Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005819.1 Hibiscus syriacus cultivar Beakdansim tig00013636_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: 637054
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:289657 original size:24 final size:24
Alignment explanation
Indices: 289604--289659 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
289594 TCCAGATCAG
* * *
289604 AAATCAGAACAGAATTCAGGTCAT
1 AAATCAGAACAAAATTCAAGTCAA
**
289628 GTATCAGAACAAAATTCAAGTCAA
1 AAATCAGAACAAAATTCAAGTCAA
289652 AAATCAGA
1 AAATCAGA
289660 TAAAATATTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.20
Consensus pattern (24 bp):
AAATCAGAACAAAATTCAAGTCAA
Found at i:295310 original size:21 final size:22
Alignment explanation
Indices: 295263--295323 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
295253 TATAGTAAAA
295263 GCATAAAATAAAAATAATATGT
1 GCATAAAATAAAAATAATATGT
295285 GCATAAAATAAAGACAT-A-AT-T
1 GCATAAAATAAA-A-ATAATATGT
295306 GCATAAAAT-AAAATAATA
1 GCATAAAATAAAAATAATA
295324 GTGACTAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
18 2 0.06
19 2 0.06
20 3 0.09
21 10 0.29
22 14 0.40
23 2 0.06
24 2 0.06
ACGTcount: A:0.61, C:0.07, G:0.08, T:0.25
Consensus pattern (22 bp):
GCATAAAATAAAAATAATATGT
Found at i:297774 original size:98 final size:98
Alignment explanation
Indices: 297603--297790 Score: 304
Period size: 98 Copynumber: 1.9 Consensus size: 98
297593 CGTTGCTCAA
* * * * *
297603 GGGGTAACTTGCAAACTTGGGACGAATACTGACAATATTTCTTTTTTTGCACAAATTGAGTCATA
1 GGGGTAACTTCCAAAATTGGGACGAATACTGACAATATTCCCTTTTTGGCACAAATTGAGTCATA
297668 ACAAATAAGATACTTTGGTATACTTTTACCAGT
66 ACAAATAAGATACTTTGGTATACTTTTACCAGT
* *
297701 GGGGTAACTTCCAAAATTGGGACGAATACTGACAATATTCCCTTTTTGGCATAGATTGAGTCATA
1 GGGGTAACTTCCAAAATTGGGACGAATACTGACAATATTCCCTTTTTGGCACAAATTGAGTCATA
*
297766 ACAGATAAGATACTTTGGTATACTT
66 ACAAATAAGATACTTTGGTATACTT
297791 ATTAAAAATG
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
98 82 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (98 bp):
GGGGTAACTTCCAAAATTGGGACGAATACTGACAATATTCCCTTTTTGGCACAAATTGAGTCATA
ACAAATAAGATACTTTGGTATACTTTTACCAGT
Found at i:298112 original size:33 final size:32
Alignment explanation
Indices: 298042--298112 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 32
298032 ATTTAAACTG
* *
298042 TAAAATAATTCATATATAAAATACAAGTTCAA
1 TAAAATCATTCATATATAAAATACAAATTCAA
*
298074 -AAAATCATTTATATATTAAGAATA-AAATTCAA
1 TAAAATCATTCATATA-TAA-AATACAAATTCAA
298106 TAAAATC
1 TAAAATC
298113 CAATAATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
31 13 0.39
32 10 0.30
33 10 0.30
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.32
Consensus pattern (32 bp):
TAAAATCATTCATATATAAAATACAAATTCAA
Found at i:302133 original size:17 final size:16
Alignment explanation
Indices: 302091--302138 Score: 64
Period size: 17 Copynumber: 3.1 Consensus size: 16
302081 TATAATCACA
302091 TAAAATATAAAAGAA-
1 TAAAATATAAAAGAAT
*
302106 T-AAACATAAAAGAAT
1 TAAAATATAAAAGAAT
302121 CTAAAATATAAAAGAAT
1 -TAAAATATAAAAGAAT
302138 T
1 T
302139 TGAGAATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 12 0.43
15 1 0.04
16 2 0.07
17 13 0.46
ACGTcount: A:0.67, C:0.04, G:0.06, T:0.23
Consensus pattern (16 bp):
TAAAATATAAAAGAAT
Found at i:303389 original size:39 final size:40
Alignment explanation
Indices: 303335--303426 Score: 116
Period size: 39 Copynumber: 2.4 Consensus size: 40
303325 TGGGGGAATT
303335 TAAGAGTCTCTTGGGAGTTAAAGT-GTTTTATTGTGAAAC
1 TAAGAGTCTCTTGGGAGTTAAAGTAGTTTTATTGTGAAAC
* * * * **
303374 TAAGATTCTCTTGGGAGTTAGAGTATTTTTATTTTGAATT
1 TAAGAGTCTCTTGGGAGTTAAAGTAGTTTTATTGTGAAAC
303414 TAAGAGT-TCTTGG
1 TAAGAGTCTCTTGG
303427 AAGATGGAGA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
39 28 0.62
40 17 0.38
ACGTcount: A:0.26, C:0.07, G:0.24, T:0.43
Consensus pattern (40 bp):
TAAGAGTCTCTTGGGAGTTAAAGTAGTTTTATTGTGAAAC
Found at i:306539 original size:39 final size:40
Alignment explanation
Indices: 306496--306583 Score: 94
Period size: 39 Copynumber: 2.2 Consensus size: 40
306486 TATGCATGAG
* * *
306496 GCAAATGAGCT-TATGGTAAGAACTTAC-CATGTGCACAAA
1 GCAAATGAGCTCTACGGTAAGAACTTACAC-TATACACAAA
*
306535 GCAAA-GAAG-TCTGCGGTAAGAACTTACACTATACACAAA
1 GCAAATG-AGCTCTACGGTAAGAACTTACACTATACACAAA
306574 GCAAATGAGC
1 GCAAATGAGC
306584 CTGAGATAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
38 2 0.05
39 36 0.90
40 2 0.05
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.19
Consensus pattern (40 bp):
GCAAATGAGCTCTACGGTAAGAACTTACACTATACACAAA
Found at i:306599 original size:39 final size:39
Alignment explanation
Indices: 306512--306605 Score: 93
Period size: 39 Copynumber: 2.4 Consensus size: 39
306502 GAGCTTATGG
* * * * *
306512 TAAGAACTTAC-CATGTGCACAAAGCAAAGAAGTCTGCGG
1 TAAGAACTTACAC-TATACACAAAGCAAAGAAGCCTGAGA
306551 TAAGAACTTACACTATACACAAAGCAAATG-AGCCTGAGA
1 TAAGAACTTACACTATACACAAAGCAAA-GAAGCCTGAGA
* *
306590 TAAGGACTTACCCTAT
1 TAAGAACTTACACTAT
306606 GCGTAGCATA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
39 44 0.96
40 2 0.04
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.20
Consensus pattern (39 bp):
TAAGAACTTACACTATACACAAAGCAAAGAAGCCTGAGA
Found at i:307662 original size:27 final size:27
Alignment explanation
Indices: 307629--307689 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
307619 TCAAAGCTCG
** * *
307629 GGGTATTTTGGTTTTTTTAAAGTTTAA
1 GGGTATTTCAGTTATTTTAAAGTTCAA
*
307656 GGGTATTTCAGTTATTTTAGAGTTCAA
1 GGGTATTTCAGTTATTTTAAAGTTCAA
307683 GGGTATT
1 GGGTATT
307690 ATAATCCTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.23, C:0.03, G:0.25, T:0.49
Consensus pattern (27 bp):
GGGTATTTCAGTTATTTTAAAGTTCAA
Found at i:307739 original size:18 final size:17
Alignment explanation
Indices: 307697--307740 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
307687 ATTATAATCC
307697 TTTCATTTAATCCATCT
1 TTTCATTTAATCCATCT
**
307714 TTTCCATTTAATTTAGTCT
1 TTT-CATTTAATCCA-TCT
307733 TTTCATTT
1 TTTCATTT
307741 TTAATCATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 3 0.13
18 14 0.61
19 6 0.26
ACGTcount: A:0.20, C:0.18, G:0.02, T:0.59
Consensus pattern (17 bp):
TTTCATTTAATCCATCT
Found at i:312311 original size:30 final size:30
Alignment explanation
Indices: 312233--312304 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
312223 ACTCTTCCAC
* * *
312233 AAGCTTCTAGAGAGTTCTACACTTCTCCGGA
1 AAGC-TCTAGAAAATTCTACACTTCTCCAGA
* *
312264 ATGTTCTAGAAAATTCTACACTTCTCCAGA
1 AAGCTCTAGAAAATTCTACACTTCTCCAGA
312294 AAGCTCTAGAA
1 AAGCTCTAGAA
312305 TTTTCTAGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
30 32 0.94
31 2 0.06
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (30 bp):
AAGCTCTAGAAAATTCTACACTTCTCCAGA
Found at i:316829 original size:10 final size:10
Alignment explanation
Indices: 316815--316844 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
316805 CTTTTCCACT
316815 CTCTTCCATA
1 CTCTTCCATA
*
316825 TTCTTCCATA
1 CTCTTCCATA
316835 CTCTTCCATA
1 CTCTTCCATA
316845 AGGTTCCACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.20, C:0.37, G:0.00, T:0.43
Consensus pattern (10 bp):
CTCTTCCATA
Found at i:316872 original size:30 final size:30
Alignment explanation
Indices: 316829--316885 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
316819 TCCATATTCT
* *
316829 TCCATACTCTTCCATAAGG-TTCCACACATC
1 TCCATAATATTCCA-AAGGATTCCACACATC
*
316859 TCCATAATATTCCAGAGGATTCCACAC
1 TCCATAATATTCCAAAGGATTCCACAC
316886 TCTTCCACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 3 0.13
30 20 0.87
ACGTcount: A:0.30, C:0.33, G:0.09, T:0.28
Consensus pattern (30 bp):
TCCATAATATTCCAAAGGATTCCACACATC
Found at i:321550 original size:21 final size:21
Alignment explanation
Indices: 321507--321550 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
321497 AATAATTTGT
* *
321507 TATATTTTTACTATTAAAGAA
1 TATATTTTAACTATTAAAAAA
321528 TATATTTTAAC-ATTATAAAAA
1 TATATTTTAACTATTA-AAAAA
321549 TA
1 TA
321551 AAAATCTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (21 bp):
TATATTTTAACTATTAAAAAA
Found at i:329185 original size:6 final size:6
Alignment explanation
Indices: 329174--329210 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
329164 ATTAACACCT
329174 TTTGCA TTTGCA TTTGGCA TTTGCA TTTGCA -TTGCA T
1 TTTGCA TTTGCA TTT-GCA TTTGCA TTTGCA TTTGCA T
329211 AAGCATTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.17
6 18 0.62
7 6 0.21
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.49
Consensus pattern (6 bp):
TTTGCA
Found at i:329195 original size:13 final size:12
Alignment explanation
Indices: 329174--329210 Score: 58
Period size: 13 Copynumber: 3.1 Consensus size: 12
329164 ATTAACACCT
329174 TTTGCATTTGCA
1 TTTGCATTTGCA
329186 TTTGGCATTTGCA
1 TTT-GCATTTGCA
329199 TTTGCA-TTGCA
1 TTTGCATTTGCA
329210 T
1 T
329211 AAGCATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 6 0.25
12 6 0.25
13 12 0.50
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.49
Consensus pattern (12 bp):
TTTGCATTTGCA
Found at i:333548 original size:34 final size:35
Alignment explanation
Indices: 333430--333565 Score: 175
Period size: 36 Copynumber: 3.9 Consensus size: 35
333420 GGGCAAGTCA
* * *
333430 ATCTTAAGCCTTCACTAGAGAGTGGTGAAGCAAACC
1 ATCTTAAGCCTTCACCAAAGAGTAGTGAAGC-AACC
* *
333466 ATCTTAAGCCTTCACCGAAGAGGAGTGAAGCAATCC
1 ATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAA-CC
* *
333502 ATTTTAAGCCTTCACTAAAGAGTAGTGAAGC-ACC
1 ATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAACC
*
333536 ATCTTAAGCCTTCACCGAAGAGTAGTGAAG
1 ATCTTAAGCCTTCACCAAAGAGTAGTGAAG
333566 GAAATCCATC
Statistics
Matches: 87, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
34 29 0.33
35 3 0.03
36 55 0.63
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (35 bp):
ATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAACC
Found at i:333563 original size:70 final size:72
Alignment explanation
Indices: 333433--333574 Score: 225
Period size: 70 Copynumber: 2.0 Consensus size: 72
333423 CAAGTCAATC
* * *
333433 TTAAGCCTTCACTAGAGAGTGGTGAAGCAAACCATCTTAAGCCTTCACCGAAGAGGAGTGAA-GC
1 TTAAGCCTTCACTAAAGAGTAGTGAAGC-AACCATCTTAAGCCTTCACCGAAGAGGAGTGAAGGA
333497 AATCCATT
65 AATCCATT
*
333505 TTAAGCCTTCACTAAAGAGTAGTGAAGC-ACCATCTTAAGCCTTCACCGAAGAGTAGTGAAGGAA
1 TTAAGCCTTCACTAAAGAGTAGTGAAGCAACCATCTTAAGCCTTCACCGAAGAGGAGTGAAGGAA
333569 ATCCAT
66 ATCCAT
333575 CCATAAAACC
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
70 31 0.48
71 8 0.12
72 26 0.40
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.23
Consensus pattern (72 bp):
TTAAGCCTTCACTAAAGAGTAGTGAAGCAACCATCTTAAGCCTTCACCGAAGAGGAGTGAAGGAA
ATCCATT
Found at i:333940 original size:214 final size:214
Alignment explanation
Indices: 333571--334822 Score: 1800
Period size: 214 Copynumber: 5.9 Consensus size: 214
333561 TGAAGGAAAT
* *
333571 CCATCCATAAAACCTTCGGGTAGGATGTTTTCATTGAATTTGAAAAT-AAGAAAATGATGTTTTA
1 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAATGAATTTGAAAATGAA-AAAATGATGTTTTA
* *
333635 AGATGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACAAATTATAAGTCCTTCG
65 AGATGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCCTCG
** * * *
333700 ATCCATCAATAAGTCTTTCGAGCATGATGCTTAAATTCTTCGGGTCATCTGTAAGCCTTTAGAGC
130 GGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
333765 AAGATGATAAGTCCTTCGAG
195 AAGATGATAAGTCCTTCGAG
*
333785 CCATCCATAAGACCTTCGGGTAGGATGTTTTCATTGAATTTGAAAAT-AAGAAAATGATGTTTTA
1 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAATGAATTTGAAAATGAA-AAAATGATGTTTTA
* * * *
333849 AGATGATGAAATTTTTGAAAACAAAGAATGCGAGTTTCAAAATTTCATAATTTATAAGTCCTTCA
65 AGATGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCCTCG
* * *
333914 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTTATCTGTAAGCCTTTAGATC
130 GGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
333979 AAGATGATAAGTCCTTC-AG
195 AAGATGATAAGTCCTTCGAG
* * *
333998 ACCATCCAAAAAACCTTCGGGTAGGATGTTTTTACATGAATTTGAAAATGAAAAAAATGATGTTT
1 -CCATCCATAAGACCTTCGGGTAGGATGTTTTCA-ATGAATTTGAAAATG-AAAAAATGATGTTT
* *
334063 TAAGAAGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAATTTTCACAATTTATAAGTCCCT
63 TAAGATGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCCT
* * *
334128 CGGGCTATCAGTAAGTCTTTCGAGCATGATGTTTAAATCATTCGGGTCATCTGTAAGTCTTTAGA
128 CGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGA
*
334193 GCAAGATGATAAGTCCTTCGGG
193 GCAAGATGATAAGTCCTTCGAG
* * *
334215 CCATCCATAAGACCTTCGGG-AGGGATGATTTCAAATAAATTTGAAAATG-AAAAATGATATTTT
1 CCATCCATAAGACCTTCGGGTA-GGATGTTTTC-AATGAATTTGAAAATGAAAAAATGATGTTTT
* * * *
334278 AAGAAGATGAATTTTTTGGAAACAAAGAATGCGATTTTCAAAATTTCACAATTTATGAGTCCCTC
64 AAGATGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCCTC
* *
334343 GGGCCATCAGTAAGTCTTTTGAGCATGATGTTTAAATCCTTCGGGTCATCTATAAGCCTTTAGAG
129 GGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAG
*
334408 CAAGATGATAAGTCCTTCGGG
194 CAAGATGATAAGTCCTTCGAG
* *
334429 CCATCCATAAGACCTTCGGGTAGGATGTTCTCACATGAATTTGAGAATGAAAAAATGATG---T-
1 CCATCCATAAGACCTTCGGGTAGGATGTTTTCA-ATGAATTTGAAAATGAAAAAATGATGTTTTA
** * * * *
334490 ---TG--G-AATTTTTGAAGGCGAATAATTCGATTTTCAAAATTTTCACAATGTATAAGTCCCTC
65 AGATGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAAA-TTTCACAATTTATAAGTCCCTC
* *
334549 GGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGAGTCATTTGTAAGCCTTTAGAG
129 GGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAG
*
334614 CAAGATGATAAGTCATTCGAG
194 CAAGATGATAAGTCCTTCGAG
* * *
334635 CCATCCATAAGACCTTCAGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAAACGATGTTTTG
1 CCATCCATAAGACCTTCGGGTAGGATGTTTTCA-ATGAATTTGAAAATGAAAAAATGATGTTTTA
* * *
334700 AGA-AATGAAATTTTTAAAAAC-GAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCCTCG
65 AGATGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCCTCG
* *
334763 GGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATTTGTAAGTCTTT
130 GGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTAAGCCTTT
334823 CGAGTGTGAT
Statistics
Matches: 939, Mismatches: 78, Indels: 43
0.89 0.07 0.04
Matches are distributed among these distances:
205 26 0.03
206 157 0.17
208 1 0.00
209 1 0.00
212 1 0.00
213 83 0.09
214 443 0.47
215 34 0.04
216 189 0.20
217 4 0.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (214 bp):
CCATCCATAAGACCTTCGGGTAGGATGTTTTCAATGAATTTGAAAATGAAAAAATGATGTTTTAA
GATGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCCTCGG
GCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCA
AGATGATAAGTCCTTCGAG
Found at i:334421 original size:430 final size:427
Alignment explanation
Indices: 333571--334810 Score: 1801
Period size: 430 Copynumber: 2.9 Consensus size: 427
333561 TGAAGGAAAT
*
333571 CCATCCATAAAACCTTCGGGTAGGATG-TTTT-CATTGAATTTGAAAAT-AAGAAAATGATGTTT
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTTACA-TGAATTTGAAAATGAAAAAAATGATGTTT
* * *
333633 TAAGATGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACAAATTATAAGTCCTT
65 TAAGA-GATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAATTTTCACAATTTATAAGTCCCT
** * *
333698 CGATCCATCAATAAGTCTTTCGAGCATGATGCTTAAATTCTTCGGGTCATCTGTAAGCCTTTAGA
129 CGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAA-TCTTCGGGTCATCTGTAAGCCTTTAGA
*
333763 GCAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTCGGGTAGGATGTTTTC-ATTGAATTTG
193 GCAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTCGGG-AGGATGTTTTCAAATGAATTTG
* * *
333827 AAAATAAGAAAATGATGTTTTAAGATGATGAAATTTTTGAAAACAAAGAATGCGAGTTTCAAAAT
257 AAAATGA-AAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAAAT
* * * *
333892 TTCATAATTTATAAGTCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGG
321 TTCACAATTTATAAGTCCCTCGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGG
* * *
333957 GTTATCTGTAAGCCTTTAGATCAAGATGATAAGTCCTTCAGA
386 GTCATCTATAAGCCTTTAGAGCAAGATGATAAGTCCTTCAGA
*
333999 CCATCCAAAAAACCTTCGGGTAGGATGTTTTTACATGAATTTGAAAATGAAAAAAATGATGTTTT
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTTACATGAATTTGAAAATGAAAAAAATGATGTTTT
334064 AAGAAGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAATTTTCACAATTTATAAGTCCCTC
66 AAG-AGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAATTTTCACAATTTATAAGTCCCTC
* *
334129 GGGCTATCAGTAAGTCTTTCGAGCATGATGTTTAAATCATTCGGGTCATCTGTAAGTCTTTAGAG
130 GGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATC-TTCGGGTCATCTGTAAGCCTTTAGAG
* * *
334194 CAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGAGGGATGATTTCAAATAAATTTGA
194 CAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTCGGGA-GGATGTTTTCAAATGAATTTGA
* * *
334259 AAATGAAAAATGATATTTTAAGAAGATGAATTTTTTGGAAACAAAGAATGCGATTTTCAAAATTT
258 AAATGAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTT
* *
334324 CACAATTTATGAGTCCCTCGGGCCATCAGTAAGTCTTTTGAGCATGATGTTTAAATCCTTCGGGT
323 CACAATTTATAAGTCCCTCGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGT
* *
334389 CATCTATAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGG
388 CATCTATAAGCCTTTAGAGCAAGATGATAAGTCCTTCAGA
* * * *
334429 CCATCCATAAGACCTTCGGGTAGGATGTTCTCACATGAATTTGAGAATG-AAAAAATGATG--TT
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTTACATGAATTTGAAAATGAAAAAAATGATGTTTT
** * * * *
334491 ----G--G-AATTTTTGAAGGCGAATAATTCGATTTTCAAAATTTTCACAATGTATAAGTCCCTC
66 AAGAGATGAAATTTTTGAAAACAAAGAATGCGATTTTC-AAATTTTCACAATTTATAAGTCCCTC
* *
334549 GGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGAGTCATTTGTAAGCCTTTAGAG
130 GGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAAT-CTTCGGGTCATCTGTAAGCCTTTAGAG
* * *
334614 CAAGATGATAAGTCATTCGAGCCATCCATAAGACCTTCAGGTAGGATGTTTTCACATGAATTTGA
194 CAAGATGATAAGTCCTTCGAGCCATCCATAAGACCTTC-GGGAGGATGTTTTCAAATGAATTTGA
* * * *
334679 AAATGAAAAAACGATGTTTTGAGAA-ATGAAATTTTTAAAAAC-GAGAATGCGATTTTCAAAATT
258 AAATG-AAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAAATT
334742 TCACAATTTATAAGTCCCTCGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGG
322 TCACAATTTATAAGTCCCTCGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGG
334807 TCAT
387 TCAT
334811 TTGTAAGTCT
Statistics
Matches: 739, Mismatches: 62, Indels: 31
0.89 0.07 0.04
Matches are distributed among these distances:
419 111 0.15
420 159 0.22
421 20 0.03
422 1 0.00
427 2 0.00
428 26 0.04
429 31 0.04
430 374 0.51
431 15 0.02
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (427 bp):
CCATCCATAAAACCTTCGGGTAGGATGTTTTTACATGAATTTGAAAATGAAAAAAATGATGTTTT
AAGAGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAATTTTCACAATTTATAAGTCCCTCG
GGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCTTCGGGTCATCTGTAAGCCTTTAGAGCA
AGATGATAAGTCCTTCGAGCCATCCATAAGACCTTCGGGAGGATGTTTTCAAATGAATTTGAAAA
TGAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTCAC
AATTTATAAGTCCCTCGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCAT
CTATAAGCCTTTAGAGCAAGATGATAAGTCCTTCAGA
Found at i:334439 original size:41 final size:42
Alignment explanation
Indices: 334335--334444 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 42
334325 ACAATTTATG
* * * * *
334335 AGTCCCTCGGGCCAT-CAGTAAGTCTTTTGAGCATGATGTTTA
1 AGTCCTTCGGGCCATCCA-TAAGCCTTTAGAGCAAGATGTATA
* * *
334377 AATCCTTCGGGTCATCTATAAGCCTTTAGAGCAAGATG-ATA
1 AGTCCTTCGGGCCATCCATAAGCCTTTAGAGCAAGATGTATA
334418 AGTCCTTCGGGCCATCCATAAGACCTT
1 AGTCCTTCGGGCCATCCATAAG-CCTT
334445 CGGGTAGGAT
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
41 21 0.38
42 33 0.60
43 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (42 bp):
AGTCCTTCGGGCCATCCATAAGCCTTTAGAGCAAGATGTATA
Found at i:334819 original size:42 final size:42
Alignment explanation
Indices: 334771--334859 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 42
334761 CGGGCCATCA
* *
334771 GTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATTT
1 GTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTT
**
334813 GTAAGTCTTTCGAGTGTGATGATTAAATCCTTCGGGTAATTT
1 GTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTT
*
334855 TTAAG
1 GTAAG
334860 CCTTCACAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.24, C:0.13, G:0.22, T:0.40
Consensus pattern (42 bp):
GTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTT
Found at i:337993 original size:20 final size:20
Alignment explanation
Indices: 337968--338012 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
337958 TTATCGAGAA
337968 AAGATAGTTAGAACTTATCT
1 AAGATAGTTAGAACTTATCT
337988 AAGATAGTTAGAACTTATCT
1 AAGATAGTTAGAACTTATCT
338008 AAGAT
1 AAGAT
338013 CTGGTCTCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (20 bp):
AAGATAGTTAGAACTTATCT
Found at i:342542 original size:23 final size:23
Alignment explanation
Indices: 342514--342558 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
342504 TATTTTTGTT
342514 ATATGTTTGATGTATTTATAGAA
1 ATATGTTTGATGTATTTATAGAA
342537 ATATGTTTGATGTATTTATAGA
1 ATATGTTTGATGTATTTATAGA
342559 CATCAATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (23 bp):
ATATGTTTGATGTATTTATAGAA
Found at i:343714 original size:45 final size:44
Alignment explanation
Indices: 343650--343746 Score: 158
Period size: 45 Copynumber: 2.2 Consensus size: 44
343640 ATCAATAAAT
343650 TTACCATTTTCCCATAAGCTCGTAAGCTTATTTTACCAACATAC
1 TTACCATTTTCCCATAAGCTCGTAAGCTTATTTTACCAACATAC
* *
343694 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTT-TCCCATAAGCTCGTAAGCTTATTTTACCAACATAC
*
343739 TTGCCATT
1 TTACCATT
343747 AACCTCATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
44 9 0.18
45 40 0.82
ACGTcount: A:0.29, C:0.25, G:0.07, T:0.39
Consensus pattern (44 bp):
TTACCATTTTCCCATAAGCTCGTAAGCTTATTTTACCAACATAC
Found at i:343943 original size:59 final size:59
Alignment explanation
Indices: 343880--343991 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 59
343870 CTTCCCCTTT
* * *
343880 CATTTTAGCACACGAAGTGCCCTAT-TCAAAAATTCATACCATTAGTATGATTTTGTTAC
1 CATTTTAACACACGAAATGCCCTATGT-AAAAATCCATACCATTAGTATGATTTTGTTAC
* * *
343939 CATTTTAATACATGAAATGCCCTATGTGAAAATCCATACCATTAGTATGATTT
1 CATTTTAACACACGAAATGCCCTATGTAAAAATCCATACCATTAGTATGATTT
343992 CCTTATATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 45 0.98
60 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.36
Consensus pattern (59 bp):
CATTTTAACACACGAAATGCCCTATGTAAAAATCCATACCATTAGTATGATTTTGTTAC
Found at i:344083 original size:59 final size:58
Alignment explanation
Indices: 343923--344304 Score: 303
Period size: 59 Copynumber: 6.5 Consensus size: 58
343913 TCATACCATT
** * ** * * *
343923 AGTATGATTTTGTTACCATTTTAATACATGAAATGCCCTATGTGAAAATCCATAC-CATT
1 AGTATGATTTCCTTATCATTTTAGCACAT-AAATGCCCTATCTGGAAATCCATACAC-TC
* * * **
343982 AGTATGATTTCCTTAT-ATTTGTAGCACCCTTAGTGCTTTATCTGGAAATCCATACACTC
1 AGTATGATTTCCTTATCATTT-TAGCA-CATAAATGCCCTATCTGGAAATCCATACACTC
* ***
344041 AGTATGATTCCCTTATCATTTTAGCACATAAAATGCCCTATCTGGAAATCCATATTTTC
1 AGTATGATTTCCTTATCATTTTAGCACAT-AAATGCCCTATCTGGAAATCCATACACTC
* * * * * **
344100 AATATGATTTCCTTATCA-TTTAGCACACTCAGTGATCC-ATATGGAAATTTATACACTC
1 AGTATGATTTCCTTATCATTTTAGCACA-TAAATG-CCCTATCTGGAAATCCATACACTC
***
344158 AGTATGATTTCTCTTA-CAATTTTAGCACATAAAAATGCCCTATCTGGAAATCCATATTTTC
1 AGTATGATTTC-CTTATC-ATTTTAGCACAT--AAATGCCCTATCTGGAAATCCATACACTC
* * * *
344219 AATATGATTTCCTTATCA-TTTAGCACACTTAGA-GCTCC-ATATGGAAATCTATACACTC
1 AGTATGATTTCCTTATCATTTTAGCACA--TAAATGC-CCTATCTGGAAATCCATACACTC
344277 AGTATGATTTCCTTATCATTTTAGCACA
1 AGTATGATTTCCTTATCATTTTAGCACA
344305 CAAAGTGTCA
Statistics
Matches: 254, Mismatches: 51, Indels: 36
0.74 0.15 0.11
Matches are distributed among these distances:
58 77 0.30
59 125 0.49
60 23 0.09
61 29 0.11
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.37
Consensus pattern (58 bp):
AGTATGATTTCCTTATCATTTTAGCACATAAATGCCCTATCTGGAAATCCATACACTC
Found at i:344218 original size:119 final size:118
Alignment explanation
Indices: 343923--344304 Score: 497
Period size: 119 Copynumber: 3.2 Consensus size: 118
343913 TCATACCATT
* * ** * * * ** *
343923 AGTATGATTT-TGTTACCATTTTAATACATGAAATGCCCTATGTGAAAATCCATACCATT-AGTA
1 AGTATGATTTCTCTTATCATTTTAGCACATAAAATGCCCTATCTGGAAATCCATA-TTTTCAATA
* ** * *
343986 TGATTTCCTTAT-ATTTGTAGCACCCTTAGTGCTTTATCTGGAAATCCATACACTC
65 TGATTTCCTTATCA-TT-TAGCACACTTAGTGCTCCATATGGAAATCTATACACTC
*
344041 AGTATGA-TTCCCTTATCATTTTAGCACATAAAATGCCCTATCTGGAAATCCATATTTTCAATAT
1 AGTATGATTTCTCTTATCATTTTAGCACATAAAATGCCCTATCTGGAAATCCATATTTTCAATAT
* * *
344105 GATTTCCTTATCATTTAGCACACTCAGTGATCCATATGGAAATTTATACACTC
66 GATTTCCTTATCATTTAGCACACTTAGTGCTCCATATGGAAATCTATACACTC
344158 AGTATGATTTCTCTTA-CAATTTTAGCACATAAAAATGCCCTATCTGGAAATCCATATTTTCAAT
1 AGTATGATTTCTCTTATC-ATTTTAGCACAT-AAAATGCCCTATCTGGAAATCCATATTTTCAAT
*
344222 ATGATTTCCTTATCATTTAGCACACTTAGAGCTCCATATGGAAATCTATACACTC
64 ATGATTTCCTTATCATTTAGCACACTTAGTGCTCCATATGGAAATCTATACACTC
344277 AGTATGATTTC-CTTATCATTTTAGCACA
1 AGTATGATTTCTCTTATCATTTTAGCACA
344305 CAAAGTGTCA
Statistics
Matches: 233, Mismatches: 24, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
117 42 0.18
118 94 0.40
119 97 0.42
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.37
Consensus pattern (118 bp):
AGTATGATTTCTCTTATCATTTTAGCACATAAAATGCCCTATCTGGAAATCCATATTTTCAATAT
GATTTCCTTATCATTTAGCACACTTAGTGCTCCATATGGAAATCTATACACTC
Found at i:346637 original size:24 final size:24
Alignment explanation
Indices: 346610--346671 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
346600 GAAACCATAA
*
346610 ATCAGAACAGAATTCAGATCAGAT
1 ATCAGAACAGAATCCAGATCAGAT
* *
346634 ATCAAAACAGAATCCATATCAGAT
1 ATCAGAACAGAATCCAGATCAGAT
*
346658 ATCAGAATAGAATC
1 ATCAGAACAGAATC
346672 TGGATCAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.48, C:0.18, G:0.13, T:0.21
Consensus pattern (24 bp):
ATCAGAACAGAATCCAGATCAGAT
Found at i:347554 original size:27 final size:28
Alignment explanation
Indices: 347505--347567 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 28
347495 AATTCTAGGG
* *
347505 TTTAGAGGTACTTTATGCCATTTAACAC
1 TTTAGGGGTACTTTAAGCCATTTAACAC
* * *
347533 TTTAGGGGTA-TTTAAGTCATTTTATAC
1 TTTAGGGGTACTTTAAGCCATTTAACAC
347560 TTTAGGGG
1 TTTAGGGG
347568 CATTATCATA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 21 0.70
28 9 0.30
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.43
Consensus pattern (28 bp):
TTTAGGGGTACTTTAAGCCATTTAACAC
Found at i:349405 original size:14 final size:14
Alignment explanation
Indices: 349369--349426 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
349359 CAGCTTGACC
*
349369 CGACTGAGTCAACA
1 CGACTGAGTCAACT
*
349383 CGCACTGAGTTAACT
1 CG-ACTGAGTCAACT
349398 CGACTGAGTCAACT
1 CGACTGAGTCAACT
* *
349412 C-ATTAAGTCAACT
1 CGACTGAGTCAACT
349425 CG
1 CG
349427 TTGACTTTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
13 11 0.30
14 14 0.38
15 12 0.32
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (14 bp):
CGACTGAGTCAACT
Found at i:349471 original size:37 final size:37
Alignment explanation
Indices: 349427--349511 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 37
349417 AGTCAACTCG
*
349427 TTGACTTTGACCGAGTCAACCCGTTGA-TCGTTGACAT
1 TTGACTTTGACCGAGTCAACCCGTTAACT-GTTGACAT
* *
349464 TTGACTTTGATCGAGTCAACCCGTTAACTGTTGACTT
1 TTGACTTTGACCGAGTCAACCCGTTAACTGTTGACAT
349501 TTG-CTTTGACC
1 TTGACTTTGACC
349512 AAAAACTCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 7 0.16
37 35 0.81
38 1 0.02
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (37 bp):
TTGACTTTGACCGAGTCAACCCGTTAACTGTTGACAT
Found at i:352205 original size:31 final size:31
Alignment explanation
Indices: 352107--352225 Score: 103
Period size: 31 Copynumber: 3.8 Consensus size: 31
352097 TAGGCTCTGC
* * * *
352107 GGCCTTGAGATCATTCTTGTGTAGGCCCTAC
1 GGCCCTGAGATCTTTCTTGCGTAGGCCCTAT
* * **
352138 GGCCCTGGGATTTTTCTTGCGTAGGCCCCGT
1 GGCCCTGAGATCTTTCTTGCGTAGGCCCTAT
* * * *
352169 AGCCCTGAGATCTTTATTGGGTAGGCCTTAT
1 GGCCCTGAGATCTTTCTTGCGTAGGCCCTAT
* * *
352200 GGCCCTAAAAACTTTCTTGCGTAGGC
1 GGCCCTGAGATCTTTCTTGCGTAGGC
352226 TCTCAAGCCC
Statistics
Matches: 66, Mismatches: 22, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
31 66 1.00
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (31 bp):
GGCCCTGAGATCTTTCTTGCGTAGGCCCTAT
Found at i:354327 original size:79 final size:79
Alignment explanation
Indices: 354188--354336 Score: 253
Period size: 79 Copynumber: 1.9 Consensus size: 79
354178 AATCGTATGT
* * *
354188 TTCCTTATTGGTTCATACATCTATAGATTTTTATGCTGAGCGGAGATCCTACGGAGATTTCAGGT
1 TTCCTTATTGGTTCAGACATCTACAGATTTTTATGCTGAGCGGAGATCCTACAGAGATTTCAGGT
354253 AGTAACAGACAATA
66 AGTAACAGACAATA
* *
354267 TTCCTTATTGGTTCAGACATCTACATATTTTTATGCTGAGCGGAGATCCTACAGATATTTCAGGT
1 TTCCTTATTGGTTCAGACATCTACAGATTTTTATGCTGAGCGGAGATCCTACAGAGATTTCAGGT
354332 AGTAA
66 AGTAA
354337 AATATAGTAA
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 65 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (79 bp):
TTCCTTATTGGTTCAGACATCTACAGATTTTTATGCTGAGCGGAGATCCTACAGAGATTTCAGGT
AGTAACAGACAATA
Found at i:354594 original size:31 final size:31
Alignment explanation
Indices: 354539--354612 Score: 105
Period size: 32 Copynumber: 2.4 Consensus size: 31
354529 GGGTTCTACA
354539 AGCCTACCCAAGAAAATTCTCAGGGCCACAG
1 AGCCTACCCAAGAAAATTCTCAGGGCCACAG
* **
354570 AGGCCTACCCAAGAAAA-TCTCAGGGTCGTAG
1 A-GCCTACCCAAGAAAATTCTCAGGGCCACAG
354601 AGCCTACCCAAG
1 AGCCTACCCAAG
354613 GGTCACCATA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
30 11 0.28
31 13 0.33
32 15 0.38
ACGTcount: A:0.34, C:0.31, G:0.22, T:0.14
Consensus pattern (31 bp):
AGCCTACCCAAGAAAATTCTCAGGGCCACAG
Found at i:354794 original size:24 final size:24
Alignment explanation
Indices: 354761--354820 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
354751 AATAAAAAAT
* * *
354761 TAGAACAGAATTCAGATCAGATA-
1 TAGAATAGAATCCAGATCAAATAG
*
354784 TCAGAATAGAATCCATATCAAATAG
1 T-AGAATAGAATCCAGATCAAATAG
354809 TAGAATAGAATC
1 TAGAATAGAATC
354821 TGGATCAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 1 0.03
24 29 0.94
25 1 0.03
ACGTcount: A:0.48, C:0.13, G:0.15, T:0.23
Consensus pattern (24 bp):
TAGAATAGAATCCAGATCAAATAG
Found at i:360969 original size:13 final size:11
Alignment explanation
Indices: 360933--360962 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
360923 AATTAACTTT
*
360933 TAATCTTAAAA
1 TAATTTTAAAA
360944 TAATTTTAAAA
1 TAATTTTAAAA
360955 TAATTTTA
1 TAATTTTA
360963 CAAAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (11 bp):
TAATTTTAAAA
Found at i:363251 original size:40 final size:40
Alignment explanation
Indices: 363196--363277 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
363186 TGCAGGTTTA
363196 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
363236 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
363276 TA
1 TA
363278 GCACTACGGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:363476 original size:47 final size:45
Alignment explanation
Indices: 363382--363507 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
363372 GTAACCATGC
* * *
363382 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATAGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
* * *
363426 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATAGGAA
*
363473 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
363508 AGATTTTATA
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 22 0.31
45 11 0.15
46 1 0.01
47 38 0.53
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
Found at i:366360 original size:29 final size:29
Alignment explanation
Indices: 366319--366440 Score: 113
Period size: 29 Copynumber: 4.4 Consensus size: 29
366309 ATATATTATA
366319 AGAAGAAGAAAAAACAGA-AGAAAA-AAAAC
1 AGAAGAAGAAAAAA-A-ATAGAAAAGAAAAC
366348 AGAAGAAGAAAAAAAATAGAAAATGAAAAC
1 AGAAGAAGAAAAAAAATAGAAAA-GAAAAC
*
366378 -GAAGAAG--AAAAAA-A-AAATGAAAAC
1 AGAAGAAGAAAAAAAATAGAAAAGAAAAC
*
366402 -GAAGAAGAAAAAAAAT-GAAAACGAGAA-
1 AGAAGAAGAAAAAAAATAGAAAA-GAAAAC
366429 AGAA-AAGAAAAA
1 AGAAGAAGAAAAA
366441 GAGAAAAAAA
Statistics
Matches: 81, Mismatches: 3, Indels: 20
0.78 0.03 0.19
Matches are distributed among these distances:
24 13 0.16
25 3 0.04
26 7 0.09
27 18 0.22
28 14 0.17
29 21 0.26
30 5 0.06
ACGTcount: A:0.75, C:0.04, G:0.18, T:0.03
Consensus pattern (29 bp):
AGAAGAAGAAAAAAAATAGAAAAGAAAAC
Found at i:366384 original size:46 final size:42
Alignment explanation
Indices: 366329--366450 Score: 117
Period size: 46 Copynumber: 2.8 Consensus size: 42
366319 AGAAGAAGAA
366329 AAAAC-AGAAGAAAAAAAACAGAAGAAGAAAAAAAATAGAAAATG
1 AAAACGAGAAGAAAAAAAA-AGAAGAAGAAAAAAAA-A-AAAATG
*
366373 AAAACGAAGAAGAAAAAAAAAATGAA-AACGAAGAAGAAAAAAAATG
1 AAAACG-AGAAG-AAAAAAAAA-GAAGAA-GAA-AAAAAAAAAAATG
366419 AAAACGAGAAAGAAAAGAAAAAG-AGAA-AAAAA
1 AAAACGAG-AAGAAAA-AAAAAGAAGAAGAAAAA
366451 TGAGAGATGA
Statistics
Matches: 67, Mismatches: 2, Indels: 20
0.75 0.02 0.22
Matches are distributed among these distances:
42 2 0.03
43 2 0.03
44 6 0.09
45 9 0.13
46 28 0.42
47 15 0.22
48 5 0.07
ACGTcount: A:0.75, C:0.04, G:0.17, T:0.03
Consensus pattern (42 bp):
AAAACGAGAAGAAAAAAAAAGAAGAAGAAAAAAAAAAAAATG
Found at i:366399 original size:24 final size:24
Alignment explanation
Indices: 366352--366440 Score: 112
Period size: 24 Copynumber: 3.7 Consensus size: 24
366342 AAAAACAGAA
*
366352 GAAGAAAAAAAATAGAAAATGAAAAC
1 GAAGAAGAAAAA-A-AAAATGAAAAC
366378 GAAGAAGAAAAAAAAAATGAAAAC
1 GAAGAAGAAAAAAAAAATGAAAAC
366402 GAAGAAG--AAAAAAAATGAAAAC
1 GAAGAAGAAAAAAAAAATGAAAAC
*
366424 G-AGAAAGAAAAGAAAAA
1 GAAG-AAGAAAAAAAAAA
366441 GAGAAAAAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
21 2 0.03
22 19 0.33
24 25 0.43
25 1 0.02
26 11 0.19
ACGTcount: A:0.74, C:0.03, G:0.18, T:0.04
Consensus pattern (24 bp):
GAAGAAGAAAAAAAAAATGAAAAC
Found at i:366412 original size:22 final size:22
Alignment explanation
Indices: 366367--366439 Score: 103
Period size: 22 Copynumber: 3.2 Consensus size: 22
366357 AAAAAAATAG
366367 AAAATGAAAACGAAGAAGAAAAAA
1 AAAATGAAAACGAAGAAG--AAAA
366391 AAAATGAAAACGAAGAAGAAAA
1 AAAATGAAAACGAAGAAGAAAA
366413 AAAATGAAAACG-AGAAAGAAAA
1 AAAATGAAAACGAAG-AAGAAAA
366435 GAAAA
1 -AAAA
366440 AGAGAAAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
21 2 0.04
22 23 0.49
23 4 0.09
24 18 0.38
ACGTcount: A:0.74, C:0.04, G:0.18, T:0.04
Consensus pattern (22 bp):
AAAATGAAAACGAAGAAGAAAA
Found at i:366422 original size:34 final size:34
Alignment explanation
Indices: 366384--366453 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 34
366374 AAACGAAGAA
*
366384 GAAAA-AAAAAATGAAAACGAAGAAGA-AAAAAAAT
1 GAAAACAAAAAA-GAAAA-GAAAAAGAGAAAAAAAT
* *
366418 GAAAACGAGAAAGAAAAGAAAAAGAGAAAAAAAT
1 GAAAACAAAAAAGAAAAGAAAAAGAGAAAAAAAT
366452 GA
1 GA
366454 GAGATGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
33 7 0.23
34 20 0.65
35 4 0.13
ACGTcount: A:0.74, C:0.03, G:0.19, T:0.04
Consensus pattern (34 bp):
GAAAACAAAAAAGAAAAGAAAAAGAGAAAAAAAT
Found at i:371820 original size:22 final size:22
Alignment explanation
Indices: 371794--371853 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
371784 TTGGTGTAGA
*
371794 GGGAATCGATACCCCCTTGA-AG
1 GGGAATCGATACCCCC-TCACAG
* *
371816 GGGAACCGATTCCCCC-CACAG
1 GGGAATCGATACCCCCTCACAG
*
371837 GGGAATTGATACCCCCT
1 GGGAATCGATACCCCCT
371854 GAGGGTTCTA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
20 1 0.03
21 15 0.50
22 14 0.47
ACGTcount: A:0.25, C:0.33, G:0.25, T:0.17
Consensus pattern (22 bp):
GGGAATCGATACCCCCTCACAG
Found at i:373457 original size:18 final size:18
Alignment explanation
Indices: 373422--373460 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
373412 TGAGCAGCAC
*
373422 GAGGAACAAGCACCTCCA
1 GAGGAACAACCACCTCCA
* *
373440 GAGGAACAACCTCGTCCA
1 GAGGAACAACCACCTCCA
373458 GAG
1 GAG
373461 TATCAAATGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.31, G:0.26, T:0.08
Consensus pattern (18 bp):
GAGGAACAACCACCTCCA
Found at i:373748 original size:17 final size:17
Alignment explanation
Indices: 373728--373761 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
373718 TTTGGATATT
373728 TGGAATGTTTGAATTTG
1 TGGAATGTTTGAATTTG
* *
373745 TGGATTGTTTGACTTTG
1 TGGAATGTTTGAATTTG
373762 AATTTGTTTG
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:0.18, C:0.03, G:0.29, T:0.50
Consensus pattern (17 bp):
TGGAATGTTTGAATTTG
Found at i:376131 original size:14 final size:14
Alignment explanation
Indices: 376112--376192 Score: 58
Period size: 14 Copynumber: 5.7 Consensus size: 14
376102 CAAAGTCAAT
*
376112 AGGTTGACTCGGAC
1 AGGTTGACTCAGAC
*
376126 AGGTTGACTTAGA-
1 AGGTTGACTCAGAC
* *
376139 TGAGTTGACTCGGAC
1 AG-GTTGACTCAGAC
376154 -GAGTTGACTCAGAC
1 AG-GTTGACTCAGAC
* *
376168 GGGTTGACTCATACC
1 AGGTTGACTCAGA-C
*
376183 AAGTTGACTC
1 AGGTTGACTC
376193 GGTGACTAGA
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
13 1 0.02
14 43 0.80
15 10 0.19
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.26
Consensus pattern (14 bp):
AGGTTGACTCAGAC
Found at i:376159 original size:28 final size:28
Alignment explanation
Indices: 376114--376177 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
376104 AAGTCAATAG
* *
376114 GTTGACTCGGACAGGTTGACTTAGATGA
1 GTTGACTCGGACAGGTTGACTCAGACGA
*
376142 GTTGACTCGGAC-GAGTTGACTCAGACGG
1 GTTGACTCGGACAG-GTTGACTCAGACGA
376170 GTTGACTC
1 GTTGACTC
376178 ATACCAAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 1 0.03
28 31 0.97
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.27
Consensus pattern (28 bp):
GTTGACTCGGACAGGTTGACTCAGACGA
Found at i:382466 original size:48 final size:46
Alignment explanation
Indices: 382367--382492 Score: 161
Period size: 48 Copynumber: 2.8 Consensus size: 46
382357 GTAAGTATGC
*
382367 AAATAAGCTTACGAGCTTAT-GAA-T-AATGGCAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGATA
* * *
382410 AAATAAGCTTACGAACTTATGGAATTTAAATGGTAAGTATTTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA-TTAAATGGTAAGTA-TATTGATA
*
382458 AAATAAGCTTACGAGCTTATGGTA-TAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAG
382493 AGATTTTATA
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
43 19 0.26
44 3 0.04
46 12 0.17
47 10 0.14
48 28 0.39
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.33
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGATA
Found at i:385668 original size:17 final size:19
Alignment explanation
Indices: 385643--385681 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
385633 ATATCTATAT
385643 TATTAATATTT-TGTTCTA
1 TATTAATATTTATGTTCTA
385661 TATT-ATATTTAATGTTCTA
1 TATTAATATTT-ATGTTCTA
385680 TA
1 TA
385682 AGTTGTTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTAATATTTATGTTCTA
Found at i:393046 original size:271 final size:271
Alignment explanation
Indices: 392563--393109 Score: 1067
Period size: 271 Copynumber: 2.0 Consensus size: 271
392553 ACCAAGCCTA
392563 ATTCAGCGACCGGTGTTGATGAGGTTTGTACGAGTTTATTGGCTTTCAATCAACCTTCCATTGCA
1 ATTCAGCGACCGGTGTTGATGAGGTTTGTACGAGTTTATTGGCTTTCAATCAACCTTCCATTGCA
392628 GTCTCTCACCAAAGCTCTAATTCCTTCTACCTTCATCATCTCGTCAAAGGATGCATCAAATTTAA
66 GTCTCTCACCAAAGCTCTAATTCCTTCTACCTTCATCATCTCGTCAAAGGATGCATCAAATTTAA
392693 GTAAATTCTGTAGTAGACAGCTCTAATTCCTGCTACCTTCATAGTCTAATCTCTTTTTTTTTTCC
131 GTAAATTCTGTAGTAGACAGCTCTAATTCCTGCTACCTTCATAGTCTAATCTCTTTTTTTTTTCC
392758 TTCTTCTGGTATTATAATTCATGCTGATGTCATATTGTGTTAAAAGTTAAAGGATCTAGATTTTA
196 TTCTTCTGGTATTATAATTCATGCTGATGTCATATTGTGTTAAAAGTTAAAGGATCTAGATTTTA
392823 ATAAAGAAGCC
261 ATAAAGAAGCC
392834 ATTCAGCGACCGGTGTTGATGAGGTTTGTACGAGTTTATTGGCTTTCAATCAACCTTCCATTGCA
1 ATTCAGCGACCGGTGTTGATGAGGTTTGTACGAGTTTATTGGCTTTCAATCAACCTTCCATTGCA
392899 GTCTCTCACCAAAGCTCTAATTCCTTCTACCTTCATCATCTCGTCAAAGGATGCATCAAATTTAA
66 GTCTCTCACCAAAGCTCTAATTCCTTCTACCTTCATCATCTCGTCAAAGGATGCATCAAATTTAA
* *
392964 GTAAATTCTGTAGTGGACAGCTCTAATTCCTGCTACCTTCATATTCTAATCTCTTTTTTTTTTCC
131 GTAAATTCTGTAGTAGACAGCTCTAATTCCTGCTACCTTCATAGTCTAATCTCTTTTTTTTTTCC
*
393029 TTCTTCTGGTATTATAATTCATGCTGATGTCATATTGTGTTAAAAGTTAAAGGATCTAGTTTTTA
196 TTCTTCTGGTATTATAATTCATGCTGATGTCATATTGTGTTAAAAGTTAAAGGATCTAGATTTTA
393094 ATAAAGAAGCC
261 ATAAAGAAGCC
393105 ATTCA
1 ATTCA
393110 ACCAGCTTTC
Statistics
Matches: 273, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
271 273 1.00
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.38
Consensus pattern (271 bp):
ATTCAGCGACCGGTGTTGATGAGGTTTGTACGAGTTTATTGGCTTTCAATCAACCTTCCATTGCA
GTCTCTCACCAAAGCTCTAATTCCTTCTACCTTCATCATCTCGTCAAAGGATGCATCAAATTTAA
GTAAATTCTGTAGTAGACAGCTCTAATTCCTGCTACCTTCATAGTCTAATCTCTTTTTTTTTTCC
TTCTTCTGGTATTATAATTCATGCTGATGTCATATTGTGTTAAAAGTTAAAGGATCTAGATTTTA
ATAAAGAAGCC
Found at i:398094 original size:2 final size:2
Alignment explanation
Indices: 398089--398122 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
398079 AAATTGAAAG
*
398089 AT AT AT AT AC 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
398123 GATTCTTACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:403079 original size:2 final size:2
Alignment explanation
Indices: 403072--403151 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
403062 GATGGAAACA
403072 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
403114 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
403152 GAAATGAAAA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:404007 original size:39 final size:39
Alignment explanation
Indices: 403941--404162 Score: 275
Period size: 39 Copynumber: 5.7 Consensus size: 39
403931 GAGATAAATA
403941 TCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGTT
1 TCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGTT
* * *
403980 TTGAGTGAAATTATCTTAAG-GAGGATAAAATCTTCTGTT
1 TCGAGTGAAACTATCTCAAGCGA-GATAAAATCTTCTGTT
* * * * * * * *
404019 TCGAGTTAAACCATCTCAAACAAGATGAAATATTTTGTA
1 TCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGTT
*
404058 TCGAGTGAAACTATCTCAAGCGAGATAAAAATCTTTTGTT
1 TCGAGTGAAACTATCTCAAGCGAGAT-AAAATCTTCTGTT
* * *
404098 TCAAGTGAAACCATCTCAAGCGAGATAAAATCTTATGTT
1 TCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGTT
*
404137 TCAAGTGAAACTATCTCAAGCGAGAT
1 TCGAGTGAAACTATCTCAAGCGAGAT
404163 GTTGATCCCT
Statistics
Matches: 155, Mismatches: 25, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
38 2 0.01
39 118 0.76
40 35 0.23
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.31
Consensus pattern (39 bp):
TCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGTT
Found at i:404115 original size:79 final size:78
Alignment explanation
Indices: 403944--404162 Score: 278
Period size: 79 Copynumber: 2.8 Consensus size: 78
403934 ATAAATATCG
* * * * *
403944 AGTGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTTGAGTGAAATTATCTTAAG-GAGGATAA
1 AGTGAAACCATCTCAAGCGAGATAAAATCTTATGTTTCGAGTGAAACTATCTCAAGCGA-GATAA
*
404008 AATCTTCTGTTTCG
65 AATCTTCTGTTTCA
* * * * * * *
404022 AGTTAAACCATCTCAAACAAGATGAAATATTTTGTATCGAGTGAAACTATCTCAAGCGAGATAAA
1 AGTGAAACCATCTCAAGCGAGATAAAATCTTATGTTTCGAGTGAAACTATCTCAAGCGAGAT-AA
*
404087 AATCTTTTGTTTCA
65 AATCTTCTGTTTCA
*
404101 AGTGAAACCATCTCAAGCGAGATAAAATCTTATGTTTCAAGTGAAACTATCTCAAGCGAGAT
1 AGTGAAACCATCTCAAGCGAGATAAAATCTTATGTTTCGAGTGAAACTATCTCAAGCGAGAT
404163 GTTGATCCCT
Statistics
Matches: 118, Mismatches: 21, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
78 48 0.41
79 70 0.59
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (78 bp):
AGTGAAACCATCTCAAGCGAGATAAAATCTTATGTTTCGAGTGAAACTATCTCAAGCGAGATAAA
ATCTTCTGTTTCA
Found at i:404163 original size:118 final size:117
Alignment explanation
Indices: 403939--404155 Score: 319
Period size: 118 Copynumber: 1.8 Consensus size: 117
403929 GTGAGATAAA
** ** *
403939 TATCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTTGAGTGAAATTATCTTAAGGAGG
1 TATCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCAAGTGAAACCATCTCAAGGAGG
* * *
404004 ATAAAATCTTCTGTTTCGAGTTAAACCATCTCAAACAAGATGAAATATTTTG
66 ATAAAATCTTATGTTTCAAGTGAAACCATCTCAAACAAGATGAAATATTTTG
*
404056 TATCGAGTGAAACTATCTCAAGCGAGATAAAAATCTTTTGTTTCAAGTGAAACCATCTCAAGCGA
1 TATCGAGTGAAACTATCTCAAGCGAGAT-AAAATCTTCTGTTTCAAGTGAAACCATCTCAAG-GA
*
404121 -GATAAAATCTTATGTTTCAAGTGAAACTATCTCAA
64 GGATAAAATCTTATGTTTCAAGTGAAACCATCTCAA
404156 GCGAGATGTT
Statistics
Matches: 88, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
117 28 0.32
118 58 0.66
119 2 0.02
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (117 bp):
TATCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCAAGTGAAACCATCTCAAGGAGG
ATAAAATCTTATGTTTCAAGTGAAACCATCTCAAACAAGATGAAATATTTTG
Found at i:404512 original size:59 final size:59
Alignment explanation
Indices: 404424--404548 Score: 153
Period size: 59 Copynumber: 2.1 Consensus size: 59
404414 TTATCCCTTA
* * *
404424 AGTGAGGCATCGCTAATTCGAAATATCGTGAATCGAGCAAAGGAAA-AGTTAACCCCTCT
1 AGTGGGGCATCACTAATTCGAAATATCGTGAATCGAACAAAGGAAATA-TTAACCCCTCT
* * * **
404483 AGTGGGGCATCACTGATTTGAAATGTCGTGAATCGAATGAAGGAAATATTAACCCCTCT
1 AGTGGGGCATCACTAATTCGAAATATCGTGAATCGAACAAAGGAAATATTAACCCCTCT
*
404542 GGTGGGG
1 AGTGGGG
404549 TGTTGTTCGT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
59 55 0.98
60 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (59 bp):
AGTGGGGCATCACTAATTCGAAATATCGTGAATCGAACAAAGGAAATATTAACCCCTCT
Found at i:404548 original size:249 final size:251
Alignment explanation
Indices: 404065--404719 Score: 931
Period size: 249 Copynumber: 2.6 Consensus size: 251
404055 GTATCGAGTG
* * * *
404065 AAACTATCTCAAGCGAGATAAAAATCTTTTGTTTCAAGTGAAACCATCTCAAGCGAGATAAAATC
1 AAACAATCTCAAGTGAGAT--AAATCTTTTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATC
* ** *
404130 TTATGTTTCAAGTGAAACTATCTCAAGCGAGATGTTGATCCCTCAAGTGAGGCGTCATTGATTTG
64 TTATGTTTCAAGTGAAACTATCTCAAGCGAGATGTTAATCCCTCAAGTGAGGCGTCGCTGATTCG
* * *
404195 AAATACCGTGAATCGAGCAAAGGAAAAGTTAACCCCTCTGGTGGGACGTCACTAATTCGAAATGC
129 AAATATCGTGAATCGAGCAAAGGAAAAGTTAACCCCTCTAGTGGGACATCACTAATTCGAAATGC
** * *
404260 CGTGAATCGTGTGAAGGAAATGTTAATCCCTCTGGTGGGGTGTTATTCGTTTTAAGAA
194 CGTGAATCGAATGAAGGAAATATTAACCCCTCTGGTGGGGTGTTATTCGTTTTAAGAA
* * *
404318 AATCAATCTCAAGTGAGATAAATCTTTT-TTT-GAGTAAAACTATCTCAAGTGAGATAAAATCTT
1 AAACAATCTCAAGTGAGATAAATCTTTTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTT
* * * * * *
404381 AT-TTTCCAAGTGAAACTACCTCAAACGAGATGTTTATCCCTTAAGTGAGGCATCGCTAATTCGA
66 ATGTTT-CAAGTGAAACTATCTCAAGCGAGATGTTAATCCCTCAAGTGAGGCGTCGCTGATTCGA
* * * *
404445 AATATCGTGAATCGAGCAAAGGAAAAGTTAACCCCTCTAGTGGGGCATCACTGATTTGAAATGTC
130 AATATCGTGAATCGAGCAAAGGAAAAGTTAACCCCTCTAGTGGGACATCACTAATTCGAAATGCC
*
404510 GTGAATCGAATGAAGGAAATATTAACCCCTCTGGTGGGGTGTTGTTCGTTTTAAGAA
195 GTGAATCGAATGAAGGAAATATTAACCCCTCTGGTGGGGTGTTATTCGTTTTAAGAA
*
404567 AAACAATCTCAAGTGAGATAAATCTTTTGTTTCGAGTGAAACTATCTCAAACGAGAT-AAATCTT
1 AAACAATCTCAAGTGAGATAAATCTTTTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTT
** * * *
404631 ATGTTTTGAGTGAAAATATCTCAAGCGAGATGTTAATCCCTCAAGTGAGGCGTTGCTGATTCAAA
66 ATGTTTCAAGTGAAACTATCTCAAGCGAGATGTTAATCCCTCAAGTGAGGCGTCGCTGATTCGAA
*
404696 ATTTCGTGAATCGAGCAAAGGAAA
131 ATATCGTGAATCGAGCAAAGGAAA
404720 TGCGTAAAAC
Statistics
Matches: 354, Mismatches: 44, Indels: 11
0.87 0.11 0.03
Matches are distributed among these distances:
248 3 0.01
249 216 0.61
250 86 0.24
251 33 0.09
253 16 0.05
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.29
Consensus pattern (251 bp):
AAACAATCTCAAGTGAGATAAATCTTTTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTT
ATGTTTCAAGTGAAACTATCTCAAGCGAGATGTTAATCCCTCAAGTGAGGCGTCGCTGATTCGAA
ATATCGTGAATCGAGCAAAGGAAAAGTTAACCCCTCTAGTGGGACATCACTAATTCGAAATGCCG
TGAATCGAATGAAGGAAATATTAACCCCTCTGGTGGGGTGTTATTCGTTTTAAGAA
Found at i:404614 original size:38 final size:38
Alignment explanation
Indices: 404567--404661 Score: 136
Period size: 38 Copynumber: 2.5 Consensus size: 38
404557 GTTTTAAGAA
* * *
404567 AAACAATCTCAAGTGAGATAAATCTTTTGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAATCTTATGTTTCGAGTG
* *
404605 AAACTATCTCAAACGAGATAAATCTTATGTTTTGAGTG
1 AAACTATCTCAAGCGAGATAAATCTTATGTTTCGAGTG
*
404643 AAAATATCTCAAGCGAGAT
1 AAACTATCTCAAGCGAGAT
404662 GTTAATCCCT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (38 bp):
AAACTATCTCAAGCGAGATAAATCTTATGTTTCGAGTG
Found at i:405141 original size:58 final size:57
Alignment explanation
Indices: 404910--405141 Score: 212
Period size: 58 Copynumber: 4.1 Consensus size: 57
404900 TGTTTTCAGT
** * * *
404910 TATCATCAAGAAACCCCTAAAAATTAGGCTTAACTTCTTTTTAAAATTCTTTGGAGA
1 TATCATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTTAAAAATTCTTTGAAAA
* * ** *
404967 TAATCATCAAGAAACCCCTGAAAATCAAACTTAGTTTC---TAAAAACTCATTTG-AAA
1 T-ATCATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTTAAAAATTC-TTTGAAAA
* * *
405022 -A-CATCAAGAAACCCCTAAAAATTAGGCTTA-TATGCTTTTAAAAATTCATTAAAAA
1 TATCATCAAGAAACCCCTAAAAATTAGGCTTAGT-TTCTTTTAAAAATTCTTTGAAAA
*
405077 GCATCATCAAGAAACCCCTAAAAATCT-GGCTTAGTTTC-TTTAAAAATTCTTTTTGAAAA
1 -TATCATCAAGAAACCCCTAAAAAT-TAGGCTTAGTTTCTTTTAAAAATTC--TTTGAAAA
405136 TATCAT
1 TATCAT
405142 GTTGTTTAGG
Statistics
Matches: 140, Mismatches: 21, Indels: 27
0.74 0.11 0.14
Matches are distributed among these distances:
51 1 0.01
52 27 0.19
53 1 0.01
54 2 0.01
55 20 0.14
56 4 0.03
57 13 0.09
58 64 0.46
59 8 0.06
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (57 bp):
TATCATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTTAAAAATTCTTTGAAAA
Found at i:411008 original size:6 final size:6
Alignment explanation
Indices: 410999--411023 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
410989 AAAAACTAAA
410999 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
411024 TTAAAAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:411014 original size:21 final size:21
Alignment explanation
Indices: 410989--411030 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
410979 ATTTTAATTA
410989 AAAAACTAAAAAAAATAAAAAT
1 AAAAA-TAAAAAAAATAAAAAT
* *
411011 AAAAATAAAAATATTAAAAA
1 AAAAATAAAAAAAATAAAAA
411031 CATTGAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (21 bp):
AAAAATAAAAAAAATAAAAAT
Found at i:411061 original size:22 final size:22
Alignment explanation
Indices: 410990--411062 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
410980 TTTTAATTAA
* *
410990 AAAACTAAAAAAAATAAAAATA-
1 AAAA-TAAAAATAATAAAAACAT
*
411012 AAAATAAAAATATTAAAAACAT
1 AAAATAAAAATAATAAAAACAT
** **
411034 TGAATAAAAATAATATGAACAT
1 AAAATAAAAATAATAAAAACAT
411056 AAAATAA
1 AAAATAA
411063 GGACATAATT
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 14 0.35
22 26 0.65
ACGTcount: A:0.73, C:0.04, G:0.03, T:0.21
Consensus pattern (22 bp):
AAAATAAAAATAATAAAAACAT
Found at i:413593 original size:98 final size:98
Alignment explanation
Indices: 413412--413604 Score: 278
Period size: 98 Copynumber: 2.0 Consensus size: 98
413402 TCCCACGTTG
* * * * * * *
413412 CTCGAGGGGTAACTTGCAAAATTGGGACGAATACTGACAATATTTCTTTTTTTGTATAGATTGAG
1 CTCGAGGGGTAACTTCCAAAATTGGGACGAATACTGACAACATTCCCTTTTTGGCACAGATTGAG
*
413477 TCATAAAAAATAATATACTTTGGTATACTTTTA
66 TCATAAAAAATAAGATACTTTGGTATACTTTTA
*
413510 CTCGCGGGGTAACTTCCAAAATTGGGACGAATACTGACAACATTCCCTTTTTGGCACAGATTGAG
1 CTCGAGGGGTAACTTCCAAAATTGGGACGAATACTGACAACATTCCCTTTTTGGCACAGATTGAG
* * *
413575 TCATTACAGATAAGATACTTTGGTATACTT
66 TCATAAAAAATAAGATACTTTGGTATACTT
413605 ATTATAAAAT
Statistics
Matches: 83, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
98 83 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Consensus pattern (98 bp):
CTCGAGGGGTAACTTCCAAAATTGGGACGAATACTGACAACATTCCCTTTTTGGCACAGATTGAG
TCATAAAAAATAAGATACTTTGGTATACTTTTA
Found at i:414549 original size:32 final size:31
Alignment explanation
Indices: 414513--414600 Score: 95
Period size: 32 Copynumber: 2.7 Consensus size: 31
414503 AGAGATTATA
* **
414513 TTGGGGCTTGAGAGCCTACCCAAGAGTGTACC
1 TTGGGGCTT-AAAGCCTACCCAAGAGAATACC
* * *
414545 TTGGGTCCTAATAGCCTACCCAAGGGAATACC
1 TTGGGGCTTAA-AGCCTACCCAAGAGAATACC
414577 TTGGGGCCTTAAAGCCTACCCAAG
1 TTGGGG-CTTAAAGCCTACCCAAG
414601 TGTCACCTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
31 1 0.02
32 41 0.89
33 4 0.09
ACGTcount: A:0.25, C:0.27, G:0.26, T:0.22
Consensus pattern (31 bp):
TTGGGGCTTAAAGCCTACCCAAGAGAATACC
Found at i:416664 original size:20 final size:20
Alignment explanation
Indices: 416610--416666 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
416600 CTGGCCAACT
*
416610 GCTCGGCTCAACTAGACGTG
1 GCTCGGCTCAACTCGACGTG
*
416630 GCTCGGCTCAACTCGATGTG
1 GCTCGGCTCAACTCGACGTG
*
416650 GCTCGGCTCAGCTCGAC
1 GCTCGGCTCAACTCGAC
416667 TCAAACAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.16, C:0.33, G:0.30, T:0.21
Consensus pattern (20 bp):
GCTCGGCTCAACTCGACGTG
Found at i:416701 original size:18 final size:19
Alignment explanation
Indices: 416672--416725 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
416662 TCGACTCAAA
416672 CAACTTGGTTTAGATCGGCT
1 CAAC-TGGTTTAGATCGGCT
* *
416692 -AA-TAGGTTTAGACCGGTT
1 CAACT-GGTTTAGATCGGCT
416710 CAACTGGTTTAGATCG
1 CAACTGGTTTAGATCG
416726 ATTCAGTCGG
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
17 1 0.04
18 12 0.43
19 14 0.50
20 1 0.04
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (19 bp):
CAACTGGTTTAGATCGGCT
Found at i:422039 original size:30 final size:29
Alignment explanation
Indices: 422005--422062 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
421995 ACATAATTAT
*
422005 CACCCTAATAGTAATTAATTACAAAACTAG
1 CACCCTAATAATAA-TAATTACAAAACTAG
**
422035 CACCCTTTTAATAATAATTACAAAACTA
1 CACCCTAATAATAATAATTACAAAACTA
422063 ACAAACGATC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.47, C:0.21, G:0.03, T:0.29
Consensus pattern (29 bp):
CACCCTAATAATAATAATTACAAAACTAG
Found at i:422147 original size:14 final size:14
Alignment explanation
Indices: 422128--422157 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
422118 ATAGGTCAGA
*
422128 TCGGTTCAGATCGG
1 TCGGTTCAGACCGG
422142 TCGGTTCAGACCGG
1 TCGGTTCAGACCGG
422156 TC
1 TC
422158 AAACCTGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (14 bp):
TCGGTTCAGACCGG
Found at i:424501 original size:39 final size:39
Alignment explanation
Indices: 424379--424501 Score: 126
Period size: 39 Copynumber: 3.2 Consensus size: 39
424369 TTTAATGGGG
* * *
424379 GAATTTAAGAGTCTCTT-GAGAGTTAAAGTGTTTTATTGT
1 GAATTTAAGAGTCTCTTGGA-AGTTAGAGTATTTTATTTT
* * *
424418 GAAATTAAGATTCTCTTGGAAGTTATAGTATTTTATTTT
1 GAATTTAAGAGTCTCTTGGAAGTTAGAGTATTTTATTTT
*
424457 GAATTTAAGAGT-TCTTGGAAGATGTAGAGT-TTTTTTTTT
1 GAATTTAAGAGTCTCTTGGAAG-T-TAGAGTATTTTATTTT
*
424496 TAATTT
1 GAATTT
424502 TTTTAGTATA
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
38 9 0.13
39 55 0.77
40 7 0.10
ACGTcount: A:0.28, C:0.04, G:0.20, T:0.48
Consensus pattern (39 bp):
GAATTTAAGAGTCTCTTGGAAGTTAGAGTATTTTATTTT
Found at i:429173 original size:27 final size:27
Alignment explanation
Indices: 429139--429204 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
429129 CAAAGCTCGT
* * *
429139 GGTATTTTGGTCATTTTAAATTTTAAG
1 GGTATTTTAGTCATTTTAAAGTTCAAG
*
429166 GGTATTTTAGTCATTTTAGAGTTCAAG
1 GGTATTTTAGTCATTTTAAAGTTCAAG
*
429193 GGTATTTCAGTC
1 GGTATTTTAGTC
429205 CTTTCAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.24, C:0.08, G:0.21, T:0.47
Consensus pattern (27 bp):
GGTATTTTAGTCATTTTAAAGTTCAAG
Found at i:437923 original size:43 final size:41
Alignment explanation
Indices: 437850--437945 Score: 104
Period size: 43 Copynumber: 2.3 Consensus size: 41
437840 ATATTTAATG
* * *
437850 ATAATATA-TCTATAATCATTTATTATATTTTAAATGATTAAA
1 ATAATATATTTTATAATAATTTATTACATTTTAAAT-ATT-AA
* * * *
437892 ATAATTTATTTTATAATAATTTGTTACATTTTTACTATTAA
1 ATAATATATTTTATAATAATTTATTACATTTTAAATATTAA
437933 ATAATATATTTTA
1 ATAATATATTTTA
437946 ACATTATAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
41 14 0.31
42 10 0.22
43 21 0.47
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (41 bp):
ATAATATATTTTATAATAATTTATTACATTTTAAATATTAA
Found at i:448769 original size:25 final size:26
Alignment explanation
Indices: 448722--448775 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
448712 TATAAAATAA
*
448722 AATAATTAATAATAATTATTA-TTAT
1 AATAATTAATAATAATTACTATTTAT
*
448747 AATAA-TAATATATAGTTACTATTTAT
1 AATAATTAATA-ATAATTACTATTTAT
448773 AAT
1 AAT
448776 GTTTCTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.20
25 13 0.52
26 7 0.28
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (26 bp):
AATAATTAATAATAATTACTATTTAT
Found at i:449077 original size:55 final size:53
Alignment explanation
Indices: 449044--449800 Score: 643
Period size: 55 Copynumber: 14.2 Consensus size: 53
449034 ATAAAACTCA
449044 AACAATCTTCATA-AAACAG-GTCTGTTCCCTATTCCTTCAGAGAGTATAGGACT
1 AACAATCTTCA-ACAAAC-GTGTCTGTTCCCTATTCCTTCAGAGAGTATAGGACT
* * *
449097 --CGATCTTCAACAAATGTGTCTGCTCCCTATTCCTTCAGAGAGTATAGGACTT
1 AACAATCTTCAACAAACGTGTCTGTTCCCTATTCCTTCAGAGAGTATAGGAC-T
* *
449149 GAACAACCTTCAACAAACGTGTCAGTTCCCTATTCCTTCAGAGAGTATAGGACT
1 -AACAATCTTCAACAAACGTGTCTGTTCCCTATTCCTTCAGAGAGTATAGGACT
*
449203 --CAATCTTCAACAAAC-TCGTCTGTTCCCTATTCTTTCAGAGAGTATAGGACTT
1 AACAATCTTCAACAAACGT-GTCTGTTCCCTATTCCTTCAGAGAGTATAGGAC-T
* * *
449255 GAACAATCTTCAAAAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATATGACT
1 -AACAATCTTCAACAAACGTGTCTGTTCCCTATTCCTTCAGAGAGTATAGGACT
* * *** *
449309 --CGATCTTCAACAAATGTGTCCACTCCCTATTCCTTCAGAGAGTATAGGGCTT
1 AACAATCTTCAACAAACGTGTCTGTTCCCTATTCCTTCAGAGAGTATAGGAC-T
* * * * *
449361 GAACAATCTTCAACAAACGTGTCCGCTCCCTATTGCTTTAGAGAGTATAAGACT
1 -AACAATCTTCAACAAACGTGTCTGTTCCCTATTCCTTCAGAGAGTATAGGACT
* * * * *
449415 CGAACAATCTTCAACAATCATGTATGCTCCCTATTCCTTCAGAGAGTATAAGACT
1 --AACAATCTTCAACAAACGTGTCTGTTCCCTATTCCTTCAGAGAGTATAGGACT
* * * * *
449470 CAAACAATCTTCAACAATCGTGTCTGCTCCTTATTCCTTAAGAGAGTATAAGACTCT
1 --AACAATCTTCAACAAACGTGTCTGTTCCCTATTCCTTCAGAGAGTATAGGA--CT
* * * * * * *
449527 AATAATGTTCAACAATCGTGTCTGCTCCTTATTCCTTCAGAGACTATAAGACT
1 AACAATCTTCAACAAACGTGTCTGTTCCCTATTCCTTCAGAGAGTATAGGACT
* * * *
449580 CGAATAATCTTCAACAATCGTGTCT-TCTCCCTATTCGTTCAGAGAGTATAAGACT
1 --AACAATCTTCAACAAACGTGTCTGT-TCCCTATTCCTTCAGAGAGTATAGGACT
* * * *
449635 CGAACAATCTTCAACAATCGTTTCTGCTCCCTATTCGTTCAGAGAGTATA--A--
1 --AACAATCTTCAACAAACGTGTCTGTTCCCTATTCCTTCAGAGAGTATAGGACT
* * * * * *
449686 GAC--TC--GAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACT
1 AACAATCTTCAACAAACGTGTCTGTTCCCTATTCCTTCAGAGAGTATAGGACT
* * * * * *
449735 CGAACAATCTTCAATAATCGTGTCTGAT-CTTAATTCCTTTAGAGAGTATAAGACT
1 --AACAATCTTCAACAAACGTGTCTGTTCCCT-ATTCCTTCAGAGAGTATAGGACT
449790 CAAACAATCTT
1 --AACAATCTT
449801 GATGCTCCAA
Statistics
Matches: 605, Mismatches: 65, Indels: 66
0.82 0.09 0.09
Matches are distributed among these distances:
45 35 0.06
47 3 0.00
49 2 0.00
50 3 0.00
51 133 0.22
52 3 0.00
53 5 0.01
54 5 0.01
55 413 0.68
56 1 0.00
57 2 0.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (53 bp):
AACAATCTTCAACAAACGTGTCTGTTCCCTATTCCTTCAGAGAGTATAGGACT
Found at i:449479 original size:110 final size:110
Alignment explanation
Indices: 449018--449800 Score: 866
Period size: 106 Copynumber: 7.3 Consensus size: 110
449008 GTTCACTCTT
* * * * *
449018 TATTCCTTCAGGGATTATAAAACTCAAACAATCTTCATA-AAACAG-GTCTGTTCCCTATTCCTT
1 TATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCA-ACAAAC-GTGTCTGCTCCCTATTCCTT
*
449081 CAGAGAGTATAGGACTCG----ATCTTCAACAAAT-GTGTCTGCTCCC
64 CAGAGAGTATAAGACTCGAACAATCTTCAAC-AATCGTGTCTGCTCCC
* * * * *
449124 TATTCCTTCAGAGAGTATAGGACTTGAACAACCTTCAACAAACGTGTCAGTTCCCTATTCCTTCA
1 TATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATTCCTTCA
* * *
449189 GAGAGTATAGGACT----CAATCTTCAACAAAC-TCGTCTGTTCCC
66 GAGAGTATAAGACTCGAACAATCTTCAACAATCGT-GTCTGCTCCC
* * * *
449230 TATTCTTTCAGAGAGTATAGGACTTGAACAATCTTCAAAAAACGTGTCTGCTCCCTATTCCTTCA
1 TATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATTCCTTCA
* **
449295 GAGAGTATATGACTCG----ATCTTCAACAAAT-GTGTCCACTCCC
66 GAGAGTATAAGACTCGAACAATCTTCAAC-AATCGTGTCTGCTCCC
* * * * * *
449336 TATTCCTTCAGAGAGTATAGGGCTTGAACAATCTTCAACAAACGTGTCCGCTCCCTATTGCTTTA
1 TATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATTCCTTCA
* *
449401 GAGAGTATAAGACTCGAACAATCTTCAACAATCATGTATGCTCCC
66 GAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCC
* * * *
449446 TATTCCTTCAGAGAGTATAAGACTCAAACAATCTTCAACAATCGTGTCTGCTCCTTATTCCTTAA
1 TATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATTCCTTCA
* * * *
449511 GAGAGTATAAGACTCTAATAATGTTCAACAATCGTGTCTGCTCCT
66 GAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCC
* * * * *
449556 TATTCCTTCAGAGACTATAAGACTCGAATAATCTTCAACAATCGTGTCTTCTCCCTATTCGTTCA
1 TATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATTCCTTCA
*
449621 GAGAGTATAAGACTCGAACAATCTTCAACAATCGTTTCTGCTCCC
66 GAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCC
* *
449666 TATTCGTTCAGAGAGTATAAGACTCGAACAA---T-------CGTGTCTGCTCCCTATTTCTTCA
1 TATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATTCCTTCA
* * *
449721 GAGAGTATAAGACTCGAACAATCTTCAATAATCGTGTCTGAT-CT
66 GAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCC
* *
449765 TAATTCCTTTAGAGAGTATAAGACTCAAACAATCTT
1 T-ATTCCTTCAGAGAGTATAAGACTCGAACAATCTT
449801 GATGCTCCAA
Statistics
Matches: 587, Mismatches: 71, Indels: 41
0.84 0.10 0.06
Matches are distributed among these distances:
99 2 0.00
100 86 0.15
103 1 0.00
105 5 0.01
106 248 0.42
107 4 0.01
109 3 0.01
110 238 0.41
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (110 bp):
TATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATTCCTTCA
GAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCC
Found at i:449711 original size:45 final size:45
Alignment explanation
Indices: 449647--449743 Score: 169
Period size: 45 Copynumber: 2.2 Consensus size: 45
449637 AACAATCTTC
*
449647 AACAATCGTTTCTGCTCCCTA-TTCGTTCAGAGAGTATAAGACTCG
1 AACAATCGTGTCTGCTCCCTATTTC-TTCAGAGAGTATAAGACTCG
449692 AACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCG
1 AACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCG
449737 AACAATC
1 AACAATC
449744 TTCAATAATC
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 47 0.94
46 3 0.06
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (45 bp):
AACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCG
Found at i:449726 original size:100 final size:100
Alignment explanation
Indices: 449592--449798 Score: 310
Period size: 100 Copynumber: 2.1 Consensus size: 100
449582 AATAATCTTC
* *
449592 AACAATCGTGTCTTCTCCCTATTCGTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTT
1 AACAATCGTGTCTGCTCCCTATTCGTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTG
* * *
449657 TCTGCTCCCT-ATTCGTTCAGAGAGTATAAGACTCG
66 TCTGAT-CCTAATTCCTTCAGAGAGTATAAGACTCA
*
449692 AACAATCGTGTCTGCTCCCTATTTC-TTCAGAGAGTATAAGACTCGAACAATCTTCAATAATCGT
1 AACAATCGTGTCTGCTCCCTA-TTCGTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGT
* *
449756 GTCTGATCTTAATTCCTTTAGAGAGTATAAGACTCA
65 GTCTGATCCTAATTCCTTCAGAGAGTATAAGACTCA
449792 AACAATC
1 AACAATC
449799 TTGATGCTCC
Statistics
Matches: 97, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
99 2 0.02
100 92 0.95
101 3 0.03
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.31
Consensus pattern (100 bp):
AACAATCGTGTCTGCTCCCTATTCGTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTG
TCTGATCCTAATTCCTTCAGAGAGTATAAGACTCA
Found at i:450870 original size:9 final size:10
Alignment explanation
Indices: 450847--450872 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
450837 TTTTGCTTCA
450847 TTTTTTCCTC
1 TTTTTTCCTC
450857 TTTTTTCCTC
1 TTTTTTCCTC
450867 TTTTTT
1 TTTTTT
450873 TATTCATTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTTCCTC
Found at i:450872 original size:32 final size:31
Alignment explanation
Indices: 450831--450900 Score: 81
Period size: 32 Copynumber: 2.3 Consensus size: 31
450821 CATCTTGAAC
* *
450831 CCTCCTTTTTGCTTCATT-TTTTCCTCTTTTTT
1 CCTCTTTTTTGATTCATTCTTTT-CTC-TTTTT
*
450863 CCTCTTTTTTTATTCATTCTTTTCTCTTTTT
1 CCTCTTTTTTGATTCATTCTTTTCTCTTTTT
450894 -CTCTTTT
1 CCTCTTTT
450901 CATTTTTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 7 0.21
31 5 0.15
32 18 0.53
33 4 0.12
ACGTcount: A:0.04, C:0.26, G:0.01, T:0.69
Consensus pattern (31 bp):
CCTCTTTTTTGATTCATTCTTTTCTCTTTTT
Found at i:450907 original size:7 final size:8
Alignment explanation
Indices: 450870--450924 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
450860 TTTCCTCTTT
450870 TTTTATTCA
1 TTTT-TTCA
450879 TTCTTTTC-
1 TT-TTTTCA
450887 TCTTTTTC-
1 T-TTTTTCA
*
450895 TCTTTTCA
1 TTTTTTCA
450903 TTTTTTCA
1 TTTTTTCA
*
450911 TTTTTTTA
1 TTTTTTCA
450919 TTTTTT
1 TTTTTT
450925 TTCTTTTTCC
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
7 5 0.12
8 27 0.68
9 6 0.15
10 2 0.05
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTTCA
Found at i:450907 original size:15 final size:15
Alignment explanation
Indices: 450880--450931 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
450870 TTTTATTCAT
450880 TCTTTTC-TCTTTTTC
1 TCTTTTCAT-TTTTTC
450895 TCTTTTCATTTTTTC
1 TCTTTTCATTTTTTC
* * *
450910 ATTTTTTTATTTTTTT
1 -TCTTTTCATTTTTTC
450926 TCTTTT
1 TCTTTT
450932 TCCTCTTCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 18 0.58
16 13 0.42
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (15 bp):
TCTTTTCATTTTTTC
Found at i:450922 original size:22 final size:21
Alignment explanation
Indices: 450857--450923 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 21
450847 TTTTTTCCTC
*
450857 TTTTTTCCTCTTTTTTTATTCA
1 TTTTTT-CTCTTTTTTTTTTCA
450879 TTCTTTTCTCTTTTTCTCTTTTCA
1 TT-TTTTCTCTTTTT-T-TTTTCA
*
450903 TTTTTTCATTTTTTTATTTTT
1 TTTTTTC-TCTTTTT-TTTTT
450924 TTTCTTTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
22 10 0.26
23 14 0.37
24 14 0.37
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTTTCTCTTTTTTTTTTCA
Found at i:450925 original size:32 final size:30
Alignment explanation
Indices: 450843--450932 Score: 92
Period size: 32 Copynumber: 2.9 Consensus size: 30
450833 TCCTTTTTGC
*
450843 TTCATTTTTTCCTCTTTTTTCCTCTTTTTTTA
1 TTCATTTTTT--TCTTTTTTTCTCTTTTTTTA
* * *
450875 TTCATTCTTTTCTCTTTTTCTCTTTTCATTTT
1 TTCATTTTTTTCTTTTTTTCTCTTTT--TTTA
*
450907 TTCATTTTTTTATTTTTTT-TCTTTTT
1 TTCATTTTTTTCTTTTTTTCTCTTTTT
450933 CCTCTTCAAG
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
29 1 0.02
30 14 0.29
31 6 0.12
32 28 0.57
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.76
Consensus pattern (30 bp):
TTCATTTTTTTCTTTTTTTCTCTTTTTTTA
Found at i:454321 original size:90 final size:89
Alignment explanation
Indices: 454215--454380 Score: 278
Period size: 90 Copynumber: 1.9 Consensus size: 89
454205 ATTTAATTTC
* * *
454215 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATTCCTGATATGATTAGGGTAACTT
1 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGACTAGGGTAACTT
454280 AGATATAAAAGGATTATTAAATTAT
65 AGATATAAAAGGATTATTAAATTAT
*
454305 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGACTAGGGTAACTTG
1 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGACTAGGGTAACTTA
*
454370 GCTATAAAAGG
66 GATATAAAAGG
454381 GTGTGTTAGG
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
89 30 0.42
90 41 0.58
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.36
Consensus pattern (89 bp):
AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGACTAGGGTAACTTA
GATATAAAAGGATTATTAAATTAT
Found at i:472535 original size:130 final size:130
Alignment explanation
Indices: 472302--472566 Score: 503
Period size: 130 Copynumber: 2.0 Consensus size: 130
472292 GTTTTGATTT
* *
472302 AGTGAGATTTGCTGAATTGGCCAACTTTGATGATGATGACAACTTCTAGAAGCATTCGACGTTGG
1 AGTGACATTTGCTGAATTAGCCAACTTTGATGATGATGACAACTTCTAGAAGCATTCGACGTTGG
472367 CTTGTTTATGGTGACAGAGGAGGCTTAGCTGGTTATCATTTAGGGTTGAGAAACCTTAACCCTTA
66 CTTGTTTATGGTGACAGAGGAGGCTTAGCTGGTTATCATTTAGGGTTGAGAAACCTTAACCCTTA
*
472432 AGTGACATTTGTTGAATTAGCCAACTTTGATGATGATGACAACTTCTAGAAGCATTCGACGTTGG
1 AGTGACATTTGCTGAATTAGCCAACTTTGATGATGATGACAACTTCTAGAAGCATTCGACGTTGG
472497 CTTGTTTATGGTGACAGAGGAGGCTTAGCTGGTTATCATTTAGGGTTGAGAAACCTTAACCCTTA
66 CTTGTTTATGGTGACAGAGGAGGCTTAGCTGGTTATCATTTAGGGTTGAGAAACCTTAACCCTTA
472562 AGTGA
1 AGTGA
472567 TCTGGGTTGG
Statistics
Matches: 132, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
130 132 1.00
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (130 bp):
AGTGACATTTGCTGAATTAGCCAACTTTGATGATGATGACAACTTCTAGAAGCATTCGACGTTGG
CTTGTTTATGGTGACAGAGGAGGCTTAGCTGGTTATCATTTAGGGTTGAGAAACCTTAACCCTTA
Found at i:485018 original size:19 final size:19
Alignment explanation
Indices: 484996--485042 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
484986 ATTTTGCATA
*
484996 TGCATTTTACTTTTCACAT
1 TGCATTTTAATTTTCACAT
**
485015 TGCATTTTAATTTTTGCAT
1 TGCATTTTAATTTTCACAT
*
485034 TGTATTTTA
1 TGCATTTTA
485043 TTCATTCATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.21, C:0.13, G:0.09, T:0.57
Consensus pattern (19 bp):
TGCATTTTAATTTTCACAT
Found at i:485500 original size:21 final size:21
Alignment explanation
Indices: 485476--485515 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
485466 TGGAGCAAAC
* *
485476 AAACAGCTGGAGGAGAAGTGG
1 AAACAACTAGAGGAGAAGTGG
*
485497 AAACAACTAGAGGGGAAGT
1 AAACAACTAGAGGAGAAGT
485516 CAGGGCTATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.10, G:0.38, T:0.10
Consensus pattern (21 bp):
AAACAACTAGAGGAGAAGTGG
Found at i:489566 original size:194 final size:189
Alignment explanation
Indices: 489366--489727 Score: 442
Period size: 194 Copynumber: 1.9 Consensus size: 189
489356 AACGTCAATA
* * ** *
489366 TATAATTAATATTCA-ATGACAACTAATTATGTCATTAAATTATGTAAAATTT-TGTTATTGATG
1 TATAATTAATATT-ATATGACAACTAATTACGTCACTAAATTAAATAAAATTTCT-TTATTGATA
* **
489429 ATTTATATCGTAACGGATAATACATTAAAATCAACCTATATGTGACGAAAGAGATATTGTCAAAT
64 AGTTATATCGTAACAAATAATACATTAAAATCAA-CT-TATGTGACGAAAGAGATATTGTCAAAT
489494 TTTTAATAACATAATATAAAT-GTTACCTAATAATATTATGAATGACATTTATGCATAAAATCAC
127 TTTTAATAAC--AATAT--ATCGTTACCTAATAATATTATGAATGACATTTATGCATAAAATCAC
489558 TT
188 TT
* * ** * *
489560 TATAATTTATATTATATGACAATTGGTTACGTCACTGAATTAAATAAGATTTCTTTATTGATAAG
1 TATAATTAATATTATATGACAACTAATTACGTCACTAAATTAAATAAAATTTCTTTATTGATAAG
* * * * *
489625 TTATATTGTCACAAATAATGCATTAAAATCAACTTATGTGACGAAAGAGATATTTTCACATTTTT
66 TTATATCGTAACAAATAATACATTAAAATCAACTTATGTGACGAAAGAGATATTGTCAAATTTTT
* *
489690 AATGACAATATATCGTTACCTATTAATATTATGAATGA
131 AATAACAATATATCGTTACCTAATAATATTATGAATGA
489728 TGATTATGTA
Statistics
Matches: 144, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
188 2 0.01
189 23 0.16
190 5 0.03
192 34 0.24
193 3 0.02
194 76 0.53
195 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (189 bp):
TATAATTAATATTATATGACAACTAATTACGTCACTAAATTAAATAAAATTTCTTTATTGATAAG
TTATATCGTAACAAATAATACATTAAAATCAACTTATGTGACGAAAGAGATATTGTCAAATTTTT
AATAACAATATATCGTTACCTAATAATATTATGAATGACATTTATGCATAAAATCACTT
Found at i:493222 original size:14 final size:14
Alignment explanation
Indices: 493203--493235 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
493193 ATTTCTATAT
*
493203 AGGGAATTATTTGC
1 AGGGAATTATTTAC
493217 AGGGAATTATTTAC
1 AGGGAATTATTTAC
493231 AGGGA
1 AGGGA
493236 TTACTCCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (14 bp):
AGGGAATTATTTAC
Found at i:493458 original size:3 final size:3
Alignment explanation
Indices: 493450--493475 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
493440 AATTAGGGTT
493450 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
493476 TTTTGTATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:494813 original size:21 final size:21
Alignment explanation
Indices: 494788--494847 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
494778 ATGAAAACAT
494788 ATAAAAAATAACTAAATTATA
1 ATAAAAAATAACTAAATTATA
* *
494809 ATAAAAATAAAACTAAA-TCTA
1 ATAAAAA-ATAACTAAATTATA
**
494830 ATAATTAATAA-TAAATTA
1 ATAAAAAATAACTAAATTA
494848 ATGTTAATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
19 4 0.13
20 4 0.13
21 15 0.48
22 8 0.26
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (21 bp):
ATAAAAAATAACTAAATTATA
Found at i:494822 original size:22 final size:24
Alignment explanation
Indices: 494788--494844 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 24
494778 ATGAAAACAT
*
494788 ATAAAAA-ATAACTAAAT-T-ATA
1 ATAAAAATAAAACTAAATCTAATA
494809 ATAAAAATAAAACTAAATCTAATA
1 ATAAAAATAAAACTAAATCTAATA
*
494833 ATTAATAATAAA
1 A-TAAAAATAAA
494845 TTAATGTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 7 0.23
22 9 0.30
23 1 0.03
24 4 0.13
25 9 0.30
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (24 bp):
ATAAAAATAAAACTAAATCTAATA
Found at i:495158 original size:23 final size:23
Alignment explanation
Indices: 495128--495177 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
495118 AAGGGATTTT
495128 TTCCATAATTACGCGCATAGTCC
1 TTCCATAATTACGCGCATAGTCC
495151 TTCCATAATTACGCGCATAGTCC
1 TTCCATAATTACGCGCATAGTCC
495174 TTCC
1 TTCC
495178 CGAAACGACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.32, G:0.12, T:0.32
Consensus pattern (23 bp):
TTCCATAATTACGCGCATAGTCC
Found at i:495652 original size:22 final size:21
Alignment explanation
Indices: 495622--495665 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
495612 AGTTTGGATT
495622 TTTCTGTTTTTTTTTCTAGTCTC
1 TTTCTG-TTTTTTTTCT-GTCTC
495645 TTTC-GTTTTTTTTCTGTCTC
1 TTTCTGTTTTTTTTCTGTCTC
495665 T
1 T
495666 CTGTCTCGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.29
21 10 0.48
22 1 0.05
23 4 0.19
ACGTcount: A:0.02, C:0.18, G:0.09, T:0.70
Consensus pattern (21 bp):
TTTCTGTTTTTTTTCTGTCTC
Found at i:496157 original size:3 final size:3
Alignment explanation
Indices: 496149--496243 Score: 122
Period size: 3 Copynumber: 31.7 Consensus size: 3
496139 TTAATATATT
* * *
496149 TAA TAA TAA TAG TAA AAA TAA TAA TAA T-A TAA TAA AAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
496196 TAA TAAA TAA TAA TGA TAA TAA TAA TAA TATA TAA TAA T-A TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
496242 TA
1 TA
496244 TGGATAAAAA
Statistics
Matches: 80, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
2 4 0.05
3 70 0.88
4 6 0.08
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:497098 original size:109 final size:113
Alignment explanation
Indices: 496534--497263 Score: 1154
Period size: 109 Copynumber: 6.6 Consensus size: 113
496524 AAACAAAGGT
* *
496534 TTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTTTTCATTCATG
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC-TTCTCATT-ATG
* * * * * *
496599 AACTTTCTCTAGCAATGTTGATCCATCAAATGAT-GAATTAAACAAAAAG
64 AACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTTAAACAAAAAG
* *
496648 TTGAAAAAGTTCTTCTCATTATGAAACCTCTTCTTCCTTCTTCAGATGAGTTCTT-TCATTATGA
1 TTGAACAAGTTCTTCTCATTATG-AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
496712 ACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTTAAAC-AAAAG
65 ACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTTAAACAAAAAG
496760 TTGAACAAG-T-TTCTCATTATGAA-TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA-TATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
496821 CTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTTAAACAAAAAG
66 CTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTTAAACAAAAAG
496869 TTG---AAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTC-TCTCA-T-TGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
496927 CTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTTAAACAAAAAG
66 CTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTTAAACAAAAAG
*
496975 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
497040 CTTTCTCTGG-AAA-ATGAT-CACCAAATGATGGATTTAAACAAAAAG
66 CTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTTAAACAAAAAG
497085 -TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* *** *
497149 CTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGG
66 CTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTTAAACAAAAAG
*
497197 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
497262 CT
66 CT
497264 CTACCTTGCA
Statistics
Matches: 579, Mismatches: 19, Indels: 37
0.91 0.03 0.06
Matches are distributed among these distances:
106 58 0.10
107 7 0.01
108 103 0.18
109 125 0.22
110 56 0.10
111 16 0.03
112 71 0.12
113 92 0.16
114 23 0.04
115 28 0.05
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.37
Consensus pattern (113 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTTAAACAAAAAG
Found at i:497218 original size:222 final size:223
Alignment explanation
Indices: 496524--497263 Score: 1125
Period size: 222 Copynumber: 3.3 Consensus size: 223
496514 AGATAATATC
**
496524 AAAC-AAAGGTTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTT
1 AAACAAAAGG-TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC-T
* * ** * *
496588 TTTCATTCATGAACTTTCTCTAGCAATGTTGATCCATCAAATGAT-GAATTAAACAAAAAGTTGA
64 TCTCATT-ATGAACTTTCTCT-GGAA-AATGATCCACCAAATGATGGATTTAAACAAAAAGTTG-
*
496652 AAAAGTTCTTCTCATTATGAAACCTCTTCTTCCTTCTTCAGATGAGTTCTT-TCATTATGAACTT
125 AAAAGTTCTTCTCATTATG-AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
496716 TCTCTGGAAAAGATGATCCACCAAATGATGGATTT
189 TCTCTGGAAAAGATGATCCACCAAATGATGGATTT
*
496751 AAACAAAA-GTTGAAC-AAGT-TTCTCATTATGAA-TTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
496812 TCA-TATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTTAAACAAAAAGTTG--AA
66 TCATTATGAACTTTCTCTGG-AAA-ATGATCCACCAAATGATGGATTTAAACAAAAAGTTGAAAA
496874 GTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTC-TCTCA-T-TGAACTTTCTCT
129 GTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
496935 GGAAAAGATGATCCACCAAATGATGGATTT
194 GGAAAAGATGATCCACCAAATGATGGATTT
* * *
496965 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTC
1 AAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
497030 TCATTATGAACTTTCTCTGGAAAATGAT-CACCAAATGATGGATTTAAACAAAAAG-TGAACAAG
66 TCATTATGAACTTTCTCTGGAAAATGATCCACCAAATGATGGATTTAAACAAAAAGTTGAA-AAG
497093 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
130 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
497158 GAAAAGATGATCCACCAAATGATGGATTC
195 GAAAAGATGATCCACCAAATGATGGATTT
***
497187 AGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
497252 TCATTATGAACT
66 TCATTATGAACT
497264 CTACCTTGCA
Statistics
Matches: 477, Mismatches: 19, Indels: 39
0.89 0.04 0.07
Matches are distributed among these distances:
214 50 0.10
215 11 0.02
216 47 0.10
217 30 0.06
218 81 0.17
219 32 0.07
220 35 0.07
221 19 0.04
222 117 0.25
223 26 0.05
224 13 0.03
225 2 0.00
226 6 0.01
227 5 0.01
228 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.37
Consensus pattern (223 bp):
AAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
TCATTATGAACTTTCTCTGGAAAATGATCCACCAAATGATGGATTTAAACAAAAAGTTGAAAAGT
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
AAAAGATGATCCACCAAATGATGGATTT
Found at i:498080 original size:82 final size:82
Alignment explanation
Indices: 497986--498214 Score: 338
Period size: 84 Copynumber: 2.8 Consensus size: 82
497976 TTATCTTTTG
* **
497986 ATTCGAATGATTGTTTCTGTACTTCCAGATC-ATAACTCAAAGAACACTTCCAGAAGATGCTATT
1 ATTC-AATGATTG-TTCTGTCCAACCAGATCAATAACTCAAAGAACACTTCCAGAAGATGCTATT
498050 GAGCACATTCATCTTCTAA
64 GAGCACATTCATCTTCTAA
* *
498069 TTTCAATGATTGGTTCTGTCCAACCATATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
1 ATTCAATGATT-GTTCTGTCCAACCAGATCA-ATAACTCAAAGAACACTTCCAGAAGATGCTATT
498134 GAGCACATTCATCTTCTAA
64 GAGCACATTCATCTTCTAA
498153 ATTC-ATGATTAGTTCTGTCCAACCAGATCAGATAACTC-AAGAACACTTCCAGAAGATGCTAT
1 ATTCAATGATT-GTTCTGTCCAACCAGATCA-ATAACTCAAAGAACACTTCCAGAAGATGCTAT
498215 GTTCTGTCCA
Statistics
Matches: 135, Mismatches: 8, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
82 44 0.33
83 36 0.27
84 55 0.41
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.31
Consensus pattern (82 bp):
ATTCAATGATTGTTCTGTCCAACCAGATCAATAACTCAAAGAACACTTCCAGAAGATGCTATTGA
GCACATTCATCTTCTAA
Found at i:498119 original size:84 final size:83
Alignment explanation
Indices: 498010--498214 Score: 353
Period size: 84 Copynumber: 2.5 Consensus size: 83
498000 TTCTGTACTT
*
498010 CCAGATC--ATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAATTTC
1 CCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAATTC
*
498073 AATGATTGGTTCTGTCCAA
66 -ATGATTAGTTCTGTCCAA
*
498092 CCATATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAATTC
1 CCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAATTC
498157 ATGATTAGTTCTGTCCAA
66 ATGATTAGTTCTGTCCAA
498175 CCAGATCAGATAACTC-AAGAACACTTCCAGAAGATGCTAT
1 CCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
498215 GTTCTGTCCA
Statistics
Matches: 117, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
82 30 0.26
83 32 0.27
84 55 0.47
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.28
Consensus pattern (83 bp):
CCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAATTC
ATGATTAGTTCTGTCCAA
Found at i:498269 original size:52 final size:52
Alignment explanation
Indices: 498164--498479 Score: 598
Period size: 52 Copynumber: 6.1 Consensus size: 52
498154 TTCATGATTA
498164 GTTCTGTCCAACCAGATCAGATAACTC-AAGAACACTTCCAGAAGATGCTAT
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
*
498215 GTTCTGTCCAAACAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
498267 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
* *
498319 TTTCTGTCCAAACAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
498371 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
498423 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
498475 GTTCT
1 GTTCT
498480 ATTCATTTGT
Statistics
Matches: 258, Mismatches: 6, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
51 26 0.10
52 232 0.90
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.24
Consensus pattern (52 bp):
GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
Found at i:499632 original size:10 final size:10
Alignment explanation
Indices: 499603--499634 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
499593 TTGACCCCCC
499603 CTTTTTTTTT
1 CTTTTTTTTT
499613 -TTTTTTTTT
1 CTTTTTTTTT
499622 CTTTTTTTTT
1 CTTTTTTTTT
499632 CTT
1 CTT
499635 CAAGCATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:507821 original size:154 final size:151
Alignment explanation
Indices: 507604--507908 Score: 517
Period size: 154 Copynumber: 2.0 Consensus size: 151
507594 GACCTCAAAA
*
507604 TTCCATTTTTGCTTTCCTTTTTCCAGGCTTTGAGTAGACGGCTATTCTTTCTTTTAGATCTTCAA
1 TTCCATTTTTGCTTTCCTTTTTCCAGGCTTTGAGTAGACGGCTATTCTTTCCTTTAGATCTTCAA
507669 CTCGTCTTTTTCTCAATGTTCAATTCT-TGGTCATATGTACCGTCGA-TGG-TGGGTCCTGATGC
66 CTCGTC-TTTTCTCAATGTTCAATTCTCTGGTC--ATGTACCGTCGATTGGTTGGGTCCTGATGC
507731 TTTTCGGGATTTGTATAACTCCTG
128 TTTTCGGGATTTGTATAACTCCTG
507755 TTCCATTTTTTGCTTTCCTTTTTCCAGGCTTTTGAGTAGAACGGCTATTCTTTCCTTTAGATCTT
1 TTCCA-TTTTTGCTTTCCTTTTTCCAGGC-TTTGAGTAG-ACGGCTATTCTTTCCTTTAGATCTT
*
507820 CAACTCGTCTTTTCTCAATGTTCAATTCTCTGGTCATGTACCGTTGATTGGTTGGGTCCTGATGC
63 CAACTCGTCTTTTCTCAATGTTCAATTCTCTGGTCATGTACCGTCGATTGGTTGGGTCCTGATGC
507885 TTTTCGGGATTTGTATAACTCCTG
128 TTTTCGGGATTTGTATAACTCCTG
507909 GTAATTTTTC
Statistics
Matches: 146, Mismatches: 2, Indels: 9
0.93 0.01 0.06
Matches are distributed among these distances:
151 5 0.03
152 34 0.23
153 32 0.22
154 75 0.51
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.45
Consensus pattern (151 bp):
TTCCATTTTTGCTTTCCTTTTTCCAGGCTTTGAGTAGACGGCTATTCTTTCCTTTAGATCTTCAA
CTCGTCTTTTCTCAATGTTCAATTCTCTGGTCATGTACCGTCGATTGGTTGGGTCCTGATGCTTT
TCGGGATTTGTATAACTCCTG
Found at i:511530 original size:23 final size:23
Alignment explanation
Indices: 511500--511545 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
511490 GATTTCTCTG
* *
511500 TTTTTTTCTATGTCTCTTTCGTT
1 TTTTTTTCTATCTCTCTCTCGTT
*
511523 TTTTTTTCTGTCTCTCTCTCGTT
1 TTTTTTTCTATCTCTCTCTCGTT
511546 GTATATATCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.02, C:0.22, G:0.09, T:0.67
Consensus pattern (23 bp):
TTTTTTTCTATCTCTCTCTCGTT
Found at i:512029 original size:3 final size:3
Alignment explanation
Indices: 512021--512123 Score: 154
Period size: 3 Copynumber: 34.7 Consensus size: 3
512011 TTTAATATAT
* *
512021 TAA TAA TAA TAG TAA -AA TAA TAA TAA TAA TAA TAA TAA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
512068 TAA TAA TAA TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
512116 TAA TAA TA
1 TAA TAA TA
512124 TGGATAAAAA
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
2 2 0.02
3 87 0.98
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:512478 original size:21 final size:21
Alignment explanation
Indices: 512454--512530 Score: 88
Period size: 21 Copynumber: 3.8 Consensus size: 21
512444 TAAATAGTTG
512454 AAGTTCGCGTTGCGATAGTCA
1 AAGTTCGCGTTGCGATAGTCA
**
512475 AAGTTCGCGTTGCGATTTTCCA
1 AAGTTCGCGTTGCGATAGT-CA
* *
512497 AA-TT--CTTTGCGATAGTCG
1 AAGTTCGCGTTGCGATAGTCA
512515 AAGTTCGCGTTGCGAT
1 AAGTTCGCGTTGCGAT
512531 TTATTCCAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
18 3 0.07
19 11 0.24
21 27 0.60
22 4 0.09
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (21 bp):
AAGTTCGCGTTGCGATAGTCA
Found at i:512519 original size:40 final size:40
Alignment explanation
Indices: 512461--512592 Score: 201
Period size: 40 Copynumber: 3.2 Consensus size: 40
512451 TTGAAGTTCG
*
512461 CGTTGCGATAGTCAAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
*
512501 CTTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
* * *
512543 AGTTGCGATAATCGAAGTTCGTGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
512583 CGTTGCGATA
1 CGTTGCGATA
512593 TCGCGTTGCG
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
40 45 0.54
41 4 0.05
42 34 0.41
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (40 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
Found at i:512584 original size:21 final size:21
Alignment explanation
Indices: 512473--512585 Score: 72
Period size: 21 Copynumber: 5.4 Consensus size: 21
512463 TTGCGATAGT
*
512473 CAAAGTTCGCGTTGCGATTTTC
1 CAAA-TTCGTGTTGCGATTTTC
**
512495 CAAATTC-T-TTGCGATAGTC
1 CAAATTCGTGTTGCGATTTTC
* * *
512514 GAAGTTCGCGTTGCGATTTATTC
1 CAAATTCGTGTTGCGA-TT-TTC
* **
512537 CAAATT--AGTTGCGATAATC
1 CAAATTCGTGTTGCGATTTTC
* *
512556 GAAGTTCGTGTTGCGATTTTC
1 CAAATTCGTGTTGCGATTTTC
512577 CAAATTCGT
1 CAAATTCGT
512586 TGCGATATCG
Statistics
Matches: 65, Mismatches: 20, Indels: 13
0.66 0.20 0.13
Matches are distributed among these distances:
19 20 0.31
20 1 0.02
21 33 0.51
22 5 0.08
23 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (21 bp):
CAAATTCGTGTTGCGATTTTC
Found at i:512733 original size:6 final size:6
Alignment explanation
Indices: 512722--512754 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
512712 GACACGTATT
512722 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
512755 CGAGACGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:513281 original size:12 final size:11
Alignment explanation
Indices: 513249--513284 Score: 56
Period size: 10 Copynumber: 3.3 Consensus size: 11
513239 TCTCATCTCG
513249 GGTCGGGTCG-
1 GGTCGGGTCGT
513259 GGTCGGGTCGT
1 GGTCGGGTCGT
513270 GGTCGTGGTCGT
1 GGTCG-GGTCGT
513282 GGT
1 GGT
513285 AATACGTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.42
11 5 0.21
12 9 0.38
ACGTcount: A:0.00, C:0.17, G:0.56, T:0.28
Consensus pattern (11 bp):
GGTCGGGTCGT
Found at i:513284 original size:6 final size:5
Alignment explanation
Indices: 513246--513280 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
513236 TCGTCTCATC
513246 TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG
513281 TGGTAATACG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.62
6 11 0.38
ACGTcount: A:0.00, C:0.20, G:0.54, T:0.26
Consensus pattern (5 bp):
TCGGG
Found at i:519114 original size:43 final size:46
Alignment explanation
Indices: 519012--519117 Score: 121
Period size: 50 Copynumber: 2.3 Consensus size: 46
519002 AGGATTAGAT
519012 TTATTATTTTATTAGGAATTAAGGTTGAGTTAAAACATTATTTTTAGTTA
1 TTATTATTTTATTAGGAATTAA-G--GAGTTAAAACATTA-TTTTAGTTA
* *
519062 TTATTATTTTATTAGGAATT-A-GAGTTAAGACA-TA-TTTAGTTTG
1 TTATTATTTTATTAGGAATTAAGGAGTTAAAACATTATTTTAG-TTA
519105 TTATTATTTTATT
1 TTATTATTTTATT
519118 CATTAATTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
42 5 0.09
43 15 0.28
44 2 0.04
45 10 0.19
49 1 0.02
50 20 0.38
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (46 bp):
TTATTATTTTATTAGGAATTAAGGAGTTAAAACATTATTTTAGTTA
Found at i:520699 original size:10 final size:9
Alignment explanation
Indices: 520687--520743 Score: 64
Period size: 8 Copynumber: 6.2 Consensus size: 9
520677 GAAAGAAAAT
*
520687 AAAAATGAA
1 AAAAAAGAA
520696 TAAAAAATGAA
1 -AAAAAA-GAA
520707 AAAAGAAGAA
1 AAAA-AAGAA
520717 AAAAAAG-A
1 AAAAAAGAA
520725 AAAAAAG-A
1 AAAAAAGAA
520733 AAAAAAGAA
1 AAAAAAGAA
520742 AA
1 AA
520744 TGAATAAAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
8 16 0.37
9 6 0.14
10 16 0.37
11 5 0.12
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.05
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:520708 original size:17 final size:17
Alignment explanation
Indices: 520688--520752 Score: 60
Period size: 16 Copynumber: 3.8 Consensus size: 17
520678 AAAGAAAATA
*
520688 AAAATGAATAAAAAATG
1 AAAATGAATAAAAAAAG
* *
520705 AAAAAAGAAGAAAAAAAAG
1 -AAAATGAA-TAAAAAAAG
* *
520724 AAAA-AAAGAAAAAAAG
1 AAAATGAATAAAAAAAG
520740 AAAATGAATAAAA
1 AAAATGAATAAAA
520753 GGAGAGTTCA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
16 12 0.32
17 8 0.21
18 11 0.29
19 7 0.18
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (17 bp):
AAAATGAATAAAAAAAG
Found at i:520709 original size:9 final size:8
Alignment explanation
Indices: 520674--520743 Score: 59
Period size: 8 Copynumber: 8.0 Consensus size: 8
520664 TATTTTGCCT
520674 AAAGAAAGA
1 AAAGAAA-A
*
520683 AAATAAAA
1 AAAGAAAA
*
520691 ATGAATAAAA
1 A--AAGAAAA
*
520701 AATGAAAAA
1 AAAG-AAAA
520710 AGAAGAAAAA
1 A-AAG-AAAA
520720 AAAGAAAA
1 AAAGAAAA
520728 AAAGAAAA
1 AAAGAAAA
520736 AAAGAAAA
1 AAAGAAAA
520744 TGAATAAAAG
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
8 23 0.43
9 14 0.26
10 16 0.30
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (8 bp):
AAAGAAAA
Found at i:525837 original size:117 final size:117
Alignment explanation
Indices: 525618--525842 Score: 299
Period size: 117 Copynumber: 1.9 Consensus size: 117
525608 CAACTCCCTA
** *
525618 TGTGATGGAATCAAGCTGAGGTTGAACAAGTTATTCTAATTATGAACTTCTTCTCCCTCGTAAGA
1 TGTGATGGAATCAAGCCAAGGTTGAACAAGTTATTCTAATTATGAACTTCTTCTCCCTCATAAGA
* * *
525683 TGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTGATCCACCTCCTTC
66 TGAGTTCTTCTCATTATAAACTATCCACTGGAAATGTTGATCCACCTCCTTC
* * * * *
525735 TGTGATGGAATCGAA-CCAAGGTTGAACAAGTTTTTCTCATTATGAATTTCTTCTCCTTCATTAG
1 TGTGATGGAATC-AAGCCAAGGTTGAACAAGTTATTCTAATTATGAACTTCTTCTCCCTCATAAG
* * * *
525799 ATGAGTTCTTCTTATTATAAACTATTCACTGGATATGTTTATCC
65 ATGAGTTCTTCTCATTATAAACTATCCACTGGAAATGTTGATCC
525843 CTTCATTCTA
Statistics
Matches: 92, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
117 90 0.98
118 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (117 bp):
TGTGATGGAATCAAGCCAAGGTTGAACAAGTTATTCTAATTATGAACTTCTTCTCCCTCATAAGA
TGAGTTCTTCTCATTATAAACTATCCACTGGAAATGTTGATCCACCTCCTTC
Found at i:525981 original size:319 final size:319
Alignment explanation
Indices: 525548--526136 Score: 844
Period size: 320 Copynumber: 1.8 Consensus size: 319
525538 GATGGACGAG
* ** * * *
525548 CAAAATGATGATGTTGATCCAACTCCTTATGTGATGGATGAGCCAAGGTCGGTGCTGTTTCAACT
1 CAAAATGATGATGTTGATCCAACTCCATATACGATGGATAAGCCAAGATCGGTGCTGTTCCAACT
* *
525613 CCCTATGTGATGGAATCAAGCTGAGGTTGAACAAGTTATTCTAATTATGAACTTC-TTCTCCCTC
66 CCCTATATGATGGAATCAAGCTAAGGTTGAACAAGTTATTCTAATTATGAAC-TCATTCTCCCTC
* * **
525677 GTA-AGATGAGTTCTTCTCATTATGAACTCT-CCATTGGAAATGTTGATCCACCTCCTTCTGTGA
130 ATAGA-ATGAGTTCTTCTCAGTATGAACTCTCCCATTGGAAATGTTGATCCACCTAATTCTGTGA
* * * *
525740 TGGAATCGAACCAAGGTTGAACAAGTTTTTCTCATTATGAATTTCTTCTCCTTCATTAG-ATGAG
194 TGGAATCGAACCAAGGTTGAACAAGTTCTTATCATTATGAAGTTCTTCTCCCTCA-TAGAATGAG
525804 TTCTTCTTATTATAAACTATTCACTGGATATGTTTATCCCTTCATTCTATGATAAAATTGAA
258 TTCTTCTTATTATAAACTATTCACTGGATATGTTTATCCCTTCATTCTATGATAAAATTGAA
* * * *
525866 CAAAGTGATGATTTTGATCCAACTCCATATACGATGGATAAGCCAAGTATTGGTGTTGTTCCAAC
1 CAAAATGATGATGTTGATCCAACTCCATATACGATGGATAAGCCAAG-ATCGGTGCTGTTCCAAC
* * * *
525931 TCCTTATATGATGGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTCATTCTCCCTC
65 TCCCTATATGATGGAATCAAGCTAAGGTTGAACAAGTTATTCTAATTATGAACTCATTCTCCCTC
* * *
525996 ATCGAATGATTTCTTCTCAGTATGAACTCTCCCATTGGAAATTTTGATCCACCTAATTCTGTGAT
130 ATAGAATGAGTTCTTCTCAGTATGAACTCTCCCATTGGAAATGTTGATCCACCTAATTCTGTGAT
* * *
526061 GGAATCGAACCAAGGTTGATCAAGTTCTTATTATTATGAAGTTCTTCTCCCTCATCGAATGAGTT
195 GGAATCGAACCAAGGTTGAACAAGTTCTTATCATTATGAAGTTCTTCTCCCTCATAGAATGAGTT
526126 CTTCTTATTAT
260 CTTCTTATTAT
526137 GAAATCTCTT
Statistics
Matches: 236, Mismatches: 30, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
318 43 0.18
319 95 0.40
320 98 0.42
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (319 bp):
CAAAATGATGATGTTGATCCAACTCCATATACGATGGATAAGCCAAGATCGGTGCTGTTCCAACT
CCCTATATGATGGAATCAAGCTAAGGTTGAACAAGTTATTCTAATTATGAACTCATTCTCCCTCA
TAGAATGAGTTCTTCTCAGTATGAACTCTCCCATTGGAAATGTTGATCCACCTAATTCTGTGATG
GAATCGAACCAAGGTTGAACAAGTTCTTATCATTATGAAGTTCTTCTCCCTCATAGAATGAGTTC
TTCTTATTATAAACTATTCACTGGATATGTTTATCCCTTCATTCTATGATAAAATTGAA
Found at i:526151 original size:118 final size:118
Alignment explanation
Indices: 525939--526158 Score: 316
Period size: 118 Copynumber: 1.9 Consensus size: 118
525929 ACTCCTTATA
* * *
525939 TGATGGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTCATTCTCCCTCATCGAATG
1 TGATGGAATCGAACCAAGGTTGAACAAGTTCTTATCATTATGAACTCATTCTCCCTCATCGAATG
* *
526004 ATTTCTTCTCAGTATGAACTCTCCCATTGGAAATTTTGATCCACCTAATTCTG
66 AGTTCTTCTCAGTATGAAATCTCCCATTGGAAATTTTGATCCACCTAATTCTG
* * *
526057 TGATGGAATCGAACCAAGGTTGATCAAGTTCTTATTATTATGAAGTTC-TTCTCCCTCATCGAAT
1 TGATGGAATCGAACCAAGGTTGAACAAGTTCTTATCATTATGAA-CTCATTCTCCCTCATCGAAT
* * **
526121 GAGTTCTTCTTATTATGAAATCTCTTATTGGAAATTTT
65 GAGTTCTTCTCAGTATGAAATCTCCCATTGGAAATTTT
526159 AACTGGTTTA
Statistics
Matches: 89, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
118 87 0.98
119 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (118 bp):
TGATGGAATCGAACCAAGGTTGAACAAGTTCTTATCATTATGAACTCATTCTCCCTCATCGAATG
AGTTCTTCTCAGTATGAAATCTCCCATTGGAAATTTTGATCCACCTAATTCTG
Found at i:532250 original size:13 final size:13
Alignment explanation
Indices: 532232--532256 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
532222 GACGCTTTTA
532232 GTCAAAGTCAAAG
1 GTCAAAGTCAAAG
532245 GTCAAAGTCAAA
1 GTCAAAGTCAAA
532257 ATTAACGTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.20, T:0.16
Consensus pattern (13 bp):
GTCAAAGTCAAAG
Found at i:533280 original size:41 final size:41
Alignment explanation
Indices: 533207--533291 Score: 107
Period size: 41 Copynumber: 2.1 Consensus size: 41
533197 ACAGTTATCA
*
533207 TCAAGAAACCCCTAAAAATTAGGCTCAACTTCTTGAAAAAT
1 TCAAGAAACCCCTAAAAATTAGACTCAACTTCTTGAAAAAT
* * * * **
533248 TCAAGAAACTCCTGAAAATTAGACTTAGCTTCTTTCAAAAT
1 TCAAGAAACCCCTAAAAATTAGACTCAACTTCTTGAAAAAT
533289 TCA
1 TCA
533292 TTTGAAGATA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.28
Consensus pattern (41 bp):
TCAAGAAACCCCTAAAAATTAGACTCAACTTCTTGAAAAAT
Done.