Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009115.1 Hibiscus syriacus cultivar Beakdansim tig00112598_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: 58023
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Found at i:4579 original size:18 final size:19
Alignment explanation
Indices: 4551--4587 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
4541 AGATGGCAAT
*
4551 CATTCTTTACATTTTTTTA
1 CATTCTTTACATTTATTTA
4570 CATT-TTTACATTTATTTA
1 CATTCTTTACATTTATTTA
4588 TTTCATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (19 bp):
CATTCTTTACATTTATTTA
Found at i:7541 original size:15 final size:12
Alignment explanation
Indices: 7505--7533 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
7495 ATATGCATAC
7505 CGAACTACTGTT
1 CGAACTACTGTT
7517 CGAACTACTGTT
1 CGAACTACTGTT
7529 CGAAC
1 CGAAC
7534 ATCTACTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (12 bp):
CGAACTACTGTT
Found at i:7998 original size:18 final size:18
Alignment explanation
Indices: 7975--8033 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
7965 ATGCTTGAAG
7975 AAAAAAAAAGAAAAAAGA
1 AAAAAAAAAGAAAAAAGA
**
7993 AAAAAATGAGAAAAAAG-
1 AAAAAAAAAGAAAAAAGA
*
8010 AAAGAAAAAGAAAAGAAGA
1 AAAAAAAAAGAAAA-AAGA
8029 AAAAA
1 AAAAA
8034 TAGGGGGTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
17 11 0.33
18 18 0.55
19 4 0.12
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (18 bp):
AAAAAAAAAGAAAAAAGA
Found at i:8012 original size:25 final size:25
Alignment explanation
Indices: 7972--8033 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
7962 ATTATGCTTG
*
7972 AAGAAAAAAAAAGAAA-AAAGAAAAA
1 AAGAAGAAAAAAGAAAGAAA-AAAAA
*
7997 AATG-AGAAAAAAGAAAGAAAAAGAA
1 AA-GAAGAAAAAAGAAAGAAAAAAAA
8022 AAGAAGAAAAAA
1 AAGAAGAAAAAA
8034 TAGGGGGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 1 0.03
25 27 0.84
26 4 0.12
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (25 bp):
AAGAAGAAAAAAGAAAGAAAAAAAA
Found at i:8015 original size:11 final size:10
Alignment explanation
Indices: 7972--8033 Score: 58
Period size: 11 Copynumber: 6.1 Consensus size: 10
7962 ATTATGCTTG
7972 AAGAAAAAAA
1 AAGAAAAAAA
7982 AAG---AAAA
1 AAGAAAAAAA
7989 AAGAAAAAAA
1 AAGAAAAAAA
*
7999 TGAGAAAAAAGA
1 -AAGAAAAAA-A
8011 AAGAAAAAGAA
1 AAGAAAAA-AA
8022 AAGAAGAAAAA
1 AAGAA-AAAAA
8033 A
1 A
8034 TAGGGGGTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
7 7 0.16
10 7 0.16
11 24 0.56
12 5 0.12
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:9469 original size:115 final size:114
Alignment explanation
Indices: 9297--9522 Score: 391
Period size: 115 Copynumber: 2.0 Consensus size: 114
9287 ATTAATTGAA
9297 GAAAGTGCCATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTG
1 GAAAGTGCCATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTG
* * *
9362 AGTTATCTGATCTGGTTTGGTATG-AACCCCAAAAACCAATCATTGGATTT
66 AGTTATATGATCTGGTTCGGTA-GAAACCAC-AAAACCAATCATTGGATTT
9412 GAAAGTGCCATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTG
1 GAAAGTGCCATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTG
*
9477 AGTTATATGATCTGGTTCGGTAGAAACCACAGAACCAATCATTGGA
66 AGTTATATGATCTGGTTCGGTAGAAACCACAAAACCAATCATTGGA
9523 ATTAAAAGAT
Statistics
Matches: 106, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
114 16 0.15
115 90 0.85
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (114 bp):
GAAAGTGCCATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTG
AGTTATATGATCTGGTTCGGTAGAAACCACAAAACCAATCATTGGATTT
Found at i:10388 original size:113 final size:114
Alignment explanation
Indices: 10254--10545 Score: 396
Period size: 113 Copynumber: 2.6 Consensus size: 114
10244 CAGCTTTTCC
* * * **
10254 AGAAGAAGTTCACAATGAGAAGAATTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACATTTTGCTTAAATTCATCATTTGATGGATCA
* * *
10319 GCATTGCCAGTTCGAGTTCATAATAAGAAGAA-C-TCATCTGAAGAAGGA
66 ACATTGCCAGGTAGAGTTCATAATAAGAAGAACCGTCATCTGAAGAA-GA
* * *
10367 AGAAGAAGTTCATAATGAGAAGAATTTGCTCAACATTTTGTTTAAATTCATCATTTGATGGATTA
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACATTTTGCTTAAATTCATCATTTGATGGATCA
*
10432 ACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGA
66 ACATTGCCAGGTAGAGTTCATAATAAGAAGAAC-CGTCATCTGAAGAAGA
* * *
10482 AG-A-AA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACATTTTGCTTAAATTCATCATTTGATGGATCA
10544 AC
66 AC
10546 TTTTCAAGAA
Statistics
Matches: 158, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
112 53 0.34
113 87 0.55
114 1 0.01
115 5 0.03
116 12 0.08
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.30
Consensus pattern (114 bp):
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACATTTTGCTTAAATTCATCATTTGATGGATCA
ACATTGCCAGGTAGAGTTCATAATAAGAAGAACCGTCATCTGAAGAAGA
Found at i:10558 original size:73 final size:74
Alignment explanation
Indices: 10478--10619 Score: 196
Period size: 74 Copynumber: 1.9 Consensus size: 74
10468 TCATCTGAAG
* * **
10478 AAGAAGAAATTCATAATGAGAAGAATTTGTTC-AACCTTTTGCTCAAATCCATCATTTGATGGAT
1 AAGAAGAAATTCACAATGAGAAGAACTTGTTCAAACCTTTTGCTCAAATCCATCATTCAATGGAT
10542 CAACTTTTC
66 CAACTTTTC
* * ** *
10551 AAGAAGAATTTCACAATGAGAAGAACTTGTTCAAACTTTTTGCTTGAATTCATCATTCAATGGAT
1 AAGAAGAAATTCACAATGAGAAGAACTTGTTCAAACCTTTTGCTCAAATCCATCATTCAATGGAT
10616 CAAC
66 CAAC
10620 ATTACCAGTT
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
73 29 0.49
74 30 0.51
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (74 bp):
AAGAAGAAATTCACAATGAGAAGAACTTGTTCAAACCTTTTGCTCAAATCCATCATTCAATGGAT
CAACTTTTC
Found at i:10696 original size:187 final size:184
Alignment explanation
Indices: 10366--10764 Score: 498
Period size: 187 Copynumber: 2.1 Consensus size: 184
10356 CTGAAGAAGG
* * * ** *
10366 AAGAAGAAGTTCATAATGAGAAGAATTTGCTCAACATTTTGTTTAAATTCATCATTTGATGGATT
1 AAGAAGAAGTTCACAATGAGAAGAACTTGCTCAACATTTTGCTTAAATTCATCATTCAATGGATC
* *
10431 AACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAGAAATTCATAATG
66 AACATTACCAGGTAGAGTTCATAATAAGAAGAAC-CGTCATCTGAAGAAGAAGAAATTCATAATG
*
10496 AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAACTTTTC
130 AGAAGAATTTGTTCAACCTTTTACTCAAATCCATCATTTGATGGATCAACTTTTC
* * * *
10551 AAGAAGAATTTCACAATGAGAAGAACTTGTTCAAACTTTTTGCTTGAATTCATCATTCAATGGAT
1 AAGAAGAAGTTCACAATGAGAAGAACTTGCTC-AACATTTTGCTTAAATTCATCATTCAATGGAT
* *
10616 CAACATTACCAGTTCGAGTTCATAATAAGAAGAA-C-TCATCTGAAGAAGGAAGAAGAAGTTCAT
65 CAACATTACCAGGTAGAGTTCATAATAAGAAGAACCGTCATCTGAAGAA-GAAG-A-AA-TTCAT
* * * * **
10679 AATGAGAAGAATTTGTTCAACCTTTTATTTAAATTCATCATTTGATGGATTAACATTGCC
126 AATGAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCATTTGATGGATCAAC-TTTTC
* * *
10739 AGGTAG-AGTTCATAATGAGAAGAACT
1 AAGAAGAAGTTCACAATGAGAAGAACT
10765 CGTCATCTGA
Statistics
Matches: 183, Mismatches: 25, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
183 12 0.07
184 5 0.03
185 29 0.16
186 58 0.32
187 72 0.39
188 7 0.04
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (184 bp):
AAGAAGAAGTTCACAATGAGAAGAACTTGCTCAACATTTTGCTTAAATTCATCATTCAATGGATC
AACATTACCAGGTAGAGTTCATAATAAGAAGAACCGTCATCTGAAGAAGAAGAAATTCATAATGA
GAAGAATTTGTTCAACCTTTTACTCAAATCCATCATTTGATGGATCAACTTTTC
Found at i:10759 original size:299 final size:295
Alignment explanation
Indices: 10222--10873 Score: 1126
Period size: 299 Copynumber: 2.2 Consensus size: 295
10212 TAGCAAAGAT
* *
10222 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAGAAGTTCACAATGAGAAGAATTTGTTCAA
1 TCAAATCCATCATTTGATGGATCAACTTTTCCAGAAGAAGTTCACAATGAGAAGAACTTGTTCAA
* *
10287 CTTTTTGCTTGAATTCATCATTCAATGGATCAGCATTGCCAGTTCGAGTTCATAATAAGAAGAAC
66 CTTTTTGCTTGAATTCATCATTCAATGGATCAACATTACCAGTTCGAGTTCATAATAAGAAGAAC
*
10352 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGCTCAACATTTTGTTTAAATTCA
131 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGCTCAACATTTTATTTAAATTCA
10417 TCATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGA
196 TCATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCT---GAAGA
*
10482 AGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
258 AGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTAC
* *
10520 TCAAATCCATCATTTGATGGATCAACTTTTCAAGAAGAATTTCACAATGAGAAGAACTTGTTCAA
1 TCAAATCCATCATTTGATGGATCAACTTTTCCAGAAGAAGTTCACAATGAGAAGAACTTGTTC-A
10585 ACTTTTTGCTTGAATTCATCATTCAATGGATCAACATTACCAGTTCGAGTTCATAATAAGAAGAA
65 ACTTTTTGCTTGAATTCATCATTCAATGGATCAACATTACCAGTTCGAGTTCATAATAAGAAGAA
* *
10650 CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTTAAATTC
130 CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGCTCAACATTTTATTTAAATTC
*
10715 ATCATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAATAAG
195 ATCATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
10780 AAATTCATAATGAGAAGAATTTGTTCAACCTTTTAC
260 AAATTCATAATGAGAAGAATTTGTTCAACCTTTTAC
* * *
10816 TCAAATCCATCACTTGATGGATCACCTTTTCCAG-AGAAAGTTCATAATGAGAAGAACT
1 TCAAATCCATCATTTGATGGATCAACTTTTCCAGAAG-AAGTTCACAATGAGAAGAACT
10874 CATCTGAAGA
Statistics
Matches: 336, Mismatches: 16, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
295 2 0.01
296 91 0.27
298 59 0.18
299 184 0.55
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.31
Consensus pattern (295 bp):
TCAAATCCATCATTTGATGGATCAACTTTTCCAGAAGAAGTTCACAATGAGAAGAACTTGTTCAA
CTTTTTGCTTGAATTCATCATTCAATGGATCAACATTACCAGTTCGAGTTCATAATAAGAAGAAC
TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGCTCAACATTTTATTTAAATTCA
TCATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGA
AATTCATAATGAGAAGAATTTGTTCAACCTTTTAC
Found at i:10937 original size:109 final size:110
Alignment explanation
Indices: 10551--11047 Score: 428
Period size: 109 Copynumber: 4.4 Consensus size: 110
10541 TCAACTTTTC
* * * * * *
10551 AAGAAGAATTTCACAATGAGAAGAACTTGTTCAAACTTTTTGCTTGAATTCATCA-TTCAATGGA
1 AAGAAGAAGTTCATAATGAGAAGAACTTGTTC-AACCTTTTACTTAAATTCATCACTT-GATGGA
* **** *
10615 TCAACATTACCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGG
64 TCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT--AGAA-G
* * * *
10665 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTTAAATTCATCATTTGATGGATT
1 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTTAAATTCATCACTTGATGGATC
* * * ***
10730 AACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTC-ATCTG
66 AACATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTAGAAG
* * * * *
10774 AATAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCACTTGATGGATC
1 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTTAAATTCATCACTTGATGGATC
* *
10839 ACCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT-GAAG
66 AACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAGAAG
* * * *
10883 AAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACCTTTTGCAT-AATTCTATCACAGAAAGAGA
1 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTTAAATTC-ATCAC---------
* * *
10947 TAGATTAGCATCAACCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
56 TTGA-T-GGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT--AGAAG
* *
11006 AAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTA
1 -AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTA
11048 AAGGACTCTA
Statistics
Matches: 315, Mismatches: 48, Indels: 30
0.80 0.12 0.08
Matches are distributed among these distances:
108 4 0.01
109 133 0.42
110 2 0.01
113 57 0.18
114 31 0.10
118 3 0.01
119 1 0.00
120 42 0.13
123 4 0.01
124 38 0.12
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (110 bp):
AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTTAAATTCATCACTTGATGGATC
AACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAGAAG
Found at i:11060 original size:124 final size:121
Alignment explanation
Indices: 10843--11135 Score: 371
Period size: 124 Copynumber: 2.4 Consensus size: 121
10833 TGGATCACCT
10843 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT---GAAG-AAGAAGAAGTTCACAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCACAATGAGA
* ** * * * * *
10904 AGAGCTTGTTCAACCTTTTGCATAATTCTATCACAGAAAGAGATAGATTAGCATCAACC
66 AGAGCTTATTCAACCTTTTAAAGAACTCTATCACAGAAAGAAATAG-GT--CAACAACC
*
10963 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCACAATGAGA
* * *
11028 AGAGCTTATTCAACCTTTTAAAGGACTCTATCACAGAAGGAAATAGGTCAACATCC
66 AGAGCTTATTCAACCTTTTAAAGAACTCTATCACAGAAAGAAATAGGTCAACAACC
** * *
11084 TCCCCAGCGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-AGAGAAGAA
1 TTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAA
11136 TTTATTCAAC
Statistics
Matches: 152, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
120 36 0.24
121 19 0.12
122 34 0.22
123 5 0.03
124 58 0.38
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (121 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCACAATGAGA
AGAGCTTATTCAACCTTTTAAAGAACTCTATCACAGAAAGAAATAGGTCAACAACC
Found at i:11283 original size:3 final size:3
Alignment explanation
Indices: 11277--11338 Score: 56
Period size: 3 Copynumber: 21.0 Consensus size: 3
11267 CTCCATTTTC
* * *
11277 TAT TAT TATT TAT TTT TAT TTT TAT T-T TAT TAT TAT T-T TAT TTT
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
11321 TAT TAA AAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT
11339 AAACGGGCCA
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
2 4 0.09
3 39 0.85
4 3 0.07
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:11301 original size:16 final size:16
Alignment explanation
Indices: 11271--11319 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
11261 TTTTTTCTCC
*
11271 ATTTTCTATTATTATTT
1 ATTTT-TATTTTTATTT
11288 ATTTTTATTTTTATTTT
1 ATTTTTATTTTTA-TTT
*
11305 ATTATTA-TTTTATTT
1 ATTTTTATTTTTATTT
11320 TTATTAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 3 0.10
16 12 0.41
17 14 0.48
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (16 bp):
ATTTTTATTTTTATTT
Found at i:11305 original size:17 final size:17
Alignment explanation
Indices: 11271--11320 Score: 59
Period size: 16 Copynumber: 3.0 Consensus size: 17
11261 TTTTTTCTCC
*
11271 ATTTTCTATTATTA-TTT
1 ATTTT-TATTTTTATTTT
11288 ATTTTTATTTTTATTTT
1 ATTTTTATTTTTATTTT
*
11305 ATTATTA-TTTTATTTT
1 ATTTTTATTTTTATTTT
11321 TATTAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
16 16 0.53
17 14 0.47
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTTTTATTTTTATTTT
Found at i:11306 original size:11 final size:11
Alignment explanation
Indices: 11279--11324 Score: 65
Period size: 11 Copynumber: 4.0 Consensus size: 11
11269 CCATTTTCTA
11279 TTATTATTTATTT
1 TTATT-TTTA-TT
11292 TTATTTTTATT
1 TTATTTTTATT
*
11303 TTATTATTATT
1 TTATTTTTATT
11314 TTATTTTTATT
1 TTATTTTTATT
11325 AAAATTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 22 0.71
12 4 0.13
13 5 0.16
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (11 bp):
TTATTTTTATT
Found at i:11321 original size:17 final size:17
Alignment explanation
Indices: 11279--11325 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
11269 CCATTTTCTA
*
11279 TTATTATTTATTTTTATT
1 TTATT-TTTATTATTATT
11297 TT-TATTTTATTATTATT
1 TTAT-TTTTATTATTATT
11314 TTATTTTTATTA
1 TTATTTTTATTA
11326 AAATTATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 22 0.85
18 4 0.15
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (17 bp):
TTATTTTTATTATTATT
Found at i:14609 original size:29 final size:30
Alignment explanation
Indices: 14540--14611 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
14530 GGTTTTTCGA
** *
14540 AAAATAAATTACTGGAATTTGAATTAATGG
1 AAAATAAATTACAAGAATTTAAATTAATGG
*
14570 AAAATAAATTACAAGAATTTAAATT-CTGG
1 AAAATAAATTACAAGAATTTAAATTAATGG
14599 AAAATAAATTACA
1 AAAATAAATTACA
14612 TTTCTGGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
29 16 0.42
30 22 0.58
ACGTcount: A:0.53, C:0.06, G:0.11, T:0.31
Consensus pattern (30 bp):
AAAATAAATTACAAGAATTTAAATTAATGG
Found at i:14616 original size:20 final size:20
Alignment explanation
Indices: 14593--14642 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
14583 AGAATTTAAA
14593 TTCTGGAAAATAAATTACAT
1 TTCTGGAAAATAAATTACAT
*
14613 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATAAATTACAT
14633 TTCTGGAAAA
1 TTCTGGAAAA
14643 CATCTGAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (20 bp):
TTCTGGAAAATAAATTACAT
Found at i:15011 original size:28 final size:27
Alignment explanation
Indices: 14971--15061 Score: 89
Period size: 30 Copynumber: 3.3 Consensus size: 27
14961 CTTTACTAAA
14971 ATATTATTTAAATATATAAATAATATTAT
1 ATATTA-TTAAATATATAAA-AATATTAT
15000 -TCATTATTAAATATATAAAAAATTTATTAT
1 AT-ATTATTAAATATAT-AAAAA--TATTAT
*
15030 ATATTATTAAA-ATA-AAAAATATAAT
1 ATATTATTAAATATATAAAAATATTAT
*
15055 ATCTTAT
1 ATATTAT
15062 ATTATTATAA
Statistics
Matches: 55, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
25 11 0.20
27 5 0.09
28 13 0.24
29 10 0.18
30 15 0.27
31 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
ATATTATTAAATATATAAAAATATTAT
Found at i:15028 original size:30 final size:28
Alignment explanation
Indices: 14971--15061 Score: 91
Period size: 28 Copynumber: 3.2 Consensus size: 28
14961 CTTTACTAAA
*
14971 ATATTATTTAAATATATAAATAATATTAT
1 ATATTA-TTAAATATATAAAAAATATTAT
15000 -TCATTATTAAATATATAAAAAATTTATTAT
1 AT-ATTATTAAATATATAAAAAA--TATTAT
*
15030 ATATTATT-AA-A-ATAAAAAATATAAT
1 ATATTATTAAATATATAAAAAATATTAT
*
15055 ATCTTAT
1 ATATTAT
15062 ATTATTATAA
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
25 11 0.20
27 8 0.15
28 17 0.31
29 6 0.11
30 12 0.22
31 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (28 bp):
ATATTATTAAATATATAAAAAATATTAT
Found at i:15153 original size:23 final size:23
Alignment explanation
Indices: 15099--15148 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
15089 TTAAACTAAA
15099 AAATA-TAATATAATATTATTAT
1 AAATATTAATATAATATTATTAT
*
15121 AAATATTAATA-AATA-TATTTT
1 AAATATTAATATAATATTATTAT
15142 AAATATT
1 AAATATT
15149 TTAATATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 12 0.46
22 9 0.35
23 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
AAATATTAATATAATATTATTAT
Found at i:20044 original size:2 final size:2
Alignment explanation
Indices: 20037--20065 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20027 GAATTGGGAA
20037 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20066 CACAAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32924 original size:3 final size:3
Alignment explanation
Indices: 32918--33003 Score: 145
Period size: 3 Copynumber: 28.7 Consensus size: 3
32908 TTTTTATCCA
*
32918 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
32966 TAT TAT TAT TAT TAT CAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
33004 AATATATATT
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:34438 original size:20 final size:21
Alignment explanation
Indices: 34392--34438 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
34382 CTGCTTTTAA
*
34392 ATATATCGTTCTAATTGTATT
1 ATATATTGTTCTAATTGTATT
* *
34413 -TTTATTGTTTTAATTGT-TT
1 ATATATTGTTCTAATTGTATT
34432 ATATATT
1 ATATATT
34439 TAAATATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.62
Consensus pattern (21 bp):
ATATATTGTTCTAATTGTATT
Found at i:34516 original size:23 final size:24
Alignment explanation
Indices: 34482--34527 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
34472 TATATATGAT
34482 AAATAATAA-TTT-ATATTTTTTA
1 AAATAATAATTTTAATATTTTTTA
*
34504 AAATAAATTATTTTAATATTTTTT
1 AAAT-AATAATTTTAATATTTTTT
34528 CAATATCGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 4 0.20
24 3 0.15
25 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
AAATAATAATTTTAATATTTTTTA
Found at i:35190 original size:18 final size:17
Alignment explanation
Indices: 35167--35218 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
35157 TTCTTTTCAA
35167 ATTTTTTATTTATTTAT
1 ATTTTTTATTTATTTAT
*
35184 -TATTTTTATAATATTTAT
1 AT-TTTTTAT-TTATTTAT
*
35202 ATGTTTTATTTTATTTA
1 ATTTTTTA-TTTATTTA
35219 CAAGTATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
16 1 0.04
17 7 0.25
18 18 0.64
19 2 0.07
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (17 bp):
ATTTTTTATTTATTTAT
Found at i:35239 original size:13 final size:15
Alignment explanation
Indices: 35208--35244 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
35198 TTATATGTTT
35208 TATTTTATTTACAAG
1 TATTTTATTTACAAG
35223 TATTTTATTT-C-AG
1 TATTTTATTTACAAG
35236 TA-TTTATTT
1 TATTTTATTT
35245 TTATGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.62
Consensus pattern (15 bp):
TATTTTATTTACAAG
Found at i:46241 original size:18 final size:17
Alignment explanation
Indices: 46203--46247 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
46193 CTATTTCAAG
*
46203 TTCAATTTA-TTTGAGA
1 TTCAATTTATTTTGAAA
46219 TTCAATTTATTTTGGAAA
1 TTCAATTTATTTT-GAAA
46237 TTCAATTTATT
1 TTCAATTTATT
46248 CTTTTCTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 9 0.35
17 3 0.12
18 14 0.54
ACGTcount: A:0.31, C:0.07, G:0.09, T:0.53
Consensus pattern (17 bp):
TTCAATTTATTTTGAAA
Found at i:47129 original size:84 final size:84
Alignment explanation
Indices: 46988--47592 Score: 1128
Period size: 84 Copynumber: 7.2 Consensus size: 84
46978 TGTGATATCT
46988 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
1 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
47053 GTTATCTGATCTGATTTGG
66 GTTATCTGATCTGATTTGG
47072 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
1 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
47137 GTTATCTGATCTGATTTGG
66 GTTATCTGATCTGATTTGG
47156 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
1 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
*
47221 GTTATTTGATCTGATTTGG
66 GTTATCTGATCTGATTTGG
47240 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
1 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
47305 GTTATCTGATCTGATTTGG
66 GTTATCTGATCTGATTTGG
47324 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
1 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
47389 GTTATCTGATCTGATTTGG
66 GTTATCTGATCTGATTTGG
47408 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
1 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
47473 GTTATCTGATCTGATTTGG
66 GTTATCTGATCTGATTTGG
47492 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTC-A-AGCATCTTCTGGAAGTGTTCTTTGA
1 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
* *
47555 GTTATCTAAT-TG-GTTGG
66 GTTATCTGATCTGATTTGG
*
47572 ACAGAACCAATCGTTGGAATT
1 -CAGAACCAATCATT-GAATT
47593 AAAGATGAAC
Statistics
Matches: 514, Mismatches: 5, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
80 4 0.01
81 15 0.03
82 39 0.08
83 1 0.00
84 455 0.89
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (84 bp):
CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGA
GTTATCTGATCTGATTTGG
Found at i:48534 original size:112 final size:112
Alignment explanation
Indices: 48294--48832 Score: 854
Period size: 112 Copynumber: 4.9 Consensus size: 112
48284 TCAAATCTTC
* *
48294 TTGATGGATCATTCATTGCCAGATAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 TTGATGGATCA-ACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
48358 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
65 AAGTTCATAATGAGAAGAACTTGTTCAAC-TTTTGTTTAAATTCATCAT
48407 TTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
48472 AGTTCATAATGAGAAGAACTTGTTCAACTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTGTTTAAATTCATCAT
48519 TTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
48584 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAAC-TTTTGTTTAAATTCATCAT
*
48632 TTGATGGATCAACATTGCCAGAG-A-----A-AGTGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * *
48690 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCAC
66 AGTTCATAATGAGAAGAACTTGTTCAA-CTTTTGTTTAAATTCATCAT
* *
48738 TTGAT---T--A-TTTGTCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* *
48797 AGTTCATAATGAGAAGAGCTTGTTCAACCTTTGTTT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTGTTT
48833 GATACTATCA
Statistics
Matches: 404, Mismatches: 12, Indels: 27
0.91 0.03 0.06
Matches are distributed among these distances:
100 8 0.02
101 2 0.00
103 1 0.00
106 89 0.22
107 59 0.15
112 125 0.31
113 120 0.30
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.29
Consensus pattern (112 bp):
TTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAACTTGTTCAACTTTTGTTTAAATTCATCAT
Found at i:48688 original size:225 final size:222
Alignment explanation
Indices: 48293--48832 Score: 861
Period size: 225 Copynumber: 2.5 Consensus size: 222
48283 TTCAAATCTT
* *
48293 CTTGATGGATCATTCATTGCCAGATAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
1 CTTGATGGATCA-ACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
48357 GAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGATCAACAT
65 GAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGATCAACAT
48422 TGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
130 TGCCAGAGAA-G---ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
48487 GAACTTGTTCAA-CTTTTGTTTAAATTCATCA
191 GAACTTGTTCAACCTTTTGTTTAAATTCATCA
*
48518 TTTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 CTTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
48583 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGATCAACATT
66 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGATCAACATT
* *
48648 GCCAGAG-A-A-AGTGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATT
131 GCCAGAGAAGATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
*
48710 TGTTCAACCTTTTGTTTGAATTCATCA
196 TGTTCAACCTTTTGTTTAAATTCATCA
* *
48737 CTTGAT---T--A-TTTGTCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 CTTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
* *
48796 AAGTTCATAATGAGAAGAGCTTGTTCAAC-CTTTGTTT
66 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTT
48833 GATACTATCA
Statistics
Matches: 302, Mismatches: 11, Indels: 17
0.92 0.03 0.05
Matches are distributed among these distances:
212 7 0.02
213 77 0.25
214 1 0.00
216 1 0.00
218 58 0.19
219 24 0.08
224 13 0.04
225 121 0.40
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.29
Consensus pattern (222 bp):
CTTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGATCAACATT
GCCAGAGAAGATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
TGTTCAACCTTTTGTTTAAATTCATCA
Found at i:49153 original size:3 final size:3
Alignment explanation
Indices: 49147--49212 Score: 109
Period size: 3 Copynumber: 22.7 Consensus size: 3
49137 TTTTTATCCA
49147 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
49193 TAT TAT CAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
49213 AATATATATT
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 4 0.07
3 55 0.93
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:49180 original size:20 final size:20
Alignment explanation
Indices: 49147--49212 Score: 105
Period size: 20 Copynumber: 3.2 Consensus size: 20
49137 TTTTTATCCA
49147 TATTATTATTATTATTATTAT
1 TATTATT-TTATTATTATTAT
49168 TATTATTTTATTATTATTAT
1 TATTATTTTATTATTATTAT
* *
49188 TATTATATTATCATTATTAT
1 TATTATTTTATTATTATTAT
49208 TATTA
1 TATTA
49213 AATATATATT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
20 36 0.84
21 7 0.16
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (20 bp):
TATTATTTTATTATTATTAT
Found at i:49223 original size:20 final size:18
Alignment explanation
Indices: 49146--49212 Score: 86
Period size: 17 Copynumber: 3.8 Consensus size: 18
49136 TTTTTTATCC
49146 ATATTATTATTATTATTA
1 ATATTATTATTATTATTA
*
49164 TTATTATTATT-TTATTA
1 ATATTATTATTATTATTA
*
49181 TTATTATTATTA-TATT-
1 ATATTATTATTATTATTA
49197 ATCATTATTATTATTA
1 AT-ATTATTATTATTA
49213 AATATATATT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
16 1 0.02
17 31 0.70
18 12 0.27
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (18 bp):
ATATTATTATTATTATTA
Found at i:50634 original size:20 final size:21
Alignment explanation
Indices: 50588--50634 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
50578 CTGCTTTTAA
*
50588 ATATATCGTTCTAATTGTATT
1 ATATATTGTTCTAATTGTATT
* *
50609 -TTTATTGTTTTAATTGT-TT
1 ATATATTGTTCTAATTGTATT
50628 ATATATT
1 ATATATT
50635 TAAATATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.62
Consensus pattern (21 bp):
ATATATTGTTCTAATTGTATT
Found at i:51895 original size:13 final size:13
Alignment explanation
Indices: 51877--51907 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
51867 TATCACCCAC
51877 CTACAAAGAAACA
1 CTACAAAGAAACA
*
51890 CTACAAAGAAATA
1 CTACAAAGAAACA
51903 CTACA
1 CTACA
51908 CCACTGCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.58, C:0.23, G:0.06, T:0.13
Consensus pattern (13 bp):
CTACAAAGAAACA
Done.