGAATAGAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 57 1.00
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (72 bp):
GCCATGTGAGTTATGAACTTATCTATTAGAAAAGAAGCCATGTGAGTTATGAACCTATCTATTAG
AGAAGTG
Found at i:60795 original size:25 final size:25
Alignment explanation
Indices: 60763--60822 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
60753 ATTTGTAGTA
60763 GAAAAATAATATTTATTATAATGAC
1 GAAAAATAATATTTATTATAATGAC
60788 GAAAAATAATATTTATTATAATGAC
1 GAAAAATAATATTTATTATAATGAC
*
60813 AAAAAATAAT
1 GAAAAATAAT
60823 GATACCATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (25 bp):
GAAAAATAATATTTATTATAATGAC
Found at i:60868 original size:38 final size:38
Alignment explanation
Indices: 60826--60931 Score: 169
Period size: 38 Copynumber: 2.8 Consensus size: 38
60816 AAATAATGAT
60826 ACCATTAATAACCCGGGTAGGTTGGTGGTTATTAATTA
1 ACCATTAATAACCCGGGTAGGTTGGTGGTTATTAATTA
60864 ACCATTAATAATCCC-GGTAGGTTGGTGGTTATTAATTA
1 ACCATTAATAA-CCCGGGTAGGTTGGTGGTTATTAATTA
** *
60902 TTCATTAATAATCCGGGTAGGTTGGTGGTT
1 ACCATTAATAACCCGGGTAGGTTGGTGGTT
60932 GAACGGGAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
37 2 0.03
38 58 0.92
39 3 0.05
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.37
Consensus pattern (38 bp):
ACCATTAATAACCCGGGTAGGTTGGTGGTTATTAATTA
Found at i:61119 original size:25 final size:25
Alignment explanation
Indices: 61086--61134 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
61076 TAGAAATTTT
*
61086 TTTATTATAATGAAGAAAAATAATA
1 TTTATTATAATGAAAAAAAATAATA
61111 TTTATTATAATGAAAAAAAATAAT
1 TTTATTATAATGAAAAAAAATAAT
61135 GGCACCAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (25 bp):
TTTATTATAATGAAAAAAAATAATA
Found at i:61194 original size:45 final size:45
Alignment explanation
Indices: 61143--61230 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
61133 ATGGCACCAA
* * *
61143 TAATTATCCATTAATAACCCGGGTAGGTTGGTTGTTGGTGGTTAT
1 TAATTATCCATTAATAACCAGGGTAGGTTGATGGTTGGTGGTTAT
61188 TAATTATCCATTAATAACCAGGGTAGGTTGATGGTTGGTGGTT
1 TAATTATCCATTAATAACCAGGGTAGGTTGATGGTTGGTGGTT
61231 GAACGGGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.24, C:0.10, G:0.27, T:0.39
Consensus pattern (45 bp):
TAATTATCCATTAATAACCAGGGTAGGTTGATGGTTGGTGGTTAT
Found at i:61282 original size:299 final size:294
Alignment explanation
Indices: 60884--61637 Score: 1000
Period size: 299 Copynumber: 2.6 Consensus size: 294
60874 ATCCCGGTAG
*
60884 GTTGGTGGTTATTAATTATTCATTAATAATCC--G-GGTAGGTTGGTGGTTGAACGGGAAAATAT
1 GTTGGTGGTTATTAATTATCCATTAATAA-CCAGGAGGTAGGTTGGTGGTTGAACGGGAAAATAT
* * *
60946 AATGAATTAGAGAGTAATAAATTCGAAGTACTAATAAGTATTTATAAAAAATATCAAGTAATAAA
65 AATGAATTAGAGAGTAATAAATTTGAAGTAATAATAAGTAATTATAAAAAATATCAAGTAATAAA
* *
61011 TTTAATCATTATTATAATGTAATCATAGTATTTAATCCGAACATATTTTGATTTATTATTTGTAG
130 TTTAATCATTATTATAATGTAATCATAGTATTTAATCCGAACATA-TTTGATTTAGTATTTGTAC
*
61076 TAGAA-ATT-T-T-TTTATTATAATGAAGAAAAATAATATTTATTATAATGAAAAAAAATAATGG
194 TAAAATATTATATATTTATTATAATGAAGAAAAATAATATTTATTATAATGAAAAAAAATAATGG
61137 CACCAATAATTATCCATTAATAACCCGGGTAGGTTGGTT
259 CACCAATAATTATCCATTAATAACCCGGGTAGG-T--TT
61176 GTTGGTGGTTATTAATTATCCATTAATAACCAGGGTAGGTTGATGGTTGGTGGTTGAACGGGAAA
1 GTTGGTGGTTATTAATTATCCATTAATAACCA-GG-AGG-T-A-GGTTGGTGGTTGAACGGGAAA
* *
61241 ATATAATGAATTAGAGAGTAATAAATTTGAAGTAATAATAAGCAATTATAAAAAAATATGAAGTA
61 ATATAATGAATTAGAGAGTAATAAATTTGAAGTAATAATAAGTAATTAT-AAAAAATATCAAGTA
*
61306 ATAAATTTAATCATTATTATAATGTAATCATACTATTTAATCCGAACATATTTGATTTAGTATTT
125 ATAAATTTAATCATTATTATAATGTAATCATAGTATTTAATCCGAACATATTTGATTTAGTATTT
* * *
61371 GTACTAAAATTTTATTATAATATTTATTATAATGACGAAGAATAATATTTATTATAATGACAAAA
190 GTACTAAAA---TATTAT-ATATTTATTATAATGAAGAAAAATAATATTTATTATAATGAAAAAA
** * * *
61436 AATAATGGCACCTTTAATTATTCATTAATAATCCGTGTAGGTTT
251 AATAATGGCACCAATAATTATCCATTAATAACCCGGGTAGGTTT
* * * *
61480 G-TGGTTGG-TATTAATTAACCATTAATAACCAGGA--TAGGTTGGTGGTTAAACAGGAAAGTAT
1 GTTGG-TGGTTATTAATTATCCATTAATAACCAGGAGGTAGGTTGGTGGTTGAACGGGAAAATAT
* *
61541 AATGAATTAGAGAGTAATAAATTTG-A--AATAATAATTAGTTATAAAAAAT-TCGAAGTAATAA
65 AATGAATTAGAGAGTAATAAATTTGAAGTAATAATAAGTAATTATAAAAAATATC-AAGTAATAA
**
61602 ATTTAAT-ATTTAGGATAATGTAATCATAGTATTTAA
129 ATTTAATCA-TTATTATAATGTAATCATAGTATTTAA
61638 GCATTATTTT
Statistics
Matches: 413, Mismatches: 29, Indels: 40
0.86 0.06 0.08
Matches are distributed among these distances:
291 4 0.01
292 75 0.18
293 13 0.03
294 1 0.00
295 1 0.00
296 49 0.12
297 2 0.00
298 2 0.00
299 87 0.21
300 63 0.15
301 1 0.00
302 2 0.00
303 28 0.07
304 7 0.02
306 2 0.00
307 76 0.18
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (294 bp):
GTTGGTGGTTATTAATTATCCATTAATAACCAGGAGGTAGGTTGGTGGTTGAACGGGAAAATATA
ATGAATTAGAGAGTAATAAATTTGAAGTAATAATAAGTAATTATAAAAAATATCAAGTAATAAAT
TTAATCATTATTATAATGTAATCATAGTATTTAATCCGAACATATTTGATTTAGTATTTGTACTA
AAATATTATATATTTATTATAATGAAGAAAAATAATATTTATTATAATGAAAAAAAATAATGGCA
CCAATAATTATCCATTAATAACCCGGGTAGGTTT
Found at i:61439 original size:22 final size:25
Alignment explanation
Indices: 61387--61441 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
61377 AAATTTTATT
61387 ATAATATTTATTATAATGACGAAGA
1 ATAATATTTATTATAATGACGAAGA
* *
61412 ATAATATTTATTATAATGACAAAAA
1 ATAATATTTATTATAATGACGAAGA
61437 ATAAT
1 ATAAT
61442 GGCACCTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.36
Consensus pattern (25 bp):
ATAATATTTATTATAATGACGAAGA
Found at i:61695 original size:27 final size:28
Alignment explanation
Indices: 61646--61698 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
61636 AAGCATTATT
*
61646 TTTTTTAAATATTGTTAATATATTTACA
1 TTTTTTAAATAATGTTAATATATTTACA
61674 TTTTTTAAA-AAT-TTAATAATATTTA
1 TTTTTTAAATAATGTTAAT-ATATTTA
61699 TTATAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 5 0.22
27 9 0.39
28 9 0.39
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (28 bp):
TTTTTTAAATAATGTTAATATATTTACA
Found at i:64581 original size:27 final size:27
Alignment explanation
Indices: 64532--64817 Score: 187
Period size: 27 Copynumber: 9.9 Consensus size: 27
64522 TTTTGACGCT
* * *
64532 ATATTTTAATGAATGTTATTAATATCA
1 ATATTTGAATTAATGTGATTAATATCA
* *
64559 ATAGTTGCATTAATGTGATTAATATCA
1 ATATTTGAATTAATGTGATTAATATCA
* * *
64586 ATATTTGAATTAATATGATTGATATTTGTTGACGCT
1 ATATTTGAATTAATGTGATT-A-A-----T-A-TCA
* * * *
64622 ATATTTTAATGAATATGAGTAATATCA
1 ATATTTGAATTAATGTGATTAATATCA
* * *
64649 ATAGTTGAATGAATGTGAATAATATCA
1 ATATTTGAATTAATGTGATTAATATCA
*
64676 ATAGTTGAATTAATGTGATTAATATCA
1 ATATTTGAATTAATGTGATTAATATCA
** * *
64703 ATATTTGAATTAATATGATGGATATTTGTTTACGCT
1 ATATTTGAATT-A-ATG-T-G--A-TT-AATA-TCA
* *
64739 ATATTTTAATGAATGTGATTAATATCA
1 ATATTTGAATTAATGTGATTAATATCA
64766 ATAGTTT-AATTAATGTGATTAATATCA
1 ATA-TTTGAATTAATGTGATTAATATCA
*
64793 ATATTTGAATTAATGTGATGAATAT
1 ATATTTGAATTAATGTGATTAATAT
64818 TAATTCAACT
Statistics
Matches: 205, Mismatches: 34, Indels: 40
0.73 0.12 0.14
Matches are distributed among these distances:
26 3 0.01
27 141 0.69
28 8 0.04
29 7 0.03
30 2 0.01
31 1 0.00
32 1 0.00
33 2 0.01
34 7 0.03
35 5 0.02
36 28 0.14
ACGTcount: A:0.38, C:0.04, G:0.14, T:0.43
Consensus pattern (27 bp):
ATATTTGAATTAATGTGATTAATATCA
Found at i:64618 original size:90 final size:90
Alignment explanation
Indices: 64499--64700 Score: 287
Period size: 90 Copynumber: 2.2 Consensus size: 90
64489 TATATATTTT
* * * * * * *
64499 TTTGCATTAATATTATGGATATTTTTTGACGCTATATTTTAATGAATGTTATTAATATCAATAGT
1 TTTGAATTAATATGATTGATATTTGTTGACGCTATATTTTAATGAATATGAGTAATATCAATAGT
* * *
64564 TGCATTAATGTGATTAATATCAATA
66 TGAATGAATGTGAATAATATCAATA
64589 TTTGAATTAATATGATTGATATTTGTTGACGCTATATTTTAATGAATATGAGTAATATCAATAGT
1 TTTGAATTAATATGATTGATATTTGTTGACGCTATATTTTAATGAATATGAGTAATATCAATAGT
64654 TGAATGAATGTGAATAATATCAATA
66 TGAATGAATGTGAATAATATCAATA
* * *
64679 GTTGAATTAATGTGATTAATAT
1 TTTGAATTAATATGATTGATAT
64701 CAATATTTGA
Statistics
Matches: 99, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
90 99 1.00
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.44
Consensus pattern (90 bp):
TTTGAATTAATATGATTGATATTTGTTGACGCTATATTTTAATGAATATGAGTAATATCAATAGT
TGAATGAATGTGAATAATATCAATA
Found at i:64678 original size:117 final size:117
Alignment explanation
Indices: 64539--64817 Score: 459
Period size: 117 Copynumber: 2.4 Consensus size: 117
64529 GCTATATTTT
* *
64539 AATGAATGTTATTAATATCAATAGTTGCATTAATGTGATTAATATCAATATTTGAATTAATATGA
1 AATGAATGTGATTAATATCAATAGTTGAATTAATGTGATTAATATCAATATTTGAATTAATATGA
*
64604 TTGATATTTGTTGACGCTATATTTTAATGAATATGAGTAATATCAATAGTTG
66 TGGATATTTGTTGACGCTATATTTTAATGAATATGAGTAATATCAATAGTTG
*
64656 AATGAATGTGAATAATATCAATAGTTGAATTAATGTGATTAATATCAATATTTGAATTAATATGA
1 AATGAATGTGATTAATATCAATAGTTGAATTAATGTGATTAATATCAATATTTGAATTAATATGA
* * * *
64721 TGGATATTTGTTTACGCTATATTTTAATGAATGTGATTAATATCAATAGTTT
66 TGGATATTTGTTGACGCTATATTTTAATGAATATGAGTAATATCAATAGTTG
* * *
64773 AATTAATGTGATTAATATCAATATTTGAATTAATGTGATGAATAT
1 AATGAATGTGATTAATATCAATAGTTGAATTAATGTGATTAATAT
64818 TAATTCAACT
Statistics
Matches: 150, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
117 150 1.00
ACGTcount: A:0.39, C:0.04, G:0.14, T:0.43
Consensus pattern (117 bp):
AATGAATGTGATTAATATCAATAGTTGAATTAATGTGATTAATATCAATATTTGAATTAATATGA
TGGATATTTGTTGACGCTATATTTTAATGAATATGAGTAATATCAATAGTTG
Found at i:64835 original size:90 final size:90
Alignment explanation
Indices: 64656--64835 Score: 263
Period size: 90 Copynumber: 2.0 Consensus size: 90
64646 TCAATAGTTG
64656 AATGAATGTGAATAATATCAATAGTTGAATTAATGTGATTAATATCAATATTTGAATTAATATGA
1 AATGAATGTGAATAATATCAATAGTTGAATTAATGTGATTAATATCAATATTTGAATTAATATGA
* ** * *
64721 TGGATATTTGTTTACGCTATATTTT
66 TGAATATTAATTAACGCTAAATTTT
* * *
64746 AATGAATGTGATTAATATCAATAGTTTAATTAATGTGATTAATATCAATATTTGAATTAATGTGA
1 AATGAATGTGAATAATATCAATAGTTGAATTAATGTGATTAATATCAATATTTGAATTAATATGA
*
64811 TGAATATTAATTCAAC-TTAAATTTT
66 TGAATATTAATT-AACGCTAAATTTT
64836 TAAAATTCAA
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
90 78 0.98
91 2 0.03
ACGTcount: A:0.39, C:0.04, G:0.13, T:0.43
Consensus pattern (90 bp):
AATGAATGTGAATAATATCAATAGTTGAATTAATGTGATTAATATCAATATTTGAATTAATATGA
TGAATATTAATTAACGCTAAATTTT
Found at i:67955 original size:25 final size:25
Alignment explanation
Indices: 67927--67978 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
67917 CATGCATTGA
*
67927 ATTATTGGTGCATAATAATGGCACC
1 ATTATTAGTGCATAATAATGGCACC
*
67952 ATTATTAGTGCCTAATAATGGCACC
1 ATTATTAGTGCATAATAATGGCACC
67977 AT
1 AT
67979 GATTCGGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (25 bp):
ATTATTAGTGCATAATAATGGCACC
Found at i:68777 original size:27 final size:24
Alignment explanation
Indices: 68726--68833 Score: 60
Period size: 25 Copynumber: 4.2 Consensus size: 24
68716 CTAAATTCAT
*
68726 AATATTTTTTATATATTTACTTTAAGA
1 AATA-TTTTT-TATATTAACTTTAA-A
*
68753 AATATTTTTTATATTAACTTGT-TA
1 AATATTTTTTATATTAACTT-TAAA
*
68777 AATATATTTTATAATTAA-TTTCAGTTAA
1 AATATTTTTTAT-ATTAACTTT-A---AA
*
68805 AATATTTTATTTTATTTAA-TTTAAA
1 AATATTTT-TTATA-TTAACTTTAAA
68830 AATA
1 AATA
68834 AATAATTTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 20
0.72 0.07 0.22
Matches are distributed among these distances:
23 1 0.02
24 14 0.21
25 21 0.32
26 6 0.09
27 4 0.06
28 10 0.15
29 10 0.15
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (24 bp):
AATATTTTTTATATTAACTTTAAA
Found at i:68783 original size:26 final size:25
Alignment explanation
Indices: 68752--68814 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 25
68742 TTACTTTAAG
*
68752 AAATATTTTTTATATTAACTT-GTTA
1 AAATATTTTATA-ATTAACTTAGTTA
*
68777 AATATATTTTATAATTAATTTCAGTTA
1 AA-ATATTTTATAATTAACTT-AGTTA
68804 AAATATTTTAT
1 AAATATTTTAT
68815 TTTATTTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
25 9 0.27
26 18 0.55
27 6 0.18
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (25 bp):
AAATATTTTATAATTAACTTAGTTA
Found at i:68786 original size:24 final size:26
Alignment explanation
Indices: 68752--68814 Score: 78
Period size: 24 Copynumber: 2.5 Consensus size: 26
68742 TTACTTTAAG
*
68752 AAATATTTTTTAT-ATTAACTT-GTT
1 AAATATATTTTATAATTAACTTAGTT
*
68776 AAATATATTTTATAATTAATTTCAGTT
1 AAATATATTTTATAATTAACTT-AGTT
68803 AAA-ATATTTTAT
1 AAATATATTTTAT
68815 TTTATTTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 12 0.35
25 7 0.21
26 9 0.26
27 6 0.18
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (26 bp):
AAATATATTTTATAATTAACTTAGTT
Found at i:68828 original size:24 final size:25
Alignment explanation
Indices: 68759--68830 Score: 69
Period size: 24 Copynumber: 2.9 Consensus size: 25
68749 AAGAAATATT
*
68759 TTTTATATTAACTT--GTTAAATATA
1 TTTTATATTAATTTAAGTTAAA-ATA
*
68783 TTTTATAATTAATTTCAGTTAAAATA
1 TTTTAT-ATTAATTTAAGTTAAAATA
* *
68809 TTTTAT-TTTATTTAATTTAAAA
1 TTTTATATTAATTTAAGTTAAAA
68831 ATAAATAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
24 19 0.46
25 7 0.17
26 9 0.22
27 6 0.15
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (25 bp):
TTTTATATTAATTTAAGTTAAAATA
Found at i:73305 original size:9 final size:8
Alignment explanation
Indices: 73281--73343 Score: 54
Period size: 9 Copynumber: 7.1 Consensus size: 8
73271 AAACATAATT
73281 AAAATAACA
1 AAAATAA-A
*
73290 ATAATAAA
1 AAAATAAA
73298 AAATATAAA
1 AAA-ATAAA
73307 AACAATAAAA
1 AA-AAT-AAA
73317 ACAAATAAA
1 A-AAATAAA
*
73326 AAATTAAA
1 AAAATAAA
73334 TAAAATAAA
1 -AAAATAAA
73343 A
1 A
73344 TAAACACAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
8 10 0.22
9 26 0.58
10 8 0.18
11 1 0.02
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (8 bp):
AAAATAAA
Found at i:73310 original size:21 final size:22
Alignment explanation
Indices: 73252--73328 Score: 81
Period size: 21 Copynumber: 3.5 Consensus size: 22
73242 TAAAGCCATG
*
73252 AAATATCAAAACAATTAATAAAC
1 AAATATAAAAACAA-TAATAAAC
73275 ATAAT-TAAAATAACAATAATAAA-
1 A-AATAT-AAA-AACAATAATAAAC
73298 AAATATAAAAACAATAA-AAAC
1 AAATATAAAAACAATAATAAAC
73319 AAATA-AAAAA
1 AAATATAAAAA
73329 TTAAATAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
20 8 0.17
21 13 0.27
22 6 0.12
23 4 0.08
24 12 0.25
25 5 0.10
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (22 bp):
AAATATAAAAACAATAATAAAC
Found at i:75084 original size:58 final size:58
Alignment explanation
Indices: 75000--75180 Score: 168
Period size: 59 Copynumber: 3.1 Consensus size: 58
74990 GGAATGTTGG
* * * * *
75000 TCCCTCAGGTGAGGCATGGCTAATTCGAAGTGTTGTGAATCGAGCACATGAAAAG-TCA
1 TCCCTCAGGTG-GGCATCGCTGATTCGAAGTGTTGTGAATCAAGCAAAGGAAAAGTTCA
* * * ** * *
75058 TCCCCTCTGGTGGGCATTGCTGATTCGAAGTATTGTGTGTCAAGCAAAGGAAATGTTGA
1 T-CCCTCAGGTGGGCATCGCTGATTCGAAGTGTTGTGAATCAAGCAAAGGAAAAGTTCA
* * * *
75117 TCCCTCAAGTGGGGCGTCGCTGATTCGAAGTGTTGTGAATCTAGCAAA-GAAAATGTTAA
1 TCCCTCAGGT-GGGCATCGCTGATTCGAAGTGTTGTGAATCAAGCAAAGGAAAA-GTTCA
75176 TCCCT
1 TCCCT
75181 TAAGTGAGGC
Statistics
Matches: 98, Mismatches: 21, Indels: 7
0.78 0.17 0.06
Matches are distributed among these distances:
58 46 0.47
59 52 0.53
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.28
Consensus pattern (58 bp):
TCCCTCAGGTGGGCATCGCTGATTCGAAGTGTTGTGAATCAAGCAAAGGAAAAGTTCA
Found at i:75327 original size:39 final size:39
Alignment explanation
Indices: 75208--75614 Score: 533
Period size: 39 Copynumber: 10.6 Consensus size: 39
75198 GTTTTAAGAA
* * * *
75208 AAACAATCTCAAGGGAGAT-AAATCTTATGTTTTGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* *
75246 AAACTATCTCAAGCGAGAT-AAATCTTCCGTTTCAAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* * * * *
75284 AAACTATCTTC-AGCAATATCAAATCTTCTGTTCCGAGTA
1 AAACTATC-TCAAGCGAGATAAAATCTTCTGTTTCGAGTG
75323 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* *
75362 AAACTATCTCAAGCGATAT-AAATCTTTTGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* * **
75400 AAACTATCTAAAGCGAGATAAAATCTTTTGTTTATAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* *
75439 AAACTATATCAAACGAGATAAATAT-TT-TGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAA-ATCTTCTGTTTCGAGTG
75477 AAACTATCTCAAGCGAGAT-AAATCTTCTGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* *
75515 AAACTATCTTAAGCGAGATAAAATCTTCTTTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
*
75554 AAACTATCTCAAGCGAGATAAAATCTTCT-TCTTCCAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGT-TTCGAGTG
75593 AAACTATCTCAAGCGAGATAAA
1 AAACTATCTCAAGCGAGATAAA
75615 CAAGATTTCA
Statistics
Matches: 326, Mismatches: 34, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
36 2 0.01
37 4 0.01
38 139 0.43
39 179 0.55
40 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (39 bp):
AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
Found at i:75385 original size:77 final size:77
Alignment explanation
Indices: 75208--75614 Score: 543
Period size: 77 Copynumber: 5.3 Consensus size: 77
75198 GTTTTAAGAA
* * * *
75208 AAACAATCTCAAGGGAGATAAATCTTATGTTTTGAGTGAAACTATCTCAAGCGAGAT-AAATCTT
1 AAACTATCTCAAGCGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTT
* *
75272 CCGTTTCAAGTG
66 CTGTTTCGAGTG
* * * *
75284 AAACTATCTTC-AGCAATATCAAATCTTCTGTTCCGAGTAAAACTATCTCAAGCGAGATAAAATC
1 AAACTATC-TCAAGCGAGAT-AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATC
75348 TTCTGTTTCGAGTG
64 TTCTGTTTCGAGTG
* * *
75362 AAACTATCTCAAGCGATATAAATCTTTTGTTTCGAGTGAAACTATCTAAAGCGAGATAAAATCTT
1 AAACTATCTCAAGCGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTT
* **
75427 TTGTTTATAGTG
66 CTGTTTCGAGTG
* * * *
75439 AAACTATATCAAACGAGATAAATATTTTGTTTCGAGTGAAACTATCTCAAGCGAGAT-AAATCTT
1 AAACTATCTCAAGCGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTT
75503 CTGTTTCGAGTG
66 CTGTTTCGAGTG
* *
75515 AAACTATCTTAAGCGAGATAAAATCTTCTTTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCT
1 AAACTATCTCAAGCGAGAT-AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCT
*
75580 TCT-TCTTCCAGTG
65 TCTGT-TTCGAGTG
75593 AAACTATCTCAAGCGAGATAAA
1 AAACTATCTCAAGCGAGATAAA
75615 CAAGATTTCA
Statistics
Matches: 290, Mismatches: 34, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
76 44 0.15
77 180 0.62
78 66 0.23
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (77 bp):
AAACTATCTCAAGCGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTT
CTGTTTCGAGTG
Found at i:77729 original size:29 final size:29
Alignment explanation
Indices: 77696--77769 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
77686 TGATATGAAG
77696 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
77725 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
77754 TGACATGAG-TACATGA
1 TGACATGAGCTACATGA
77770 ACATATGAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.16
29 38 0.84
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (29 bp):
TGACATGAGCTACATGATCACAAGAGAAA
Found at i:77872 original size:15 final size:15
Alignment explanation
Indices: 77854--77886 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
77844 GAGGGTATAA
77854 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
77869 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
77884 TAG
1 TAG
77887 GAGTCCTACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.21, G:0.33, T:0.30
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:84830 original size:60 final size:60
Alignment explanation
Indices: 84688--84830 Score: 151
Period size: 60 Copynumber: 2.4 Consensus size: 60
84678 TAGTGTAAAA
* * * * * * *
84688 TACACAAATGGTCACTTAATTAAAGGATATTATTTTGTTGAGTTCCCTAACTATTAAAAGT
1 TACA-AAATGGTCACTCAACTATAGGATAATATTTTATTGAGTCCCCCAACTATTAAAAGT
* * * * * * *
84749 TATAAAATGATCTCCCGACTATAGGGTAATATTTTATTGAGTCCCCCGACTATTAAAAGT
1 TACAAAATGGTCACTCAACTATAGGATAATATTTTATTGAGTCCCCCAACTATTAAAAGT
84809 TACAAAATGGTCACTCAACTAT
1 TACAAAATGGTCACTCAACTAT
84831 TCATATATTC
Statistics
Matches: 63, Mismatches: 19, Indels: 1
0.76 0.23 0.01
Matches are distributed among these distances:
60 60 0.95
61 3 0.05
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (60 bp):
TACAAAATGGTCACTCAACTATAGGATAATATTTTATTGAGTCCCCCAACTATTAAAAGT
Done.